NATIONAL OPEN UNIVERSITY OF NIGERIA

SCHOOL OF SCIENCE AND TECHNOLOGY

COURSE CODE: BIO 307

COURSE TITLE: EVOLUTION

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 BIO 307: EVOLUTION

TEAM WRITERS: Mr Kofi O. Renner

Nigerian Institute for Oceanography and

Marine Research,
No 3 Wilmot Point Road, Bar-beach Bus-stop,
Victoria Island,
Lagos, Nigeria.

Mr O. S. Fakayode

Nigerian Institute for Oceanography and

Marine Research,
No 3 Wilmot Point Road, Bar-beach Bus-stop,
Victoria Island,
Lagos, Nigeria.

BIO 307 COURSE GUIDE

Introduction

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Evolution (307) is a first semester course. It is a two credit unit compulsory course which all
students offering Bachelor of Science (BSc) in Biology must take.

Evolution is an important area of study for scientists. It is described as series of changes

across successive generations in the heritable characteristics of biological populations.
Processes in evolution give rise to diversity at every level of biological organisation, which
include species, individual organisms and at the molecular level, such as proteins and DNA.
Since this course evolution involve changes across generation of life (either plant or animal),
we will focus on the various heritable characteristics in evolution of both plants and animals
and how their genetic make-up supports their existence.

This course deals with the historical concept of evolution, Population genetics, and gene
frequency/equilibrium. Hardey Weinberg Principle, Polymorphism, Mutation; origin and
types. Polyploidy, isolation mechanism, adaptation; origin of life; evolution of organic
molecules, Polymer synthesis, origin of species, Evidence of evolution; fossils (carbon
dating), comparative anatomy, Taxonomy, Comparative-biochemistry, physiology,
immunology, cell biology. Evolution of the plants, role of oxygen, multicellular development,
Phylogeny and geological periods and epochs.

What you will learn in this course

In this course, you have the course units and a course guide. The course guide will tell you
briefly what the course is all about. It is a general overview of the course materials you will
be using and how to use those materials. It also helps you to allocate the appropriate time to
each unit so that you can successfully complete the course within the stipulated time limit.

The course guide also helps you to know how to go about your Tutor-Marked-Assignment
which will form part of your overall assessment at the end of the course. Also, there will be
tutorial classes that are related to this course, where you can interact with your facilitators and
other students. Please I encourage you to attend these tutorial classes.

This course exposes you to Evolution, a sub-discipline and very interesting field of Biology.

Course Aims

This course aims to enable you to know/understand different theories of evolution postulated
and genetic basis of evolution in animals and plant related to their development.

Course Objectives

To achieve the aim set above, there are objectives. Each unit has a set of objectives presented
at the beginning of the unit. These objectives will give you what to concentrate and focus on
while studying the unit and during your study to check your progress.

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The Comprehensive Objectives of the Course are given below. At the end of the course/after
going through this course, you should be able to:

• Differentiate one evolutionary mechanism from another

• Define biological evolution?

• Explain how theories of microevolution and macroevolution related?

• Understand the various mechanisms governing evolution

• Explain in detail the mechanisms of evolution.

• Discuss extensively on Isolation mechanisms

• Discuss pre and post zygotic isolation

• How reproductive isolation important to speciation and what forms can it take?

• Explain mutation, its types and what causes it.

• Discuss the outcomes of evolution and how these outcomes affect the changes in our

environment, related to species existence.

• Define Population Genetics

• Describe the History of Population Genetics

• Define genetic frequency

• Explain the significance of genetic frequency

• Relate genetic frequency and the Hardy-Weinberg Principle

• Define the Ecology and discuss its significance to Evolution

• Differentiate the types of Ecology

• Define polymorphism

• State and discuss types of polymorphism

• Describe variation and understand the basis for variation: Evolution

• Highlight the importance of natural selection

• Explain genetic recombination

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Working through the Course

To successfully complete this course. You are required to read each study unit, read the
textbooks and other materials provided by the National Open University.

Reading the reference materials can also be of great assistance.

Each unit has self –assessment exercise which you are advised to do. At certain periods
during the course you will be required to submit your assignments for the purpose of
assessment.

There will be a final examination at the end of the course. The course should take you
about17 weeks to complete.

This course guide provides you with all the components of the course, how to go about
studying and how you should allocate your time to each unit so as to finish on time and
successfully.

The Course Materials

The main components of the course are:

1 The Study Guide

2 Study Units

3 Reference/ Further Readings

4 Assignments

5 Presentation Schedule

Study Units

The study units in this course are given below:

BIO 307 EVOLUTION (2 UNITS)

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MODULE: 1 THEORIES OF EVOLUTION
Unit 1: History of Evolutionary Thought
Unit 2: Mechanisms of Evolution
Unit 3: Isolation Mechanisms
Unit 4: Mutation
Unit 5: Outcome of Evolution

MODULE 2: POPULATION GENETICS

Unit 1: History of Population Genetics
Unit 2: Processes of Population Genetics
Unit 3: Hardey-Weinberg Principle

Unit 4: Gene Frequency/Equilibrium

MODULE 3: POLYMORPHISM

Unit 1: Ecology
Unit 2: Introduction to Polymorphism
Unit 3: Examples of Polymorphism

MODULE 4: VARIATION: TYPES AND CAUSES

Unit 1: Evolution and Variation

Unit 2: Genetic variation

Unit 3: Reshuffling of genes

Unit 4: Polyploidy

MODULE 5: EVOLUTION OF LIFE

Unit 1: Origin of Life
Unit 2: Evidence of evolution, adaptation and Speciation
Unit 3: Classification and phylogeny
Unit 4: Geological periods and epoch
Unit 5: Evolution of the plants
In module one, unit one and two deal with the history of Evolutionary Thought and
mechanism of evolution, unit three to five deal with isolation mechanisms, mutation and
outcome of evolution.

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Module Two is concerned with the history of population genetics as well as their processes.
Application of Hardey-Weinberg Principle in analyzing population genetics for gene
frequency, sex linkage, equilibrium, and heterozygote frequency.

Module Three unit one to three deal with ecology as it related to polymorphism with
examples. Polymorphism is related to biodiversity, genetic variation and adaptation and is
common in nature.

In Module Four, the first two units deal with Evolution and Variation with further
explanation on genetic variation. Unit three and four; reshuffling of genes and polyploidy is
further explained to understand genetic variation in evolution.
Module Five, unit one and two focused on Origin of Life, evidence of evolution, adaptation
and Speciation in organisms. Classification and phylogeny, Geological periods and epoch and
Evolution of the plants are extensively discussed in unit three, four and five.

Each unit will take a week or two lectures, will include an introduction, objectives, reading
materials, self assessment question(s), conclusion, summary, tutor-marked assignments
(TMAs), references and other reading resources.

There are activities related to the lecture in each unit which will help your progress and
comprehension of the unit. You are required to work on these exercises which together with
the TMAs will enable you to achieve the objective of each unit.

Presentation Schedule

There is a time-table prepared for the early and timely completion and submissions of your
TMAs as well as attending the tutorial classes. You are required to submit all your
assignments by the stipulated date and time. Avoid falling behind the schedule time.

Assessment

There are three aspects to the assessment of this course.

The first one is the self-assessment exercises. The second is the tutor-marked assignments
and the third is the written examination or the examination to be taken at the end of the
course.

Do the exercises or activities in the unit applying the information and knowledge you
acquired during the course. The tutor-marked assignments must be submitted to your
facilitator for formal assessment in accordance with the deadlines stated in the presentation
schedule and the assignment file.

The work submitted to your tutor for assessment will account for 30% of your total work.

At the end of this course you have to sit for a final or end of course examination of about a
three hour duration which will account for 70% of your total course mark.

Tutor Marked Assignment

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This is the continuous assessment component of this course and it accounts for 30% of the
total score. You will be given four (4) TMAs by your facilitator to answer. Three of which
must be answered before you are allowed to sit for the end of the course examination.

These answered assignments must be returned to your facilitator.

You are expected to complete the assignments by using the information and material in your
reading references and study units.

Reading and researching into the references will give you a wider view point and give you a
deeper understanding of the subject.

1 Make sure that each assignment reaches your facilitator on or before the deadline
given in the presentation schedule and assignment file. If for any reason you are not
able to complete your assignment, make sure you contact your facilitator before the
assignment is due to discuss the possibility of an extension. Request for extension will
not be granted after the due date unless there is an exceptional circumstance.
2 Make sure you revise the whole course content before sitting for examination. The
self-assessment activities and TMAs will be useful for this purposes and if you have
any comments please do before the examination. The end of course examination
covers information from all parts of the course.

Course Marking Scheme

Assignment Marks
Assignment 1-4 Four assignments, best three marks of the
four count at 10% each - 30% of course
marks.
End of course examination 70% of overall course marks
Total 100% of course materials

Facilitators/ Tutors and Tutorials

Sixteen (16) hours are provided for tutorials for this course. You will be notified of the
dates, times and location for these tutorial classes.

As soon as you are allocated a tutorial group, the name and phone number of your
facilitator will be given to you.

These are the duties of your facilitator:

• He or she will mark and comment on your assignment

• He will monitor your progress and provide any necessary assistance you need.
• He or she will mark your TMAs and return to you as soon as possible.

(You are expected to mail your tutored assignment to your facilitators at least two days
before the schedule date).

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Do not delay to contact your facilitator by telephone or e-mail for necessary assistance if

• You do not understand any part of the study in the course material.
• You have difficulty with the self assessment activities.
• You have a problem or question with an assignment or with the grading of the
assignment.

It is important and necessary you attend the tutorial classes because this is the only chance to
have face to face contact with your facilitator and to ask questions which will be answered
instantly. It is also a period where you can point out any problem encountered in the course of
your study.

Summary

Evolution (307) is a course that introduces you to the concepts and principles of how living
things gradually change from one form into another over the course of time, the origin of
species and lineages by descent of living forms from ancestral forms, and the generation of
diversity. This emphasizes the appearance of new, physically distinct life forms that can be
grouped with similar appearing life forms in a taxonomic hierarchy. It commonly is referred
to as macroevolution. It can also be defined as changes in the genetic composition of a
population with the passage of each generation.

On the completion of this course, you will have an understanding of basic knowledge of
historical theories of evolution, population genetics, genetic variation, polymorphism and
evolution of life etc you will be able to understand the concept behind evolution. In addition
you will be able to answer the following questions:

• Discuss three schools of thought for the History of Evolution?

• For or against; Charles Darwin’s Theory of Evolution?
• State and elaborate on three of these mechanisms?
• What are the different types of mutation?
• How important is mutation to the evolutionary process?

• Identify keys areas of biological and environmental conservation where a genetic

approach benefits outcomes of management?
• Explain polymorphism and niche diversity?
• Discuss mechanism of balancing selection?
• What are the mechanisms that affect genetic variation?
• Describe polyploidy in animals and plants?
• List 5 probable stages involved in the origin of life?
• The RNA- first hypothesis for the origin of cells is supported by the discovery of--
-------

The list of questions you are expected to answer is not limited to the above list.

I believe you will agree with me that Evolution is a very interesting field of biology.

I wish you success in this course.

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MODULE 1: THEORIES OF EVOLUTION

Unit 1: History of Evolutionary Thought

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Unit 2: Mechanisms of Evolution

Unit 3: Isolation Mechanisms

Unit 4: Mutation

Unit 5: Outcomes of Evolution

UNIT 1: HISTORY OF EVOLUTIONARY THOUGHT

CONTENTS

1.0 Introduction

2.0 Objectives

3.0 Main Focus

3.1 Different schools of evolutionary thought

3.2 Darwin’s theory of natural selection

3.3 Modern synthesis of evolutionary theory

4.0 Conclusion

5.0 Summary

6.0 Tutor-Marked Assignment

7.0 Reference/Further Readings

UNIT 1: HISTORY OF EVOLUTIONARY THOUGHT

1.0 Introduction

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Evolution has been described as series of changes across successive generations in the

heritable characteristics of biological populations. Processes in evolution give rise to diversity

at every level of biological organisation, which include species, individual organisms and at

the molecular level, such as proteins and DNA. Approximately 3.7billion years ago, life on

Earth originated and then evolved from a universal common ancestor. The divergence and

repeated speciation of life can be traced through shared sets of biochemical and

morphological traits, or by shared DNA sequences. Existing patterns of biodiversity have

been shaped both by speciation and by extinction. The theory of evolution by natural

selection was formulated by Charles Darwin, who was the first to recognise natural selection

as an important cause of evolution.

2.0 Objectives

At the conclusion of this unit, students should be able to:

• Give an account of the history of evolution,

• Describe the different schools of thought of the evolutionary process,

• Differentiate one school of thought of the evolutionary process from the other

• Understand Darwin’s theory of natural selection.

3.0 Main Focus

3.1 Evolution Pre-Darwin

Contrary to many assumptions, evolutionary theory did not begin in 1859 with Charles

Darwin and The Origin of Species. Rather, evolution-like ideas had existed since the times of

the Greeks, and had been in and out of favour in the periods between ancient Greece and

Victorian England. Indeed, by Darwin's time the idea of evolution - called "descent with

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modification" - was not especially controversial, and several other evolutionary theories had

already been proposed. Darwin may stand at the beginning of a modern tradition, but he is

also the final culmination of an ancient speculation.

3.2 Greek Evolution

Many examples of societies that postulated the history of evolution include the Greeks, who

did not specifically refer to their concepts as "evolution", they did have a philosophical

notion of descent with modification. Several different Greek philosophers subscribed to a

concept of origination, arguing that all things originated from water or air. Another common

concept was the idea that all things descended from one central, guiding principle. Aristotle

suggests a transition between the living and the nonliving, and theorizes that in all things

there is a constant desire to move from the lower to the higher, finally becoming the divine.

3.3 Medieval Evolution

Medieval theories argued that all living things came into existence in unchanging forms due

to divine will, was notably in opposition to the concept of evolution. Medieval thinking was

also, oddly enough, confused by the idea of spontaneous generation, which stated that living

things can appear fully formed from inorganic matter. In this view, maggots came from

rotting meat; frogs came from slime, etc. This sort of a concept prevented both genetic

thinking and speculation about evolution or descent with modification. Nevertheless, a few

philosophers theorized about some sort of teleological principle by which species might

derive from a divine form.

3.4 Immanuel Kant

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Immanuel Kant the German philosopher Immanuel Kant developed a concept of descent that

is relatively close to modern thinking; he did in a way anticipate Darwinian thinking. Based

on similarities between organisms, Kant speculated that they may have come from a single

ancestral source. In a thoroughly modern speculation, he mused that "an orang-utan or a

chimpanzee may develop the organs which serve for walking, grasping objects, and speaking-

in short, that lie may evolve the structure of man, with an organ for the use of reason, which

shall gradually develop itself by social culture"

3.5 Biological Conceptions of Evolution.

Preceding discussion has focused on the philosophical components of evolutionary theory,

but precursors exist for its biological aspects as well. Indeed, as mentioned above, by

Darwin's time the concept of descent with modification was hardly controversial - it was only

the mechanism, the rate of modification, and the ultimate origin of life that were being

debated. Darwin's major breakthrough consisted in providing a plausible mechanism to drive

change in organisms.

3.6 Carolus Linnaeus.

Carolus Linnaeus (1707-1778), is considered the father of modern taxonomy for his work in

hierarchical classification of various organisms. At first, he believed in the fixed nature of

species, but he was later swayed by hybridization experiments in plants, which could produce

new species. However, he maintained his belief in special creation in the Garden of Eden,

consistent with the Christian doctrine to which he was quite devoted. He still saw the new

species created by plant hybridization to have been part of God's plan, and never considered

the idea of open-ended, undirected evolution not mediated by the divine.

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3.7 Erasmus Darwin.

Charles Darwin's grandfather Erasmus Darwin (1731-1802) was also a distinguished

naturalist with his own intriguing ideas about evolution. While he never thought of natural

selection, he did argue that all life could a have a single common ancestor, though he

struggled with the concepts of a mechanism for this descent. He also discussed the effects of

competition and sexual selection on possible changes in species. Like Lamarck, Erasmus

Darwin subscribed to a theory stating that the use or disuse of parts could in itself make them

grow or shrink, and that unconscious striving by the organism was responsible for adaptation.

3.8 Jean-Baptiste. Lamarck

Jean-Baptiste Lamarck's (1744-1829) theory of evolution was a good try for his time, but has

now been discredited by experimental evidence and the much more plausible mechanism of

modification proposed by Darwin. Lamarck saw species as not being fixed and immutable,

but rather in a constantly changing state. He presented a multitude of different theories that he

believed combined to explain descent with modification of these changing species. Lamarck

subscribed to a number of what we now know to be false beliefs about inheritance. First, like

Erasmus Darwin, he argued for strong effects of the use and disuse of parts, which he thought

would make the relevant parts change size or shape in accordance with their use. Second,

Lamarck believed that all organisms fundamentally wanted to adapt themselves to their

environment, and so they strove to become better adapted. The belief most commonly

associated with Lamarck today is his idea of the inheritance of acquired characteristics. This

theory stated that an organism could pass on to its offspring any characteristics it had

acquired in its lifetime. For example, if a man exercised and thus developed strong muscles,

his offspring would then have strong muscles at birth.

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3.9 Thomas Malthus.

Thomas Malthus' (1766-1834) theory of population growth was in the end what inspired

Darwin to develop the theory of natural selection. According to Malthus, populations produce

many more offspring than can possibly survive on the limited resources generally available.

According to Malthus, poverty, famine, and disease were natural outcomes that resulted from

overpopulation. However, Malthus believed that divine forces were ultimately responsible for

such outcomes, which, though natural, were designed by God.

3.10 Charles Darwin and Alfred Russel Wallace.

Figure 1. Charles Darwin

1809-1882 Alfred Wallace
1823-1913

Charles Darwin and Alfred Russel Wallace both independently developed the idea of the

mechanism of natural selection after reading Thomas Malthus' Essay on the Principle of

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Population (1798). However, Darwin had been turning the problem over in his mind for some

twenty years before he first published The Origin of Species. Moreover, Darwin was much

more willing to explore the implications of natural selection, particularly in relation to

humans, than Wallace was. In addition, Wallace was a champion of rather radical social

causes and later openly embraced spiritualism - all elements that resulted in the downplay of

his role in the discovery of natural selection.

Darwin’s was a part of an expedition on board the HMS Beagle in 1831. He embarked on a 5

week visit to the Galápagos Islands in the Eastern Pacific Ocean. It was there that he made

the observations that eventually led him to comprehend what causes plants and animals to

evolve, but he apparently did not clearly formulate his views on this until 1837. At the time

he left the Galápagos Islands, he apparently still believed in a traditional Biblical creation of

all life forms.

Darwin's Beagle Diary

audio recording of excerpts from
Darwin's popular account of his
voyage of exploration.

Figure 2.

The Galápagos Islands have species found in no other part of the world. Darwin was

surprised that the birds were slightly different from one island to another. He realized that

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the key to why this difference existed was connected with the fact that the various species

live in different kinds of environments.

Figure 3.

On his return to England, Darwin and an ornithologist identified 13 species of finches that he

had collected on the Galápagos Islands. This was surprising since he knew of only one

species of this bird on the mainland of South America, nearly 600 miles to the east, where

they had all presumably originated. He observed that the Galápagos species differed from

each other in beak size and shape. He noted that the beak varieties were associated with diets

based on different foods. He concluded that when the original South American finches

reached the islands, they dispersed to different environments where they had to adapt to

different conditions. Over many generations, they changed anatomically in ways that

allowed them to get enough food and survive to reproduce. This observation was verified by

intensive field research in the last quarter of the 20th century.

Galapágos Creatures--some of the unusual animals that Darwin

saw on the Galapágos islands. Video clip from "Evolution:
Constant Change and Common Threads". (Howard Hughes
Medical Institute, 2005)

Figure 4

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Today the term adaptive radiation is used to refer to this sort of branching evolution in which

different populations of a species become reproductively isolated from each other by adapting

to different ecological niches and eventually become separate species.

Figure 5

Darwin understood that any population is made up of individuals that are all slightly different

from one another. Individuals having variation that gives them an advantage in staying alive

long enough to successfully reproduce are the ones that pass on their traits more frequently to

the next generation. Subsequently, their traits become more common and the population

evolves. Darwin called this "descent with modification."

The Galápagos finches provide an excellent example of this process. Among the birds that

ended up in arid environments, the ones with beaks better suited for eating cactus got more

food. As a result, they were in better condition to mate. Similarly, those with beak shapes

that were better suited to getting nectar from flowers or eating hard seeds in other

environments were at an advantage there. In a very real sense, nature selected the best

adapted varieties to survive and to reproduce. This process has come to be known as natural

selection.

In 1859, Darwin's publication of On the Origin of Species explained natural selection in detail

and in a way that lead to an increasingly wide acceptance of Darwinian evolution. Thomas

Henry Huxley applied Darwin's ideas to humans, using palaeontology and comparative

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anatomy to provide strong evidence that humans and apes shared a common ancestry. Some

were disturbed by this since it implied that humans did not have a special place in the

universe. Due to the fact that the exact mode for reproductive heritability and the origin of

new traits remained a mystery, Darwin developed his provisional theory of pangenesis. In

1865 Gregor Mendel reported that traits were inherited in a predictable manner through the

independent assortment and segregation of elements. All plants and animals receive their

specific characteristics from their parents by inheriting particular combinations of genes.

Molecular biologists have discovered that genes are, in fact, segments of DNA molecules

in our cells.

Figure 6 section of a DNA molecule

Mendel's laws of inheritance eventually supplanted most of Darwin's pangenesis theory.

August Weismann made the important distinction between germ cells and somatic cells of the

body, demonstrating that heredity passes through the germ line only. Hugo de Vries

connected Darwin's pangenesis theory to Wiesman's germ/somatic cell distinction and

proposed that Darwin's pangenes were concentrated in the cell nucleus and when expressed

they could move into the cytoplasm to change the cells structure. De Vries was also one of

the researchers who made Mendel's work well-known, believing that Mendelian traits

corresponded to the transfer of heritable variations along the germ line. To explain how new

variants originate; De Vries developed a mutation theory that led to a temporary rift between

those who accepted Darwinian evolution and biometricians who allied with de Vries. At the

turn of the 20th century, pioneers in the field of population genetics, such as J.B.S. Haldane,

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Sewall Wright, and Ronald Fisher, set the foundations of evolution onto a robust statistical

philosophy. The false contradiction between Darwin's theory, genetic mutations, and

Mendelian inheritance was thus reconciled.

An evolutionary synthesis in the 1930s connected natural selection, mutation theory, and

Mendelian inheritance into a unified theory that applied generally to any branch of biology.

The modern synthesis was able to explain patterns observed across species in populations,

through fossil transitions in palaeontology, and even complex cellular mechanisms in

developmental biology. The publication of the structure of DNA by James Watson and

Francis Crick in 1953 demonstrated a physical basis for inheritance. Molecular biology

improved our understanding of the relationship between genotype and phenotype.

Advancements were also made in phylogenetic systematics, mapping the transition of traits

into a comparative and testable framework through the publication and use of evolutionary

trees. Theodosius Dobzhansky an evolutionary biologist in 1973 penned that "nothing in

biology makes sense except in the light of evolution", because it has brought to light the

relations of what first seemed disjointed facts in natural history into a coherent explanatory

body of knowledge that describes and predicts many observable facts about life on this

planet. Since then, the modern synthesis has been further extended to explain biological

phenomena across the full and integrative scale of the biological hierarchy, from genes to

species.

4.0 Conclusion

The student shall be able to give a thorough account of the History of evolution as well as to

discuss major highlights of evolution especially Pre-Darwinian era and to establish

similarities and differences amongst the different schools of thought. The student should be

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able to discuss for and against the different theories of evolution which are thought to have

led to our current existence.

5.0 Summary

The concept of evolution has been the centre of debate for over a century. Evolution has been

called the cornerstone of biology, and for good reasons. It is possible to do research in

biology with little or no knowledge of evolution. Most biologists do. But, without evolution

biology becomes a disparate set of fields. Evolutionary explanations pervade all fields in

biology and bring them together under one theoretical umbrella. After the publication of On

the Origin of Species in 1859, the idea that life had evolved was an active source of academic

debate centred on the philosophical, social and religious implications of evolution.

Nowadays, the modern evolutionary synthesis is accepted by a vast majority of scientists.

However, evolution remains a contentious concept for some theists.

6.0 Tutor-Marked Assignment

• What do you understand by History of Evolutionary Thought?

• Discuss three schools of thought for the History of Evolution?

• For or against; Charles Darwin’s Theory of Evolution?

7.0 Reference/Further Readings

The Descent of Man by Charles Darwin; The Origin of Species by Charles Darwin; Evolution

from The Internet Encyclopedia of Philosophy; A History of Evolutionary Thought; Timeline

of Evolutionary Thought; Lamarck and his Theory of Evolution by Thomas E. Hart from The

Victorian Web.

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UNIT2: MECHANISMS OF EVOLUTION

CONTENTS

1.0 Introduction

2.0 Objectives

3.0 Evolution and its many forms

3.1 Natural selection

3.2 Genetic Drift

3.3 Genetic Hitch-Hiking

3.4 Gene Flow

4.0 Conclusion

5.0 Summary

6.0 Tutor-Marked Assignment

7.0 Reference/Further Readings

1.0 Introduction

Based on the Neo-Darwinian perspective, evolution occurs when there are changes in the

frequencies of alleles within a population of interbreeding organisms. A good example is the

allele for black colour in a population of moths becoming more common. Mechanisms that

can lead to changes in allele frequencies include natural selection, genetic drift, genetic

hitchhiking, mutation and gene flow.

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2.0 Objectives

At the end of this unit, the student should be able to:

• Differentiate one evolutionary mechanism from another

• Define biological evolution?

• How are theories of microevolution and macroevolution related?

• Understand the various mechanisms governing evolution

• Explain in detail the mechanisms of evolution.

3.0 Evolution and its many forms

The word "evolution" does not apply exclusively to biological evolution. The universe and

our solar system have developed out of the explosion of matter that began our known

universe. Chemical elements have evolved from simpler matter. Life has evolved from non-

life, and complex organisms from simpler forms. Languages, religions, and political systems

all evolve. Hence, evolution is an appropriate theme for a course on global change. The core

aspects of evolution are "change" and the role of history, in that past events have an influence

over what changes occur subsequently. In biological evolution this might mean that complex

organisms arise out of simpler ancestors - though be aware that this is an over-simplification

not acceptable to a more advanced discussion of evolution. A full discussion of evolution

requires a detailed explanation of genetics, because science has given us a good

understanding of the genetic basis of evolution. It also requires an investigation of the

differences that characterize species, genera, indeed the entire tree of life, because these are

the phenomena that the theory of evolution seeks to explain. We will begin with observed

patterns of similarities and differences among species, because this is what Darwin knew

about. The genetic basis for evolution only began to be integrated into evolutionary theory in

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the 1930's and 1940's. We will add genetics into our understanding of evolution through a

discussion activity.

Definitions of Biological Evolution

We begin with two working definitions of biological evolution, which capture these two

facets of genetics and differences among life forms. Then we will ask what is a species, and

how does a species arise?

• Definition 1:

Changes in the genetic composition of a population with the passage of each

generation

• Definition 2:

The gradual change of living things from one form into another over the course of
time, the origin of species and lineages by descent of living forms from ancestral
forms, and the generation of diversity

Note that the first definition emphasizes genetic change. It commonly is referred to as

microevolution. The second definition emphasizes the appearance of new, physically distinct

life forms that can be grouped with similar appearing life forms in a taxonomic hierarchy. It

commonly is referred to as macroevolution.

3.1 Natural Selection

Natural selection is the process by which genetic mutations that enhance reproduction

become and remain, more common in successive generations of a population. It has often

been called a "self-evident" mechanism because it necessarily follows from three simple

facts:

• Heritable variation exists within populations of organisms.

• Organisms produce more offspring than can survive.

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 • These offspring vary in their ability to survive and reproduce.

These conditions produce competition between organisms for survival and reproduction.

Consequently, organisms with traits that give them an advantage over their competitors pass

these advantageous traits on, while traits that do not confer an advantage are not passed on to

the next generation. Natural selection is based on a concept of evolutionary fitness. This

fitness is measured by an organism's ability to survive and reproduce, which determines the

size of its genetic contribution to the next generation. A good example is if an organism could

survive well and reproduces rapidly, but its offspring were all too small and weak to survive,

this organism would make little genetic contribution to future generations and would thus

have low fitness.

The idea that species could change over time was not immediately acceptable to many: the

lack of a mechanism hampered the acceptance of the idea as did its implications regarding the

biblical views of creation.

Charles Darwin and Alfred Wallace both worked independently of each other, travelled

extensively, and eventually developed similar ideas about the change in life over time as well

as a mechanism for that change: natural selection.

Ancient Greek philosophers such as Anaximander postulated the development of life from

non-life and the evolutionary descent of man from animal. Charles Darwin simply brought

something new to the old philosophy -- a plausible mechanism called "natural selection."

Natural selection acts to preserve and accumulate minor advantageous genetic mutations.

Suppose a member of a species developed a functional advantage – let us assume it grew

wings and learned to fly. Its offspring would inherit that advantage and pass it on to their

offspring. The inferior or disadvantaged members of the same species would gradually die

26
out, leaving only the superior or advantaged members of the species. Natural selection is the

preservation of a functional advantage that enables a species to compete better in the wild.

Natural selection is the naturalistic equivalent to domestic breeding. Over the centuries,

human breeders have produced dramatic changes in domestic animal populations by selecting

individuals to breed. Breeders eliminate undesirable traits gradually over time. Similarly,

natural selection eliminates inferior species gradually over time. Some types of organisms

within a population leave more offspring than others. Over time, the frequency of the more

prolific type will increase. The difference in reproductive capability is called natural

selection. Natural selection is the only mechanism of adaptive evolution; it is defined as

differential reproductive success of pre- existing classes of genetic variants in the gene pool.

The most common action of natural selection is to remove unfit variants as they arise via

mutation. In other words, natural selection usually prevents new alleles from increasing in

frequency. This led a famous evolutionist, George Williams, to say "Evolution proceeds in

spite of natural selection."

Natural selection can maintain or deplete genetic variation depending on how it acts. When

selection acts to weed out deleterious alleles, or causes an allele to sweep to fixation, it

depletes genetic variation. When heterozygotes are fit than either of the homozygotes,

however, selection causes genetic variation to be maintained. This is called balancing

selection. An example of this is the maintenance of sickle-cell alleles in human populations

subject to malaria. Variation at a single locus determines whether red blood cells are shaped

normally or sickled. If a human has two alleles for sickle-cell, he/she develops anaemia -- the

shape of sickle-cells precludes those carrying normal levels of oxygen. However,

heterozygotes that have one copy of the sickle-cell allele, coupled with one normal allele

enjoy some resistance to malaria -- the shape of sickled cells makes it harder for the

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plasmodia to enter the cell. Thus, individuals homozygous for the normal allele suffer more

malaria than heterozygotes. Individuals homozygous for the sickle- cell are anaemic.

Heterozygotes have the highest fitness of these three types. Heterozygotes pass on both

sickle-cell and normal alleles to the next generation. Thus, neither allele can be eliminated

from the gene pool. The sickle-cell allele is at its highest frequency in regions of Africa

where malaria is most pervasive.

Balancing selection is rare in natural populations. Only a handful of other cases beside the

sickle-cell example have been found. At one time population geneticists thought balancing

selection could be a general explanation for the levels of genetic variation found in natural

populations. That is no longer the case. Balancing selection is only rarely found in natural

populations. And, there are theoretical reasons why natural selection cannot maintain

polymorphisms at several loci via balancing selection.

Individuals are selected. The example I gave earlier was an example of evolution via natural

selection. Dark colored moths had a higher reproductive success because light colored moths

suffered a higher predation rate. The decline of light colored alleles was caused by light

colored individuals being removed from the gene pool Individual organisms either reproduce

or fail to reproduce and are hence the unit of selection. One way alleles can change in

frequency is to be housed in organisms with different reproductive rates. Genes are not the

unit of selection; neither are groups of organisms a unit of selection. There are some

exceptions to this "rule," but it is a good generalization.

Organisms do not perform any behaviour that is for the good of their species. An individual

organism competes primarily with others of it own species for its reproductive success.

Natural selection favours selfish behaviour because any truly altruistic act increases the

recipient's reproductive success while lowering the donors. Altruists would disappear from a

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population as the non- altruists would reap the benefits, but not pay the costs, of altruistic

acts. Much behaviour appears altruistic. Biologists, however, can demonstrate that this

behaviour is only apparently altruistic. Cooperating with or helping other organisms is often

the most selfish strategy for an animal. This is called reciprocal altruism. A good example of

this is blood sharing in vampire bats. In these bats, those lucky enough to find a meal will

often share part of it with an unsuccessful bat by regurgitating some blood into the other's

mouth. Biologists have found that these bats form bonds with partners and help each other

out when the other is needy. If a bat is found to be a "cheater," (he accepts blood when

starving, but does not donate when his partner is) his partner will abandon him. The bats are

thus not helping each other altruistically; they form pacts that are mutually beneficial.

Helping closely related organisms can appear altruistic; but this is also a selfish behaviour.

Reproductive success (fitness) has two components; direct fitness and indirect fitness. Direct

fitness is a measure of how many alleles, on average, a genotype contributes to the

subsequent generation's gene pool by reproducing. Indirect fitness is a measure of how many

alleles identical to its own it helps to enter the gene pool. Direct fitness plus indirect fitness is

inclusive fitness. J. B. S. Haldane once remarked he would gladly drown, if by doing so he

saved two siblings or eight cousins. Each of his siblings would share one half his alleles; his

cousins, one eighth. They could potentially add as many of his alleles to the gene pool as he

could.

Natural selection favours traits or behaviour that increase a genotype's inclusive fitness.

Closely related organisms share many of the same alleles. In diploid species, siblings share

on average at least 50% of their alleles. The percentage is higher if the parents are related. So,

helping close relatives to reproduce gets an organism's own alleles better represented in the

gene pool. The benefit of helping relatives increases dramatically in highly inbred species. In

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some cases, organisms will completely forgo reproducing and only help their relatives

reproduce. Ants, and other eusocial insects, have sterile castes that only serve the queen and

assist her reproductive efforts. The sterile workers are reproducing by proxy.

The words selfish and altruistic have connotations in everyday use that biologists do not

intend. Selfish simply means behaving in such a way that one's own inclusive fitness is

maximized; altruistic means behaving in such a way that another's fitness is increased at the

expense of one’s' own. Use of the words selfish and altruistic is not meant to imply that

organisms consciously understand their motives.

The opportunity for natural selection to operate does not induce genetic variation to appear --

selection only distinguishes between existing variants. Variation is not possible along every

imaginable axis, so all possible adaptive solutions are not open to populations. To pick a

somewhat ridiculous example, a steel shelled turtle might be an improvement over regular

turtles. Turtles are killed quite a bit by cars these days because when confronted with danger,

they retreat into their shells -- this is not a great strategy against a two ton automobile.

However, there is no variation in metal content of shells, so it would not be possible to select

for a steel shelled turtle.

Here is a second example of natural selection. Geospiza fortis lives on the Galapagos Islands

along with fourteen other finch species. It feeds on the seeds of the plant Tribulus cistoides,

specializing on the smaller seeds. Another species, G. Magnirostris, has a larger beak and

specializes on the larger seeds. The health of these bird populations depends on seed

production. Seed production, in turn, depends on the arrival of wet season. In 1977, there was

a drought. Rainfall was well below normal and fewer seeds were produced. As the season

progressed, the G. fortis population depleted the supply of small seeds. Eventually, only

larger seeds remained. Most of the finches starved; the population plummeted from about

30
twelve hundred birds to less than two hundred. Peter Grant, who had been studying these

finches, noted that larger beaked birds fared better than smaller beaked ones. These larger

birds had offspring with correspondingly large beaks. Thus, there was an increase in the

proportion of large beaked birds in the population the next generation. To prove that the

change in bill size in Geospiza fortis was an evolutionary change, Grant had to show that

differences in bill size were at least partially genetically based. He did so by crossing finches

of various beak sizes and showing that a finch's beak size was influenced by its parent's

genes. Large beaked birds had large beaked offspring; beak size was not due to

environmental differences.

Natural selection may not lead a population to have the optimal set of traits. In any

population, there would be a certain combination of possible alleles that would produce the

optimal set of traits (the global optimum); but there are other sets of alleles that would yield a

population almost as adapted (local optima). Transition from a local optimum to the global

optimum may be hindered or forbidden because the population would have to pass through

less adaptive states to make the transition. Natural selection only works to bring populations

to the nearest optimal point. This idea is Sewall Wright's adaptive landscape. This is one of

the most influential models that shape how evolutionary biologists view evolution.

Natural selection does not have any foresight. It only allows organisms to adapt to their

current environment. Structures or behaviours do not evolve for future utility. An organism

adapts to its environment at each stage of its evolution. As the environment changes, new

traits may be selected for. Large changes in populations are the result of cumulative natural

selection. Changes are introduced into the population by mutation; the small minority of these

changes that result in a greater reproductive output of their bearers are amplified in frequency

by selection.

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Complex traits must evolve through viable intermediates. For many traits, it initially seems

unlikely that intermediates would be viable. What good is half a wing? Half a wing may be

no good for flying, but it may be useful in other ways. Feathers are thought to have evolved

as insulation and/or as a way to trap insects. Later, proto-birds may have learned to glide

when leaping from tree to tree. Eventually, the feathers that originally served as insulation

now became co-opted for use in flight. A trait's current utility is not always indicative of its

past utility. It can evolve for one purpose, and be used later for another. A trait evolved for its

current utility is an adaptation; one that evolved for another utility is an exaptation. An

example of an exaptation is a penguin's wing. Penguins evolved from flying ancestors; now

they are flightless and use their wings for swimming.

3.2 Genetic Drift

Genetic drift is the change in allele frequency from one generation to the next that occurs

because alleles are subject to sampling error. Due to this, when selective forces are absent or

relatively weak, allele frequencies tend to drift upward or downward randomly. This drift

halts when an allele eventually becomes fixed, either by disappearing from the population, or

replacing the other alleles entirely. Genetic drift therefore may eliminate some alleles from a

population due to chance alone. Even in the absence of selective forces, genetic drift can

cause two separate populations that began with the same genetic structure to drift apart into

two divergent populations with different sets of alleles. Usually, it is difficult to measure the

relative importance of selection and neutral processes, including drift. The comparative

importance of adaptive and non-adaptive forces in driving evolutionary change is an area of

current research

Allele frequencies can change due to chance alone. This is called genetic drift. Drift is a

binomial sampling error of the gene pool. This implies that the alleles that form the next

32
generation's gene pool are a sample of the alleles from the current generation. When sampled

from a population, the frequency of alleles differs slightly due to chance alone.

Alleles can increase or decrease in frequency due to drift. The average expected change in

allele frequency is zero, since increasing or decreasing in frequency is equally probable. A

small percentage of alleles may continually change frequency in a single direction for several

generations just as flipping a fair coin may, on occasion, result in a string of heads or tails. A

very few new mutant alleles can drift to fixation in this manner.

In small populations, the variance in the rate of change of allele frequencies is greater than in

large populations. However, the overall rate of genetic drift is independent of population size.

If the mutation rate is constant, large and small populations lose alleles to drift at the same

rate. This is because large populations will have more alleles in the gene pool, but they will

lose them more slowly. Smaller populations will have fewer alleles, but these will quickly

cycle through. This assumes that mutation is constantly adding new alleles to the gene pool

and selection is not operating on any of these alleles.

Sharp drops in population size can change allele frequencies substantially. In the event of a

population crashing, the alleles in the surviving sample may not be representative of the pre-

crash gene pool. This change in the gene pool is called the founder effect, due to the fact that

small populations of organisms that invade a new territory are subject to this. Many biologists

feel the genetic changes brought about by founder effects may contribute to isolated

populations developing reproductive isolation from their parent populations. In sufficiently

small populations, genetic drift can counteract selection.

3.3 Genetic Hitchhiking

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The recombination of genes allows alleles on the same strand of DNA to become separated.

However, the rate of recombination is low-approximately two events per chromosome per

generation. As a result of this, genes close together on a chromosome may not always be

shuffled away from each other and genes that are close together tend to be inherited together.

This is referred to as linkage. This is measured by finding how often two alleles occur

together on a single chromosome compared to expectations, which is called their linkage

disequilibrium. A set of alleles that is usually inherited in a group is called a haplotype. This

can be important when one allele in a particular haplotype is strongly beneficial: natural

selection can drive a selective sweep that will also cause the other alleles in the haplotype to

become more common in the population; this effect is called genetic hitchhiking or genetic

draft. Genetic draft caused by the fact that some neutral genes are genetically linked to others

that are under selection can be partially captured by an appropriate effective population size.

3.4 Gene Flow

Gene flow is the exchange of genes between populations and between species. The presence

or absence of gene flow fundamentally changes the course of evolution. As a result of the

complexity of organisms, any two completely isolated populations will eventually evolve

genetic incompatibilities through neutral processes, even if both populations remain

essentially identical in terms of their adaptation to the environment.

If genetic differentiation between populations develops, gene flow between populations can

introduce traits or alleles which are disadvantageous in the local population and this may lead

to organism within these populations to evolve mechanisms that prevent mating with

genetically distant populations, eventually resulting in the appearance of new species. Thus,

exchange of genetic information between individuals is fundamentally important for the

development of the biological species concept.

34
During the development of the modern synthesis, Sewall Wright's developed his shifting

balance theory that gene flow between partially isolated populations was an important aspect

of adaptive evolution. However, recently there has been substantial criticism of the

importance of the shifting balance theory.

In some closely related species, fertile hybrids can result from interspecific matings. These

hybrids can vector genes from species to species. Gene flow between more distantly related

species occurs infrequently. This is called horizontal transfer. One interesting case of this

involves genetic elements called P elements. Margaret Kidwell found that P elements were

transferred from some species in the Drosophila willistoni group to Drosophila

melanogaster. These two species of fruit flies are distantly related and hybrids do not form.

Their ranges do, however, overlap. The P elements were vectored into Drosophila.

melanogaster via a parasitic mite that targets both these species. This mite punctures the

exoskeleton of the flies and feeds on the "juices". Material, including DNA, from one fly can

be transferred to another when the mite feeds. Since P elements actively move in the genome,

one incorporated itself into the genome of a melanogaster fly and subsequently spread

through the species. Laboratory stocks of melanogaster caught prior to the 1940's lack of P

elements. All natural populations today harbour them.

4.0 Conclusion

It is important to note that Darwin's book "The Origin of Species by Means of Natural

Selection" did two things. It summarized all of the evidence in favour of the idea that all

organisms have descended with modification from a common ancestor, and thus built a

strong case for evolution. In addition Darwin advocated natural selection as a mechanism of

evolution. Biologists no longer question whether evolution has occurred or is occurring. That

part of Darwin's book is now considered to be so overwhelmingly demonstrated that is is

35
often referred to as the fact of evolution. However, the MECHANISM of evolution is still

debated. We have learned much since Darwin's time and it is no longer appropriate to claim

that evolutionary biologists believe that Darwin's theory of Natural Selection is the best

theory of the mechanism of evolution. I can understand why this point may not be

appreciated by the average non-scientist because natural selection is easy to understand at a

superficial level. It has been widely promoted in the popular press and the image of "survival

of the fittest" is too powerful and too convenient.

5.0 Summary

During the first part of this century the incorporation of genetics and population biology into

studies of evolution led to a Neo-Darwinian theory of evolution that recognized the

importance of mutation and variation within a population. Natural selection then became a

process that altered the frequency of genes in a population and this defined evolution. This

point of view held sway for many decades but more recently the classic Neo-Darwinian view

has been replaced by a new concept which includes several other mechanisms in addition to

natural selection.

6.0 Tutor-Marked Assignment

• What is/are the importance of mechanisms governing evolution

• State and elaborate on three of these mechanisms.

7.0 Reference/Further Readings

Ewens W.J. (2004). Mathematical Population Genetics (2nd Edition). Springer-Verlag, New

York..,

36
Hurst LD (2009). "Fundamental concepts in genetics: genetics and the understanding of

selection". Nat. Rev. Genet. 10 (2): 83–93.

Morjan C, Rieseberg L (2004). "How species evolve collectively: implications of gene flow

and selection for the spread of advantageous alleles". Mol. Ecol. 13 (6): 1341–56.,

Gillespie, John H. (2001). "Is the population size of a species relevant to its evolution?".

Evolution 55. Barton,

N H (2000). "Genetic hitchhiking". Philosophical Transactions of the Royal Society of

London. Series B, Biological Sciences 355 (1403): 1553–1562.

Coyne; Barton, Turelli (1997). "Perspective: A Critique of Sewall Wright's Shifting Balance

Theory of Evolution". Evolution. 3 51: 643–671.

Masel J (2011). "Genetic drift". Current Biology 21 (20): R837-R838.,

Mitchell-Olds, Thomas; Willis, JH; Goldstein, DB (2007). "Which evolutionary processes

influence natural genetic variation for phenotypic traits?". Nature Reviews Genetics 8 (11):

845–856.,

Nei M (2005). "Selectionism and neutralism in molecular evolution". Mol. Biol. Evol. 22

(12): 2318–42..,

Hartl, Daniel L. & Andrew G. Clark. (1997). Principles of Population Genetics. Sunderland,

Mass

Crow, James F. & Motoo Kimura. (1970). Introduction to Population Genetics Theory.

Edina, Minn.: Burgess Publishing Company.,

37
Graur, Dan & Wen-Hsiung Li. (2000). Fundamentals of Molecular Evolution. Sunderland,

Mass.: Sinauer Associates.

FUTUYMA, D. 1998. Evolutionary biology (3ª edición). Sinauer, Sunderland.

Mayr, E. 1963. Animal species and evolution. Harvard University Press, Cambridge.

Levine, L. 1979. Biología del gen. Ed. Omega, Barcelona. ISBN 84-282-0551-5.

Wiens, J. 2004. SPECIATION AND ECOLOGY REVISITED: PHYLOGENETIC NICHE

CONSERVATISM AND THE ORIGIN OF SPECIES. Evolution 58: 193-197. DOI:

10.1111/j.0014-3820.2004.tb01586.x

UNIT 3: ISOLATION MECHANISMS

1.0 Introduction

2.0 Objectives

3.0 Morphological species concept:

3.1 Pre-zygotic

3.1.1 Temporal isolation

3.1.2 Sexual isolation by behaviour or conduct

3.1.3 Mechanical isolation

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3.1.4 Gametic isolation

3.2 Post-zygotic isolation

3.2.1 Zygote mortality and non-viability of hybrids

3.2.2 Hybrid sterility

3.2.3 Multiple mechanisms

3.2.4 Hybrid gender

3.3 Genetics of isolation barriers

3.3.1 Pre-Copulatory isolation mechanisms in animals

3.3.2 Post copulation or fertilization isolation mechanisms in animals

3.3.3. Post copulation or fertilization isolation mechanisms in plants

3.4 Selection for reproductive isolation

4.0 Conclusion

5.0 Summary

6.0 Tutor-Marked Assignment

7.0 References/Further Reading

UNIT 3: ISOLATION MECHANISMS

1.0 Introduction

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The biological species concept helps us ask how species are formed, because it focuses our

attention on the question of how reproductive isolation comes about.

There are many barriers to reproduction. Each species may have its own courtship displays,

or breeding season, so that members of the two species do not have the opportunity to

interbreed, or the two species may be unable to interbreed successfully because of failure of

the egg to become fertilized or to develop.

2.0 Objectives

At the end of this unit, the student should be able to:

• Discuss extensively on Isolation mechanisms

• Discuss pre and post zygotic isolation

• How is reproductive isolation important to speciation and what forms can it take?

3.0 Morphological species concept:

Oak trees look like oak trees, tigers look like tigers. Morphology refers to the form and

structure of an organism or any of its parts. The morphological species concept supports the

widely held view that "members of a species are individuals that look similar to one another."

This school of thought was the basis for Linneaus' original classification, which is still

broadly accepted and applicable today.

This concept became criticized by biologists because it was arbitrary. Many examples were

found in which individuals of two populations were very hard to tell apart but would not mate

with one another, suggesting that they were in fact different species. Mimicry complexes

supplied further evidence against the concept, as organisms of the same species can look very

different, depending upon where they are reared or their life cycle stage (some insects

40
produce a spring brood that looks like one host plant and a summer brood that looks like

another). The morphological species concept was replaced by another viewpoint that puts

more emphasis on the biological differences between species.

Biological species concept: This concept states that "a species is a group of actually or

potentially interbreeding individuals who are reproductively isolated from other such

groups." This definition was attractive to biologists and became widely adopted by the

1940's. It suggested a critical test of species-hood: two individuals belong to the same species

if their gametes can unite with each other under natural conditions to produce fertile

offspring. This concept also emphasized that a species is an evolutionary unit. Members share

genes with other members of their species, and not with members of other species.

Most scientists feel that the biological species concept should be kept, but with some

qualifications. It can only be used with living species, and cannot always be applied to

species that do not live in the same place. The real test applies to species that have the

potential to interbreed.

Most importantly, the biological species concept helps us ask how species are formed,

because it focuses our attention on the question of how reproductive isolation comes about.

Let us first examine types of reproductive isolation, because there are quite a few.

There are many barriers to reproduction. Each species may have its own courtship displays,

or breeding season, so that members of the two species do not have the opportunity to

interbreed. Or, the two species may be unable to interbreed successfully because of failure of

the egg to become fertilized or to develop.

This suggests a simple and useful dichotomy, between pre-mating or prezygotic (i.e., pre-

zygote formation) reproductive isolating mechanisms, and post-mating or postzygotic

41
isolating mechanisms. Remember that a zygote is the cell formed by the union of two

gametes and is the basis of a developing individual.

Despite our increasing ability to understand the finest details of organisms, there is still

debate about what constitutes a species. Definitions of species tend to fall into two main

camps, the morphological and the biological species concepts.

3.1 Pre-zygotic

The mechanisms of reproductive isolation or hybridization barriers are a collection of

mechanisms, behaviors and physiological processes that prevent the members of two

different species that cross or mate from producing offspring, or which ensure that any

offspring that may be produced is not fertile. These barriers maintain the integrity of a species

over time, reducing or directly impeding gene flow between individuals of different species,

allowing the conservation of each species’ characteristics

Pre-zygotic isolation mechanisms are the most economic in terms of the biological efficiency

of a population, as resources are not wasted on the production of a descendent that is weak,

non-viable or sterile.

3.1.1 Temporal isolation

Any of the factors that prevent potentially fertile individuals from meeting will

reproductively isolate the members of distinct species. The types of barriers that can cause

this isolation include: different habitats, physical barriers, and a difference in the time of

sexual maturity or flowering. When factors change, especially physical barriers, often, species

will branch off.

An example of the ecological or habitat differences that impede the meeting of potential pairs

occurs in two fish species of the family Gasterosteidae (sticklebacks). One species lives all

42
year round in fresh water, mainly in small streams. The other species lives in the sea during

winter, but in spring and summer individuals migrate to river estuaries to reproduce. The

members of the two populations are reproductively isolated due to their adaptations to

distinct salt concentrations. An example of reproductive isolation due to differences in the

mating season are found in the toad species Bufo americanus and Bufo fowleri . The members

of these species can be successfully crossed in the laboratory producing healthy, fertile

hybrids. However, mating does not occur in the wild even though the geographical

distribution of the two species overlaps. The reason for the absence of inter-species mating is

that B. americanus mates in early summer and B. fowleri in late summer. Certain plant

species, such as Tradescantia canaliculata and T. subaspera, are sympatric throughout their

geographic distribution yet they are reproductively isolated as they flower at different times

of the year. In addition, one species grows in sunny areas and the other in deeply shaded

areas.

3.1.2 Sexual isolation by behaviour or conduct

The different mating rituals of animal species creates extremely powerful reproductive

barriers, termed sexual or behavior isolation, that isolate apparently similar species in the

majority of the groups of the animal kingdom. In dioecious species, males and females have

to search for a partner, be in proximity to each other, carry out the complex mating rituals and

finally copulate or release their gametes into the environment in order to breed.

Mating dances, the songs of males to attract females or the mutual grooming of pairs, are all

examples of typical courtship behavior that allows both recognition and reproductive

isolation. This is because each of the stages of courtship depend on the behavior of the

partner. The male will only move onto the second stage of the exhibition if the female shows

certain responses in her behavior. He will only pass onto the third stage when she displays a

43
second key behavior. The behaviors of both interlink, are synchronized in time and lead

finally to copulation or the liberation of gametes into the environment. No animal that is not

physiologically suitable for fertilization can complete this demanding chain of behavior. In

fact, the smallest difference in the courting patterns of two species is enough to prevent

mating (for example, a specific song pattern acts as an isolation mechanism in distinct species

of grasshopper of the genus Chorthippus. Even where there are minimal morphological

differences between species, differences in behavior can be enough to prevent mating. For

example, Drosophila melanogaster and D. simulans which are considered twin species due to

their morphological similarity, do not mate even if they are kept together in a laboratory.

Drosophila ananassae and D. pallidosa are twin species from Melanesia. In the wild they

rarely produce hybrids, although in the laboratory it is possible to produce fertile offspring.

Studies of their sexual behavior show that the males court the females of both species but the

females show a marked preference for mating with males of their own species. A different

regulator region has been found on Chromosome II of both species that affects the selection

behavior of the females.

Pheromones play an important role in the sexual isolation of insect species. These compounds

serve to identify individuals of the same species and of the same or different sex. Evaporated

molecules of volatile pheromones can serve as a wide-reaching chemical signal. In other

cases, pheromones may be detected only at a short distance or by contact

In species of the melanogaster group of Drosophila, the pheromones of the females are

mixtures of different compounds, there is a clear dimorphism in the type and/or quantity of

compounds present for each sex. In addition, there are differences in the quantity and quality

of constituent compounds between related species, it is assumed that the pheromones serve to

distinguish between individuals of each species. An example of the role of pheromones in

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sexual isolation is found in 'corn borers' in the genus Ostrinia. There are two twin species in

Europe that occasionally cross. The females of both species produce pheromones that contain

a volatile compound which has two isomers, E and Z; 99% of the compound produced by the

females of one species is in the E isomer form, while the females of the other produce 99%

isomer Z. The production of the compound is controlled by just one locus and the

interspecific hybrid produces an equal mix of the two isomers. The males, for their part,

almost exclusively detect the isomer emitted by the females of their species, such that the

hybridization although possible is scarce. The perception of the males is controlled by one

gene, distinct from the one for the production of isomers, the heterozygous males show a

moderate response to the odour of either type. In this case, just 2 'loci' produce the effect of

ethological isolation between species that are genetically very similar.

Sexual isolation between two species can be asymmetrical. This can happen when the mating

that produces descendants only allows one of the two species to function as the female

progenitor and the other as the male, while the reciprocal cross does not occur. For instance,

half of the wolves tested in the Great Lakes area of America show mitochondrial DNA

sequences of coyotes. While mitochondrial DNA from wolves is never found in coyote

populations. This probably reflects an asymmetry in inter-species mating due to the

difference in size of the two species as male wolves take advantage of their greater size in

order to mate with female coyotes, while female wolves and male coyotes do not mate.

3.1.3 Mechanical isolation

Mating pairs may not be able to couple successfully if their genitals are not compatible. The

relationship between the reproductive isolation of species and the form of their genital organs

was signaled for the first time in 1844 by the French entomologist Léon Dufour. Insects' rigid

carapaces act in a manner analogous to a lock and key, as they will only allow mating

45
between individuals with complementary structures, that is, males and females of the same

species (termed co-specifics).

Evolution has led to the development of genital organs with increasingly complex and

divergent characteristics, which will cause mechanical isolation between species. Certain

characteristics of the genital organs will often have converted them into mechanisms of

isolation. However, numerous studies show that organs that are anatomically very different

can be functionally compatible, indicating that other factors also determine the form of these

complicated structures.

Mechanical isolation also occurs in plants and this is related to the adaptation and coevolution

of each species in the attraction of a certain type of pollinator (where pollination is zoophilic)

through a collection of morphophysiological characteristics of the flowers (called floral

syndrome), in such a way that the transport of pollen to other species does not occur.

3.1.4 Gametic isolation

The synchronous spawning of many species of coral in marine reefs means that inter-species

hybridization can take place as the gametes of hundreds of individuals of tens of species are

liberated into the same water at the same time. Approximately a third of all the possible

crosses between species are compatible, in the sense that the gametes will fuse and lead to

individual hybrids. This hybridization apparently plays a fundamental role in the evolution of

coral species. However, the other two-thirds of possible crosses are incompatible. It has been

observed that in sea urchins of the genus Strongylocentrotus the concentration of

spermatocytes that allow 100% fertilization of the ovules of the same species is only able to

fertilize 1.5% of the ovules of other species. This inability to produce hybrid offspring,

46
despite the fact that the gametes are found at the same time and in the same place, is due to a

phenomenon known as gamete incompatibility, which is often found between marine

invertebrates, and whose physiological causes are not fully understood.

In some Drosophila crosses, the swelling of the female's vagina has been noted following

insemination. This has the effect of consequently, preventing the fertilization of the ovule by

sperm of a different species.

In plants the pollen grains of a species can germinate in the stigma and grow in the style of

other species. However, the growth of the pollen tubes may be detained at some point

between the stigma and the ovules, in such a way that fertilization does not take place. This

mechanism of reproductive isolation is common in the Angiosperms and is called cross-

incompatibility or incongruence. A relationship exists between self-incompatibility and the

phenomenon of cross-incompatibility. In general crosses between individuals of a self-

compatible species (SC) with individuals of a self-incompatible (SI) species give hybrid

offspring. On the other hand, a reciprocal cross (SI x SC) will not produce offspring, because

the pollen tubes will not reach the ovules. This is known as unilateral incompatibility, which

also occurs when two SC or two SI species are crossed.

3.2 Post-zygotic isolation

3.2.1 Zygote mortality and non-viability of hybrids

A type of incompatibility that is found as often in plants as in animals occurs when the ovule

is fertilized but the zygote does not develop, or it develops and the resulting individual has a

reduced viability. This is the case for crosses between species of the frog genus, where widely

differing results are observed depending of the species involved. In some crosses there is no

segmentation of the zygote. In others, normal segmentation occurs in the blastula but

47
gastrulation fails. Finally, in other crosses, the initial stages are normal but errors occur in the

final phases of embryo development. This indicates differentiation of the embryo

development genes (or gene complexes) in these species and these differences determine the

non-viability of the hybrids.

Similar results are observed in mosquitos of the Culex genus, but the differences are seen

between reciprocal crosses, from which it is concluded that the same effect occurs in the

interaction between the genes of the cell nucleus (inherited from both parents) as occurs in

the genes of the cytoplasmic organelles which are inherited solely from the female progenitor

through the cytoplasm of the ovule.

In Angiosperms, the successful development of the embryo depends on the normal

functioning of its endosperm.

The failure of endosperm development and its subsequent abortion has been observed in

many interploidal crosses (that is, those between populations with a particular degree of intra

or interspecific ploidy and in certain crosses in species with the same level of ploidy. The

collapse of the endosperm, and the subsequent abortion of the hybrid embryo is one of the

most common post-fertilization reproductive isolation mechanism found in angiosperms.

3.2.2 Hybrid sterility

A hybrid has normal viability but is deficient in terms of reproduction or is sterile. This is

demonstrated by the mule and in many other well known hybrids. In all of these cases

sterility is due to the interaction between the genes of the two species involved; to

chromosomal imbalances due to the different number of chromosomes in the parent species;

or to nucleus-cytoplasmic interactions such as in the case of Culex described above.

48
Hinnies and mules are hybrids resulting from a cross between a horse and an ass or between a

mare and a donkey, respectively. These animals are nearly always sterile due to the difference

in the number of chromosomes between the two parent species. Both horses and donkeys

belong to the genus Equus, but Equus caballus has 64 chromosomes, while Equus asinus

only has 62. A cross will produce offspring (mule or hinny) with 63 chromosomes, that will

not form pairs, which means that they do not divide in a balanced manner during meiosis. It

is curious that they can cross with each other but the mule and the hinny are actually animals

created by humans, as in the wild the species ignore each other and do not cross. In order to

obtain mules or hinnies it is necessary to train the progenitors to accept copulation between

the species or create them through artificial insemination.

The sterility of many of the interspecific hybrids among the angiosperms is a widely

recognised and studied phenomenon. There are a variety of causes that can determine the

interspecific sterility of hybrids in plants, these may be genetic, related to the genomes or the

interaction between nuclear and cytoplasmic factors, as will be discussed in the

corresponding section. Nevertheless, it should be pointed out that - on the contrary to the

situation in animals - hybridization in plants is a stimulus for the creation of new species.

Indeed, although the hybrid may be sterile it can continue to multiply in the wild through the

mechanisms of asexual reproduction, be they vegetative propagation or apomixis or the

production of seeds. Indeed, interspecific hybridization can be associated with polyploidia

and, in this way, the origin of new species that are called allopolyploids. Rosa canina, for

example, is the result of multiple hybridizations. or there is a type of wheat that is an

allohexaploid that contains the genomes of three different species.

3.2.3 Multiple mechanisms

49
In general, the barriers that separate species do not consist of just one mechanism. The twin

species of Drosophila, D. pseuoobscura and D. persimilis, are isolated from each other by

habitat (persimilis generally lives in colder regions at higher altitudes), by the timing of the

mating season (persimilis is generally more active in the morning and pseuoobscura at night)

and by behavior during mating (the females of both species prefer the males of their

respective species). In this way, although the distribution of these species overlaps in wide

areas of the west of the United States of America, these isolation mechanisms are sufficient to

keep the species separated. Such that, only a few fertile females have been found amongst the

other species among the thousands that have been analyzed. However, when hybrids are

produced between both species, the gene flow between the two will continue to be impeded

as the hybrid males are sterile. Also, and in contrast with the great vigor shown by the sterile

males, the descendants of the backcrosses of the hybrid females with the parent species are

weak and notoriously non-viable. This last mechanism restricts even more the genetic

interchange between the two species of fly in the wild.

3.2.4 Hybrid gender

Haldane's Rule states that when one of the two sexes is absent in interspecific hybrids

between two specific species and then the gender that is not produced, is rare or is sterile is

the heterozygous (or heterogametic) sex. In mammals, at least, there is growing evidence to

suggest that this is due to high rates of mutation of the genes determining masculinity in the

Y chromosome.

It has been suggested that Haldane's Rule simply reflects the fact that the male gender is more

sensitive than the female when the sex-determining genes are included in a hybrid genome.

But there are also organisms in which the heterozygous sex is the female: birds and

50
butterflies and the law is followed in these organisms. Therefore, it is not a problem related to

sexual development, nor with the sex chromosomes. Haldane proposed that the stability of

hybrid individual development requires the full gene complement of each parent species, so

that the hybrid of the heterozygous sex is unbalanced (i.e. missing at least one chromosome

from each of the parental species). For example, the hybrid male obtained by crossing D.

melanogaster females with D. simulans males, which is non-viable, lacks the X chromosome

of D. simulans.

3.3 Genetics of isolation barriers

3.3.1 Pre-copulatory isolation mechanisms in animals

The genetics of ethological isolation barriers will be discussed first. Pre-copulatory isolation

occurs when the genes necessary for the sexual reproduction of one species differ from the

equivalent genes of another species, such that if a male of species A and a female of species

B are placed together they are unable to copulate. Study of the genetics involved in this

reproductive barrier tries to identify the genes that govern distinct sexual behaviors in the two

species. The males of Drosophila melanogaster and those of D. simulans conduct an

elaborate courtship with their respective females, which are different for each species, but the

differences between the species are more quantitative than qualitative. In fact the simulans

males are able to hybridize with the melanogaster females. Although there are lines of the

latter species that can easily cross there are others that are hardly able to. Using this

difference, it is possible to assess the minimum number of genes involved in pre-copulatory

isolation between the melanogaster and simulans species and their chromosomal location.

In experiments, flies of the D. melanogaster line, which hybridizes readily with simulans,

were crossed with another line that it does not hybridize with, or rarely. The females of the

51
segregated populations obtained by this cross were placed next to simulans males and the

percentage of hybridization was recorded, which is a measure of the degree of reproductive

isolation. It was concluded from this experiment that 3 of the 8 chromosomes of the haploid

complement of D. melanogaster carry at least one gene that affects isolation, such that

substituting one chromosome from a line of low isolation with another of high isolation

reduces the hybridization frequency. In addition, interactions between chromosomes are

detected so that certain combinations of the chromosomes have a multiplying effect. Cross

incompatibility or incongruence in plants is also determined by major genes that are not

associated at the self-incompatibility S locus.

3.3.2 Post copulation or fertilization isolation mechanisms in animals

Reproductive isolation between species appears, in certain cases, a long time after

fertilization and the formation of the zygote, as happens - for example - in the twin species

Drosophila pavani and D. gaucha. The hybrids between both species are not sterile, in the

sense that they produce viable gametes, ovules and spermatozoa. However, they cannot

produce offspring as the sperm of the hybrid male do not survive in the semen receptors of

the females, be they hybrids or from the parent lines. In the same way, the sperm of the males

of the two parent species do not survive in the reproductive tract of the hybrid female.[12] This

type of post copulatory isolation appears as the most efficient system for maintaining

reproductive isolation in many species.

In fact, the development of a zygote into an adult is a complex and delicate process of

interactions between genes and the environment that must be carried out precisely, and if

there is any alteration in the usual process, caused by the absence of a necessary gene or the

presence of a different one, it can arrest the normal development causing the non-viability of

the hybrid or its sterility. It should be borne in mind that half of the chromosomes and genes

52
of a hybrid are from one species and the other half come from the other. If the two species are

genetically different, there is little possibility that the genes from both will act harmoniously

in the hybrid. From this perspective, only a few genes would be required in order to bring

about post copulatory isolation, as opposed to the situation described previously for pre-

copulatory isolation.

In many species where pre-copulatory reproductive isolation does not exist, hybrids are

produced but they are of only one sex. This is the case for the hybridization between females

of Drosophila simulans and Drosophila melanogaster males: the hybridized females die early

in their development so that only males are seen among the offspring. However, populations

of D. simulans have been recorded with genes that permit the development of adult hybrid

females, that is, the viability of the females is “rescued”. It is assumed that the normal

activity of these speciation genes is to “inhibit” the expression of the genes that allow the

growth of the hybrid. There will also be regulator genes.

A number of these genes have been found in the melanogaster species group. The first to be

discovered was “Lhr” (Lethal hybrid rescue) located in Chromosome II of D. simulans. This

dominant allele allows the development of hybrid females from the cross between simulans

females and melanogaster males. A different gene, also located on Chromosome II of D.

simulans is “Shfr” that also allows the development of female hybrids, its activity being

dependent on the temperature at which development occurs. Other similar genes have been

located in distinct populations of species of this group. In short, only a few genes are needed

for an effective post copulatory isolation barrier mediated through the non-viability of the

hybrids.

As important as identifying an isolation gene is knowing its function. The Hmr gene, linked

to the X chromosome and implicated in the viability of male hybrids between D.

53
melanogaster and D. simulans, is a gene from the proto-oncogene family myb, that codes for

a transcriptional regulator. Two variants of this gene function perfectly well in each separate

species, but in the hybrid they do not function correctly, possibly due to the different genetic

background of each species. Examination of the allele sequence of the two species shows that

change of direction substitutions are more abundant than synonymous substitutions,

suggesting that this gene has been subject to intense natural selection.

The Dobzhansky-Muller model proposes that reproductive incompatibilities between species

are caused by the interaction of the genes of the respective species. It has been demonstrated

recently that Lhr has functionally diverged in D. simulans and will interact with Hmr which,

in turn, has functionally diverged in D. melanogaster to cause the lethality of the male

hybrids. Lhr is located in a heterochromatic region of the genome and its sequence has

diverged between these two species in a manner consistent with the mechanisms of positive

selection. An important unanswered question is whether the genes detected correspond to old

genes that initiated the speciation favoring hybrid non-viability, or are modern genes that

have appear post-speciation by mutation, that are not shared by the different populations and

that suppress the effect of the primitive non-viability genes. The OdsH (abbreviation of

Odysseus) gene causes partial sterility in the hybrid between Drosophila simulans and a

related species, D. mauritiana, which is only encountered on Mauritius, and is of recent

origin. This gene shows monophyly in both species and also has been subject to natural

selection. It is thought that it is a gene that intervenes in the initial stages of speciation, while

other genes that differentiate the two species show polyphyly. Odsh originated by duplication

in the genome of Drosophila and has evolved at very high rates in D. mauritania, while its

paralogue, unc-4, is nearly identical between the species of the group melanogaster.

Seemingly, all these cases illustrate the manner in which speciation mechanisms originated in

nature, therefore they are collectively known as “speciation genes”, or possibly, gene

54
sequences with a normal function within the populations of a species that diverge rapidly in

response to positive selection thereby forming reproductive isolation barriers with other

species. In general, all these genes have functions in the transcriptional regulation of other

genes.

The Nup96 gene is another example of the evolution of the genes implicated in post-

copulatory isolation. It regulates the production of one of the approximately 30 proteins

required to form a nuclear pore. In each of the simulans groups of Drosophila the protein

from this gene interacts with the protein from another, as yet undiscovered, gene on the X

chromosome in order to form a functioning pore. However, in a hybrid the pore that is

formed is defective and causes sterility. The differences in the sequences of Nup96 have been

subject to adaptive selection, similar to the other examples of speciation genes described

above.

Post-copulatory isolation can also arise between chromosomally differentiated populations

due to chromosomal translocations and inversions. If, for example, a reciprocal translocation

is fixed in a population, the hybrid produced between this population and one that does not

carry the translocation will not have a complete meiosis. This will result in the production of

unequal gametes containing unequal numbers of chromosomes with a reduced fertility. In

certain cases, complete translocations exist that involve more than two chromosomes, so that

the meiosis of the hybrids is irregular and their fertility is zero or nearly zero. Inversions can

also give rise to abnormal gametes in heterozygous individuals but this effect has little

importance compared to translocations. An example of chromosomal changes causing

sterility in hybrids comes from the study of Drosophila nasuta and D. albomicans which are

twin species from the Indo-Pacific region. There is no sexual isolation between them and the

F1 hybrid is fertile. However, the F2 hybrids are relatively infertile and leave few

55
descendants which have a skewed ratio of the sexes. The reason is that the X chromosome of

albomicans is translocated and linked to an autosome which causes abnormal meiosis in

hybrids. Robertsonian translocations are variations in the numbers of chromosomes that arise

from either: the fusion of two acrocentric chromosomes into a single chromosome with two

arms, causing a reduction in the haploid number, or conversely; or the fission of one

chromosome into two acrocentric chromosomes, in this case increasing the haploid number.

The hybrids of two populations with differing numbers of chromosomes can experience a

certain loss of fertility, and therefore a poor adaptation, because of irregular meiosis.

3.3.3. Post copulation or fertilization isolation mechanisms in plants

In plants, hybrids often suffer from an autoimmune syndrome known as hybrid necrosis. In

the hybirds, specific gene products contributed by one of the parents may be inappropriately

recognized as foreign and pathogenic, and thus trigger pervasive cell death throughout the

plant. In at least one case, a pathogen receptor, encoded by the most variable gene family in

plants, was identified as being responsible for hybrid necrosis.

3.4 Selection for reproductive isolation

In 1950 K. F. Koopman reported results from experiments designed to examine the

hypothesis that selection can increase reproductive isolation between populations. He used D.

pseudoobscura and D. persimilis in these experiments. When the flies of these species are

kept at 16°C approximately a third of the matings are interspecific. In the experiment equal

numbers of males and females of both species were placed in containers suitable for their

survival and reproduction. The progeny of each generation were examined in order to

determine if there were any interspecific hybrids. These hybrids were then eliminated. An

equal number of males and females of the resulting progeny were then chosen to act as

56
progenitors of the next generation. As the hybrids were destroyed in each generation the flies

that solely mated with members of their own species produced more surviving descendants

than the flies that mated solely with individuals of the other species. In the table to the right it

can be seen that for each generation the number of hybrids continuously decreased up to the

tenth generation when hardly any interspecific hybrids were produced. It is evident that

selection against the hybrids was very effective in increasing reproductive isolation between

these species. From the third generation, the proportions of the hybrids were less than 5%.

This confirmed that selection acts to reinforce the reproductive isolation of two genetically

divergent populations if the hybrids formed by these species are less well adapted than their

parents.

These discoveries allowed certain assumptions to be made regarding the origin of

reproductive isolation mechanisms in nature. Namely, if selection reinforces the degree of

reproductive isolation that exists between two species due to the poor adaptive value of the

hybrids, it is expected that the populations of two species located in the same area will show a

greater reproductive isolation than populations that are geographically separated. This

mechanism for “reinforcing” hybridization barriers in sympatric populations is called the

"Wallace Effect", as it was first proposed by Alfred Russell Wallace at the end of the 19th

century, and it has been experimentally demonstrated in both plants and animals.

The sexual isolation between Drosophila miranda and D. pseudoobscura, for example, is

more or less pronounced according to the geographic origin of the flies being studied. Flies

from regions where the distribution of the species is superimposed show a greater sexual

isolation than exists between populations originating in distant regions.

On the other hand, interspecific hybridization barriers can also arise as a result of the adaptive

divergence that accompanies allopatric speciation. This mechanism has been experimentally

57
proved by an experiment carried out by Diane Dodd on D. pseudoobscura. A single

population of flies was divided into two, with one of the populations fed with starch-based

food and the other with maltose-based food. This meant that each sub population was adapted

to each food type over a number of generations. After the populations had diverged over

many generations, the groups were again mixed; it was observed that the flies would mate

only with others from their adapted population. This indicates that the mechanisms of

reproductive isolation can arise even though the interspecific hybrids are not selected against.

4.0 Conclusion

In this student the student learnt the following:

• Mechanism of isolation

• Pre and Post-zygotic isolation

• Mechanisms governing isolation mechanisms

• Genetics of isolation barriers

5.0 Summary

Isolating mechanisms are the reproductive characteristics which prevent species from fusing.

Isolating mechanisms are particularly important in the biological species concept, in which

species of sexual organisms are defined by reproductive isolation, i.e. a lack of gene mixture.

Two broad kinds of isolating mechanisms between species are typically distinguished,

together with a number of sub-types.

6.0 Tutor-Marked Assignment

• What do you understand by isolation mechanisms?

58
 • What is the relationship between isolation mechanisms and the biological species

concept?

7.0 References/Further Reading

Mayr E. (1970) Populations, Species, and Evolution. Harvard University Press, Cambridge,

Mass.

Futuyma, D.J. 1986. Evolutionary Biology. Sunderland, Mass: Sinauer Associates, Inc.

Wessells, N.K. and J.L. Hopson. 1988. Biology. New York: Random House. Chapter 43.

Rosenzweig, M.L. 1995. Species Diversity in Space and Time. Cambridge: Cambridge

University Press.

Wu, C. I.; Hollocher, H.; Begun, D. J.; Aquadro, C. F.; Xu, Y.; Wu, M. L. (1995), "Sexual

isolation in Drosophila melanogaster: a possible case of incipient speciation", Proceedings of

the National Academy of Sciences of the United States of America 92 (7): 2519–2523,

doi:10.1073/pnas.92.7.2519, PMC 42249, PMID 7708677

West-eberhard, M.J. (1983), "Sexual Selection, Social Competition, and Speciation", The

Quarterly Review of Biology 58 (2): 155, doi:10.1086/413215

Mendelson, T.C. (2003), "Sexual Isolation Evolves Faster Than Hybrid Inviability in a

Diverse and Sexually Dimorphic enus of", Evolution 57 (2): 317–327, doi:10.1111/j.0014-

3820.2003.tb00266.x, PMID 12683528

59
Perdeck, A.C. (1958), "The Isolating Value of Specific Song Patterns in Two Sibling Species

of Grasshoppers (Chorthippus brunneus Thunb. and C. biguttulus L.)", Behaviour 12 (1-2):

1–75, doi:10.1163/156853957X00074

Casares, P. 2008. Genética de poblaciones y evolutiva. Capítulo 17. Genética del aislamiento

reproductivo. Universidad de Oviedo, España. [1]

Coyne, J.A.; Crittenden, A.P.; Mah, K. (1994), "Genetics of a pheromonal difference

contributing to reproductive isolation in Drosophila", Science 265 (5177): 1461–1464,

doi:10.1126/science.8073292, PMID 8073292

LEHMAN N; Eisenhawer, A.; Hansen, K.; David Mech, L.; Peterson, R. O.; Gogan, P. J. P.;

Wayne, R. K. (1991), "Introgression of coyote mitochondrial DNA into sympatric North

American gray wolf populations", Evolution 45 (1): 104–119, doi:10.2307/2409486,

JSTOR 2409486.

UNIT 4: MUTATION

1.0 Introduction

2.0 Objectives

3.0 Mutation

3.1 Causes of mutation

60
3.2 Classifying Mutations

3.3 Harmful mutations

3.4 Beneficial Mutations

4.0 Conclusion

5.0 Summary

6.0 Tutor-Marked Assignment

7.0 Reference/Further Reading

Unit 4 Mutation

1.0 Introduction

In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA

sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as

sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses and

61
mutagenic chemicals, as well as errors that occur during meiosis or DNA replication. They

can also be induced by the organism itself, by cellular processes such as hyper-mutation. A

mutation is passed to the offspring stably, unless it is a dynamic mutation.

2.0 Objectives

At the end of this unit, the student should know the following:

• Definition of mutation

• What causes mutation

• Types of mutation

3.0 Mutation

62
Duplication of part of a chromosome

The cellular machinery that copies DNA sometimes makes mistakes. These mistakes change

the sequence of a gene. This is called a mutation. There are many kinds of mutations. A point

mutation is a mutation in which one "letter" of the genetic code is changed to another.

Lengths of DNA can also be deleted or inserted in a gene; these are also mutations. Finally,

genes or parts of genes can become inverted or duplicated. Typical rates of mutation are

between 10-10 and 10-12 mutations per base pair of DNA per generation.

Most mutations are thought to be neutral with regards to fitness. Only a small portion of the

genome of eukaryotes contains coding segments, although some non-coding DNA is involved

in gene regulation or other cellular functions, it is probable that most base changes would

have no fitness consequence.

Most mutations that have any phenotypic effect are deleterious. Mutations that result in

amino acid substitutions can change the shape of a protein, potentially changing or

eliminating its function. This can lead to inadequacies in biochemical pathways or interfere

with the process of development. Organisms are sufficiently integrated that most random

changes will not produce a fitness benefit. Only a very small percentage of mutations are

63
beneficial. The ratio of neutral to deleterious to beneficial mutations is unknown and

probably varies with respect to details of the locus in question and environment.

Mutation limits the rate of evolution. The rate of evolution can be expressed in terms of

nucleotide substitutions in a lineage per generation. Substitution is the replacement of an

allele by another in a population. This is a two step process: First a mutation occurs in an

individual, creating a new allele. This allele subsequently increases in frequency to fixation in

the population.

The rate of evolution is k = 2Nvu (in diploids)

Where

k is nucleotide substitutions,

N is the effective population size,

v is the rate of mutation and

u is the proportion of mutants that eventually fix in the population.

Mutation need not be limiting over short time spans. The rate of evolution expressed above is

given as a steady state equation; it assumes the system is at equilibrium. Given the time

frames for a single mutant to fix, it is unclear if populations are ever at equilibrium. A change

in environment can cause previously neutral alleles to have selective values; in the short term

evolution can run on "stored" variation and thus is independent of mutation rate. Other

mechanisms can also contribute selectable variation. Recombination creates new

combinations of alleles (or new alleles) by joining sequences with separate micro-

evolutionary histories within a population. Gene flow can also supply the gene pool with

variants. Of course, the ultimate source of these variants is mutation.

3.1 Causes of mutation

64
Two classes of mutations are spontaneous mutations and induced mutations caused by

mutagens.

Spontaneous mutation

Spontaneous mutations on the molecular level can be caused by:

• Tautomerism – A base is changed by the repositioning of a hydrogen atom, altering

the hydrogen bonding pattern of that base resulting in incorrect base pairing during

replication.

• Depurination – Loss of a purine base (A or G) to form an apurinic site (AP site).

• Deamination – Hydrolysis changes a normal base to an atypical base containing a

keto group in place of the original amine group. Examples include C → U and A →

HX (hypoxanthine), which can be corrected by DNA repair mechanisms; and 5MeC

(5-methylcytosine) → T, which is less likely to be detected as a mutation because

thymine is a normal DNA base.

• Slipped strand mispairing - Denaturation of the new strand from the template during

replication, followed by renaturation in a different spot ("slipping"). This can lead to

insertions or deletions.

Induced mutation

Induced mutations on the molecular level can be caused by:

• Chemicals

o Hydroxylamine NH2OH

o Base analogs (e.g. BrdU)

65
 o Alkylating agents (e.g. N-ethyl-N-nitrosourea) These agents can mutate both

replicating and non-replicating DNA. In contrast, a base analog can only

mutate the DNA when the analog is incorporated in replicating the DNA. Each

of these classes of chemical mutagens has certain effects that then lead to

transitions, transversions, or deletions.

o Agents that form DNA adducts (e.g. ochratoxin A metabolites)

o DNA intercalating agents (e.g. ethidium bromide)

o DNA crosslinkers

o Oxidative damage

o Nitrous acid converts amine groups on A and C to diazo groups, altering their

hydrogen bonding patterns which leads to incorrect base pairing during

replication.

• Radiation

o Ultraviolet radiation (nonionizing radiation). Two nucleotide bases in DNA –

cytosine and thymine – are most vulnerable to radiation that can change their

properties. UV light can induce adjacent pyrimidine bases in a DNA strand to

become covalently joined as a pyrimidine dimer. UV radiation, particularly

longer-wave UVA, can also cause oxidative damage to DNA.

o Ionizing radiation

o Radioactive decay, such as 14C in DNA

• Viral infections

DNA has so-called hotspots, where mutations occur up to 100 times more frequently than the

normal mutation rate. A hotspot can be at an unusual base, e.g., 5-methylcytosine.

66
Mutation rates also vary across species. Evolutionary biologists have theorized that higher

mutation rates are beneficial in some situations, because they allow organisms to evolve and

therefore adapt more quickly to their environments. For example, repeated exposure of

bacteria to antibiotics, and selection of resistant mutants, can result in the selection of bacteria

that have a much higher mutation rate than the original population.

3.2 Classifying Mutations

67
Five types of chromosomal mutations.

1. Structural Effects

68
The sequence of a gene can be altered in a number of ways. Gene mutations have varying

effects on health depending on where they occur and whether they alter the function of

essential proteins. Structurally, mutations can be classified as:

Small-scale mutations. These are mutations that affecting one or a few nucleotides. These

include:

Point mutations. Point mutations involve an exchange of a single nucleotide for another one.

Most common is the transition that exchanges a purine for a purine (A ↔ G) or a pyrimidine

for a pyrimidine, (C ↔ T). Point mutations are often caused by chemicals or malfunction of

DNA replication. A transition can be caused by nitrous acid, base mis-pairing, or mutagenic

base analogs such as 5-bromo-2-deoxyuridine (BrdU). Less common is a transversion, which

exchanges a purine for a pyrimidine or a pyrimidine for a purine (C/T ↔ A/G). A point

mutation can be reversed by another point mutation, in which the nucleotide is changed back

to its original state (true reversion) or by second-site reversion (a complementary mutation

elsewhere that results in regained gene functionality). These changes are classified as

transitions or transversions. An example of a transversion is adenine (A) being converted into

a cytosine (C). There are also many other examples that can be found. Another Point

mutation that occur within the protein coding region of a gene may be classified into three

kinds, depending upon what the erroneous codon codes for:

Silent mutations. Silent mutations are those that code for the same amino acid, because of

the redundancy of the genetic code. That is, there is a change in the bases but the altered

triplet still inserts the same amino acid as before into the protein.

Missense mutations. Missense mutations code for a different amino acid.

Nonsense mutations. Nonsense mutations code for a "stop" and can truncate the protein.

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Insertions. Insertions are mutations that add one or more extra nucleotides into the DNA.

They are usually caused by transposable elements, or errors during replication of repeating

elements (e.g. AT repeats). Insertions in the coding region of a gene may alter splicing of the

mRNA (splice site mutation), or cause a shift in the reading frame (frameshift), both of which

can significantly alter the gene product. Insertions can be reverted by excision of the

transposable element.

Deletions. Deletions remove one or more nucleotides from the DNA. Like insertions, these

mutations can alter the reading frame of the gene. They are irreversible.

Large-scale mutations. Large scale mutations in chromosomal structure may include:

Amplifications. Amplifications (or gene duplications) lead to multiple copies of all

chromosomal regions, increasing the dosage of the genes located within them.

Deletions. Deletions of large chromosomal regions lead to loss of the genes within those

regions.

Juxtaposing mutations. Mutations whose effect is to juxtapose previously separate pieces of

DNA, potentially bringing together separate genes to form functionally distinct fusion genes

(e.g. bcr-abl). These include:

Chromosomal translocations. Chromosomal translocations interchange genetic parts from

nonhomologous chromosomes.

Interstitial deletions. Intersitional deletions involve an intra-chromosomal deletion that

removes a segment of DNA from a single chromosome, thereby apposing previously distant

genes. For example, cells isolated from a human astrocytoma, a type of brain tumor, were

found to have a chromosomal deletion removing sequences between the "fused in

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glioblastoma" (fig) gene and the receptor tyrosine kinase "ros," producing a fusion protein

(FIG-ROS). The abnormal FIG-ROS fusion protein has constitutively active kinase activity

that causes oncogenic transformation (a transformation from normal cells to cancer cells).

Chromosomal inversions. Chromosomal inversions involve reversing the orientation of a

chromosomal segment.

Loss of heterozygosity. Loss of heterozygosity involves the loss of one allele, either by a

deletion or recombination event, in an organism that previously had two different alleles.

2 Functional Effects

Loss-of-function mutations. Loss-of-function mutations are the result of gene product

having less or no function. When the allele has a complete loss of function (null allele) it is

often called an amorphic mutation. Phenotypes associated with such mutations are most often

recessive. Exceptions are when the organism is haploid, or when the reduced dosage of a

normal gene product is not enough for a normal phenotype (this is called haploinsufficiency).

Gain-of-function mutations. Gain-of-function mutations change the gene product such that

it gains a new and abnormal function. These mutations usually have dominant phenotypes.

Often called a neo-morphic mutation.

Dominant negative mutations. Dominant negative mutations (also called anti-morphic

mutations) have an altered gene product that acts antagonistically to the wild-type allele.

These mutations usually result in an altered molecular function (often inactive) and are

characterized by a dominant or semi-dominant phenotype. In humans, Marfan syndrome is an

example of a dominant negative mutation occurring in an autosomal dominant disease. In this

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condition, the defective glycoprotein product of the fibrillin gene (FBN1) antagonizes the

product of the normal allele.

Lethal mutations. Lethal mutations are mutations that lead to a phenotype incapable of

effective reproduction.

3 By aspect of phenotype affected

Morphological mutations. Morphological mutations usually affect the outward appearance

of an individual. Mutations can change the height of a plant or change it from smooth to

rough seeds.

Biochemical mutations. Biochemical mutations result in lesions stopping the enzymatic

pathway. Often, morphological mutants are the direct result of a mutation due to the

enzymatic pathway.

4 By inheritance

The human genome contains two copies of each gene—a paternal and a maternal allele.

• Wildtype or Homozygous non-mutated. This occurs when neither of the alleles are

mutated.

• A Heterozygous mutation. Heterozygous mutations occurs when only one allele is

mutated.

• A Homozygous mutation. Homozygous mutation is when both the paternal and

maternal alleles have an identical mutation.

• Compound heterozygous mutations. Compound heterozygous mutations or a genetic

compound is when the paternal and maternal alleles have two different mutations.

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5 Special classes

• Conditional mutation. Conditional mutation is a mutation that has wild-type (or less

severe) phenotype under certain "permissive" environmental conditions and a mutant

phenotype under certain "restrictive" conditions. For example, a temperature-sensitive

mutation can cause cell death at high temperature (restrictive condition), but might

have no deleterious consequences at a lower temperature (permissive condition).

3.3 Harmful mutations

Changes in DNA caused by mutation can cause errors in protein sequence, creating partially

or completely non-functional proteins. To function correctly, each cell depends on thousands

of proteins to function in the right places at the right times. When a mutation alters a protein

that plays a critical role in the body, a medical condition can result. A condition caused by

mutations in one or more genes is called a genetic disorder. However, only a small

percentage of mutations cause genetic disorders; most have no impact on health. For

example, some mutations alter a gene's DNA base sequence but do not change the function of

the protein made by the gene.

If a mutation is present in a germ cell, it can give rise to offspring that carries the mutation in

all of its cells. This is the case in hereditary diseases. On the other hand, a mutation can occur

in a somatic cell of an organism. Such mutations will be present in all descendants of this

cell, and certain mutations can cause the cell to become malignant, and thus cause cancer.

Often, gene mutations that could cause a genetic disorder are repaired by the DNA repair

system of the cell. Each cell has a number of pathways through which enzymes recognize and

repair mistakes in DNA. Because DNA can be damaged or mutated in many ways, the

process of DNA repair is an important way in which the body protects itself from disease.

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3.4 Beneficial Mutations

A very small percentage of all mutations actually have a positive effect. These mutations lead

to new versions of proteins that help an organism and its future generations better adapt to

changes in their environment.

For example, a specific 32 base pair deletion in human CCR5 (CCR5-∆32) confers HIV

resistance to homozygotes and delays AIDS onset in heterozygotes. The CCR5 mutation is

more common in those of European descent. One theory for the etiology of the relatively high

frequency of CCR5-∆32 in the European population is that it conferred resistance to the

bubonic plague in mid-fourteenth century Europe. People who had this mutation were able to

survive infection thus its frequency in the population increased. It could also explain why this

mutation is not found in Africa where the bubonic plague never reached. A more recent

theory says the selective pressure on the CCR5 Delta 32 mutation has been caused by

smallpox instead of bubonic plague.

4.0 Conclusion

At the end of this unit, the student learnt the following:

• Definition of mutation

• Causes and Classifications of mutation.

5.0 Summary

Mutation is the alteration of DNA sequence, whether it is in a small way by the alteration of a

single base pair, or whether it be a gross event such as the gain or loss of an entire

chromosome. It may be caused through the action of damaging chemicals, or radiation, or

through the errors inherent in the DNA replication and repair reactions. One consequence

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may be genetic disease. However, although in the short term mutation may seem to be a BAD

THING, in the long term it is essential to our existence. Without mutation there could be no

change and without change life cannot evolve. If it had not been for mutation the world

would still be covered in primeval slime.

6.0 Tutor-Marked Assignment

• What is mutation?

• What are the different types of mutation?

• How important is mutation to the evolutionary process?

7.0 Reference/Further Reading

Types of genetic mutations. http://ghr.nlm.nih.gov/

Leroi, A. M. 2003. Mutants: On Genetic Variety and the Human Body. New York: Viking.

ISBN 0670031100.

Maki, H. 2002. Origins of spontaneous mutations: specificity and directionality of base-

substitution, frameshift, and sequence-substitution mutageneses. Annual Review of Genetics

36: 279-303.

Mayr, E. What Evolution Is. New York: Basic Books, 2001. ISBN 0465044255

Taggart, R., and C. Starr. 2006. Biology The Unity and Diversity of Life. Thompson

Brooks/Cole

Bertram J (2000). "The molecular biology of cancer". Mol. Aspects Med. 21 (6): 167–223.

doi:10.1016/S0098-2997(00)00007-8. PMID 11173079.

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Aminetzach YT, Macpherson JM, Petrov DA (2005). "Pesticide resistance via transposition-

mediated adaptive gene truncation in Drosophila". Science 309 (5735): 764–7.

doi:10.1126/science.1112699. PMID 16051794.

Burrus V, Waldor M (2004). "Shaping bacterial genomes with integrative and conjugative

elements". Res. Microbiol. 155 (5): 376–86. doi:10.1016/j.resmic.2004.01.012.

PMID 15207870.

Sawyer SA, Parsch J, Zhang Z, Hartl DL (2007). "Prevalence of positive selection among

nearly neutral amino acid replacements in Drosophila". Proc. Natl. Acad. Sci. U.S.A. 104

(16): 6504–10. doi:10.1073/pnas.0701572104. PMC 1871816. PMID 17409186.

76
UNIT 5: OUTCOMES OF EVOLUTION

CONTENTS

1.0 Introduction

2.0 Objectives

3.0 Main Focus

3.1 Adaptation

3.2 Speciation

3.3 Extinction

4.0 Conclusion

5.0 Summary

6.0 Tutor-Marked Assignment

7.0 Reference/Further Readings

1.0 Introduction

Entirely, every aspect of the behaviour and form of organisms are influenced by evolution.

Importantly, the most prominent are the specific behavioural and physical adaptations that are

the outcome of natural selection. Certain activities are aided by these adaptations which

increase fitness. Such activities include; finding food, avoiding predators or attracting mates.

Organisms can also respond to selection by co-operating with each other, usually by aiding

their relatives or engaging in mutually beneficial symbiosis. Evolution produces new species

through splitting ancestral populations of organisms into new groups that cannot or will not

interbreed in the longer term.

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2.0 Objectives

Based on the theories of evolution, at the end of this study; the student should be able to

discuss the outcomes of evolution and how these outcomes affect the changes in our

environment, related to species existence.

3.0Main focus

The outcomes of evolution are sometimes divided into macroevolution. Macroevolution

occurs at or above the level of species, such as extinction and speciation and microevolution,

which refers to smaller evolutionary changes, such as adaptations, within a species or

population. Generally, the outcome of long periods of microevolution is referred

macroevolution. Hence, the distinction between micro- and macroevolution is not a

fundamental one – the time involved is simply the difference. In macroevolution however,

the traits of the entire species may be important. For example, a large amount of variation

among individuals allows a species to rapidly adapt to new habitats, reducing the possibility

of the species going extinct, while a wide geographic range increases the chance of

speciation, by making it more likely that part of the population will become isolated. In this

regard, microevolution and macroevolution might involve selection at different levels –

microevolution acting on genes and organisms, against macroevolution processes which

include species selection acting on entire species and affecting their rates of speciation and

extinction.

It is often misconceived that evolution has goals or long-term plans; in the real sense of it

however, evolution has no long-term goal and does not necessarily produce greater

complexity. Inspite of the fact that complex species have evolved, they occur as a side effect

of the overall number of organisms increasing and simple forms of life still remain more

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common in the biosphere. A good example is that the overwhelming majority of species are

microscopic prokaryotes, which form about half the world's biomass despite their small size

and constitute the vast majority of Earth's biodiversity. Simple organisms therefore have been

the dominant form of life on Earth throughout its history and continue to be the main form of

life up to the present day, with complex life only appearing more diverse because it is more

noticeable. Importantly, the evolution of microorganisms is particularly important to modern

evolutionary research, since their rapid reproduction allows the study of experimental

evolution and the observation of evolution and adaptation in real time.

In 1859 the English naturalist Charles Darwin published The Origin of Species. The book

pointed at two major arguments: First, Charles Darwin presented a dearth of evidence of

evolution. He said that all living things on earth today are the descendants of earlier species.

Second, he proposed a mechanism of natural selection to explain how evolution takes place.

Evolution involves two interrelated phenomena; adaptation and speciation.

3.1 Adaptation

Over a period of time, species modify their phenotypes in certain ways that allow them to

succeed in their environment. Adaptation is a process that ensures organisms are better suited

to their habitat. Adaptation may also refer to a trait that is key to an organism's survival. A

good example is the adaptation of horses' teeth to the grinding of grass. By using the term

adaptation for the evolutionary process and adaptive trait for the product the two senses of

the word may be distinguished. Adaptations are produced by natural selection. Theodosius

Dobzhansky brought about the following definitions;

1. Adaptation is the evolutionary process whereby an organism becomes better able to

live in its habitat or habitats.

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 2. Adaptedness is the state of being adapted: the degree to which an organism is able to

live and reproduce in a given set of habitats.

3. An adaptive trait is an aspect of the developmental pattern of the organism which

enables or enhances the probability of that organism surviving and reproducing.

Adaptation may cause either the loss of an ancestral feature or the gain of a new feature. An

example that shows both types of change is bacterial adaptation to antibiotic selection, with

genetic changes causing antibiotic resistance by either modifying the target of the drug, or

increasing the activity of transporters that pump the drug out of the cell. A controversial but

interesting idea is that some adaptations might increase the ability of organisms to generate

genetic diversity and adapt by natural selection

A baleen whale skeleton, a and b label flipper bones, which were adapted from front leg bones: while

c indicates vestigial leg bones, suggesting an adaptation from land to sea.

Adaptation occurs through the gradual modification of existing structures. Consequently,

structures with similar internal organisation may have different functions in related

organisms. This is the result of a single ancestral structure being adapted to function in

different ways. The bones within bat wings, for example, are very similar to those in mice

feet and primate hands, due to the descent of all these structures from a common mammalian

ancestor. However, since all living organisms are related to some extent, even organs that

appear to have little or no structural similarity, such as arthropod, squid and vertebrate eyes,

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or the limbs and wings of arthropods and vertebrates, can depend on a common set of

homologous genes that control their assembly and function; this is called deep homology.

During evolution, some structures may lose their original function and become vestigial

structures. Such structures may have little or no function in a current species, yet have a clear

function in ancestral species, or other closely related species. Examples include pseudogenes,

the non-functional remains of eyes in blind cave-dwelling fish wings in flightless birds, and

the presence of hip bones in whales and snakes. Examples of vestigial structures in humans

include wisdom teeth, the coccyx, the vermiform appendix, and other behavioural vestiges

such as goose bumps and primitive reflexes

An area of current investigation in evolutionary developmental biology is the developmental

basis of adaptations and exaptations. This research looks at the origin and evolution of

embryonic development and how modifications of development and developmental processes

produce novel features. This study has shown that evolution can change a development to

produce new structures, such as embryonic bone structures that develop into the jaw in other

animals instead forming part of the middle ear in mammals. It is also possible for structures

that have been lost in evolution to reappear due to changes in developmental genes, such as a

mutation in chickens causing embryos to grow teeth similar to those of crocodiles. It is now

becoming apparent that most alterations in the form of organisms are due to changes in a

small set of conserved genes.

3.2 Speciation

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The four Mechanisms of Speciation

When a species diverges into two or more descendant species, the process is called

Speciation. In attempting to define what a species is, we find multiple ways of doing so. The

choice of definition is dependent on the particularities of the species concerned. A good

example is that some species concepts apply more readily toward sexually reproducing

organisms while others lend themselves better toward asexual organisms. Although there are

a variety of species concepts, these various concepts can be placed into one of three
thre broad

philosophical approaches: interbreeding, ecological and phylogenetic.

Barriers to reproduction between two diverging sexual populations are required for the

populations to become new species.

species. Gene flow may slow this process by spreading the new

genetic variants also to the other populations. Depending on how far two species have

diverged since their most recent common ancestor,

ancestor, it may still be possible for them to

produce offspring, as with horses and donkeys mating to produce mules.

mules Such hybrids are

generally infertile.. In this case, closely related species may regularly interbreed, but hybrids

will be selected against and the species will remain distinct. However, viable hybrids are

occasionally formed and these new species can either have properties intermediate between

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their parent species, or possess a totally new phenotype. The importance of hybridisation in

producing new species of animals is unclear, although cases have been seen in many types of

animals, with the gray tree frog being a particularly well-studied example.

Speciation has been observed under controlled laboratory conditions and in nature. In

sexually reproducing organisms, speciation results from reproductive isolation followed by

genealogical divergence. There are four mechanisms for speciation. The most common in

animals is allopatric speciation, which occurs in populations initially isolated geographically,

such as by habitat fragmentation or migration. Selection under these conditions can produce

very rapid changes in the appearance and behaviour of organisms. As selection and drift act

independently on populations isolated from the rest of their species, separation may

eventually produce organisms that cannot interbreed.

The second mechanism of speciation is peripatric speciation, which occurs when small

populations of organisms become isolated in a new environment. This differs from allopatric

speciation in that the isolated populations are numerically much smaller than the parental

population. Here, the founder effect causes rapid speciation after an increase in inbreeding

increases selection on homozygotes, leading to rapid genetic change.

The third mechanism of speciation is parapatric speciation. This is similar to peripatric

speciation in that a small population enters a new habitat, but differs in that there is no

physical separation between these two populations. Instead, speciation results from the

evolution of mechanisms that reduce gene flow between the two populations. This occurs

when there has been a drastic change in the environment within the parental species' habitat.

One example is the grass Anthoxanthum odoratum, which undergoes parapatric speciation in

response to localised metal pollution from mines. In this instance, plants that have resistance

to high levels of metals in the soil evolve. Selection against interbreeding with the metal-

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sensitive parental population produced a gradual change in the flowering time of the metal-

resistant plants, which eventually produced complete reproductive isolation. Selection against

hybrids between the two populations may cause reinforcement, which is the evolution of

traits that promote mating within a species, as well as character displacement, which is when

two species become more distinct in appearance.

Lastly, sympatric speciation is where species diverge without geographic isolation or changes

in habitat. This is rare since even a small amount of gene flow may remove genetic

differences between parts of a population. Generally, sympatric speciation in animals requires

the evolution of both genetic differences and non-random mating, to allow reproductive

isolation to evolve.

The cross-breeding of two related species to produce a new hybrid species is one type of

sympatric speciation. This is not common in animals as animal hybrids are usually sterile.

This is because during meiosis the homologous chromosomes from each parent are from

different species and cannot successfully pair. However, it is more common in plants because

plants often double their number of chromosomes, to form polyploids. This allows the

chromosomes from each parental species to form matching pairs during meiosis, since each

parent's chromosomes are represented by a pair already. An example of such a speciation

event is when the plant species Arabidopsis thaliana and Arabidopsis arenosa cross-bred to

give the new species Arabidopsis suecica. This happened about 20,000 years ago and the

speciation process has been repeated in the laboratory, which allows the study of the genetic

mechanisms involved in this process. Indeed, chromosome doubling within a species may be

a common cause of reproductive isolation, as half the doubled chromosomes will be

unmatched when breeding with undoubled organisms.

3.3 Extinction

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The disappearance of an entire species is called Extinction . It is not an unusual event,

however species regularly appear through speciation and disappear through extinction. Most

animal and plant species that have lived on Earth millions of years ago are now extinct, and

this appears to be the ultimate fate of all species. These extinctions have been continuous and

have happened through the course of our history in the world, although the rate of extinction

spikes in occasional mass extinction events. The Cretaceous–Tertiary extinction event, during

which the non-avian dinosaurs went extinct is the most well-known, but the earlier

approximately 96% of species driven to extinction during the Permian–Triassic extinction

event was even more severe. The Holocene extinction event is an ongoing mass extinction

associated with humanity's expansion across the globe over the past few thousand years.

Present-day extinction rates are 100–1000 times greater than the background rate and up to

30% of species may be extinct by the mid 21st century. Human activities are now the primary

cause of the ongoing extinction event; global warming may further accelerate it in the future.

The role of extinction in evolution is not very well understood and may depend on which type

of extinction is considered. The major reasons for the continuous "low-level" extinction

events, which form the majority of extinctions, may be the result of competition between

species for limited resources. If one species can out-compete another, this could produce

species selection, with the fitter species surviving and the other species being driven to

extinction. The intermittent mass extinctions are also important, but instead of acting as a

selective force, they drastically reduce diversity in a nonspecific manner and promote bursts

of rapid evolution and speciation in survivors.

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4.0 Conclusion

The student should be able to adequately discuss the outcomes of evolution and how it has

shaped the existence of present day species in our world today. The student should also be

able to elaborate on the major aspects that have determined the existence of species.

5.0 Summary

Evolutionary outcomes have shaped the way our world is today. As evolution has influenced

and shaped organisms in terms of behaviour and form, natural selection has resulted in

physical adaptations and specific behavioural patterns. The outcomes including adaptation,

speciation and extinction have been key factors that have ensured the changes and survival of

species.

6.0 Tutor-Marked Assignment

• What are the outcomes of Evolution

• What do you understand by Speciation and Adaptation

• What are the mechanisms in Speciation

7.0 Reference/Further Readings

Scott EC, Matzke NJ (2007). "Biological design in science classrooms". Proc. Natl. Acad.

Sci. U.S.A.. 104 1 (suppl_1): 8669–76

Hendry AP, Kinnison MT (2001). "An introduction to microevolution: rate, pattern, process".

Genetica 112–113: 1–8

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Jablonski, D. (2000). "Micro- and macroevolution: scale and hierarchy in evolutionary

biology and paleobiology". Paleobiology 26 (sp4): 15–52.

Mayr, Ernst 1982. The growth of biological thought. Harvard. p483: "Adaptation... could no

longer be considered a static condition, a product of a creative past and became instead a

continuing dynamic process."

Dobzhansky, T.; Hecht, MK; Steere, WC (1968). "On some fundamental concepts of

evolutionary biology". Evolutionary biology volume 2 (1st ed.). New York: Appleton-

Century-Crofts. pp. 1–34.

Dobzhansky, T. (1956). "Genetics of natural populations XXV. Genetic changes in

populations of Drosophila pseudoobscura and Drosphila persimilis in some locations in

California". Evolution 10 (1): 82–92.

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/S/Speciation.html

http://anthro.palomar.edu/evolve/default.htm

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MODULE 2: POPULATION GENETICS

Unit 1: History of Population Genetics

Unit 2: Processes of Population Genetics

Unit 3: Hardey-Weinberg Principle

Unit 4: Gene Frequency/Equilibrium

UNIT 1: HISTORY OF POPULATION GENETICS

Content

I.0 Introduction

2.0 Objectives

3.0 Population

3.1 History of Population Genetics

4.0 Conclusion

5.0 Summary

6.0 Tutor-Marked Assignment

7.0 Reference/Further Readings

Unit 1 History of Population Genetics

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1.0 Introduction

The study of allele frequency, distribution and change under the influence of the four main

evolutionary processes namely: natural selection, genetic drift, mutation and gene flow. It

takes into account the factors of recombination, population subdivision and population

structure. Population genetics attempts to explain adaptation and speciation.

The emergence of the modern evolutionary synthesis was due in part to Population genetics.

Its primary founders were Sewall Wright, J. B. S. Haldane and R. A. Fisher, who also laid the

foundations for the related discipline of quantitative genetics.

2.0 Objectives

At the end of this unit, students should be able to

• Define Population Genetics

• Describe the History of Population Genetics

3.0 Population Genetics

Population genetics is a field of biology that studies the genetic composition of biological

populations and the observed changes in the genetic composition that result from the

operation of various factors, including natural selection. Experts in population genetics

pursue their goals by employing the following methods; development of mathematical

models of gene frequency dynamics, extraction of conclusions from those models about the

likely patterns of genetic variation in actual populations and testing the conclusions against

empirical data. A number of the more robust generalizations to emerge from population-

genetic analysis include;

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Population genetics as being bound with the study of evolution and natural selection, which is

often referred to as the theoretical cornerstone of modern Darwinism. This is as a result of the

fact that natural selection is one of the most important factors that can affect a population's

genetic composition. Natural selection occurs when some variants in a population out-

reproduce other variants, as a result of being better adapted to the environment, or ‘fitter’.

Presuming the fitness differences are at least partly due to genetic differences, this will cause

the population's genetic makeup to be altered over time. While studying the formal models of

gene frequency change, population genetics experts hope to shed light on the evolutionary

process and permit the consequences of different evolutionary hypotheses to be explored in a

quantitatively precise way.

In the 1920s and 1930s the field of population genetics came into light due to the work of

R.A. Fisher, J.B.S. Haldane and Sewall Wright. Their achievement was to integrate the

principles of Mendelian genetics, which had been rediscovered at the turn of century, with

Darwinian natural selection. Many of the early Mendelians did not accept Darwin's

‘gradualist’ account of evolution, believing instead that novel adaptations must arise in a

single mutational step; conversely, many of the early Darwinians did not believe in

Mendelian inheritance, often because of the erroneous belief that it was incompatible with the

process of evolutionary modification as described by Darwin. By working out mathematically

the consequences of selection acting on a population obeying the Mendelian rules of

inheritance, Fisher, Haldane and Wright showed that Darwinism and Mendelism were not

just compatible but excellent bed fellows; this played a key part in the formation of the ‘neo-

Darwinian synthesis’, and explains why population genetics came to occupy so pivotal a role

in evolutionary theory.

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Population genetics is the study of the frequency and interaction of alleles and genes in

populations. A sexual population is a set of organisms in which any pair of members can

breed together. This implies that all members belong to the same species and live near each

other.

A good example is; all of the moths of the same species living in an isolated forest are a

population. A gene in this population may have several alternate forms, which account for

variations between the phenotypes of the organisms. An example might be a gene for

coloration in moths that has two alleles: black and white. A gene pool is the complete set of

alleles for a gene in a single population; the allele frequency for an allele is the fraction of the

genes in the pool that is composed of that allele. Evolution occurs when there are changes in

the frequencies of alleles within a population; for example, the allele for black colour in a

population of moths becoming more common.

3.1 History of Population Genetics

Population genetics began as attempting to reconcile the Mendelian and biometrician models.

A major step was the work of the British biologist and statistician R.A. Fisher. In a series of

papers starting in 1918 and culminating in his 1930 book The Genetical Theory of Natural

Selection. Fisher showed that the continuous variation measured by the biometricians could

be produced by the combined action of many discrete genes, and that natural selection could

change allele frequencies in a population, resulting in evolution. In 1924, a series of papers

by J.B.S. Haldane worked out the mathematics of allele frequency change at a single gene

locus under a broad range of conditions. Haldane also applied statistical analysis to real-

world examples of natural selection, such as the evolution of industrial melanism in peppered

moths, and showed that selection coefficients could be larger than Fisher assumed, leading to

more rapid adaptive evolution.

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Sewall Wright an American biologist, who had a background in animal breeding

experiments, centred his research on combinations of interacting genes and the effects of

inbreeding on small, relatively isolated populations that exhibited genetic drift. In 1932,

Wright introduced the concept of an adaptive landscape and argued that genetic drift and

inbreeding could drive a small, isolated sub-population away from an adaptive peak, allowing

natural selection to drive it towards different adaptive peaks.

Population genetics as a discipline was based on the work of Fisher, Haldane and Wright.

This integrated natural selection with Mendelian genetics, which was the critical first step in

developing a unified theory of how evolution worked.

John Maynard Smith was Haldane's pupil, whilst W.D. Hamilton was heavily influenced by

the writings of Fisher. The American George R. Price worked with both Hamilton and

Maynard Smith. American Richard Lewontin and Japanese Motoo Kimura were heavily

influenced by Wright.

Ordinary genetics in comparism with population genetics, looks at how one selects breeding

stock to produce the best possible offspring. Population genetics looks at the statistical

distribution of genes in a particular breeding population, such as a breed of dog, and how

different kinds of selection can affect that gene distribution. Ordinary genetics is seen as

predicting the phenotypic makeup of the next generation, while population genetics predicts

the genetic makeup of the breed as a whole, often several generations away.

Population genetics is concerned with gene and genotype frequencies, the factors that tend to

keep them constant, and the factors that tend to change them in populations. It is largely

concerned with the study of polymorphisms. It directly impacts counselling, forensic

medicine, and genetic screening.

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The mathematics of population genetics was originally developed as the beginning of the

modern evolutionary synthesis. According to Beatty (1986), population genetics defines the

core of the modern synthesis. In the first few decades of the 20th century, most field

naturalists continued to believe that Lamarckian and orthogenic mechanisms of evolution

provided the best explanation for the complexity they observed in the living world. However,

as the field of genetics continued to develop, those views became less tenable. During the

modern evolutionary synthesis, these ideas were purged, and only evolutionary causes that

could be expressed in the mathematical framework of population genetics were retained.

Consensus was reached as to which evolutionary factors might influence evolution, but not as

to the relative importance of the various factors.

Theodosius Dobzhansky, a postdoctoral worker in T. H. Morgan's lab, had been influenced

by the work on genetic diversity by Russian geneticists such as Sergei Chetverikov. He

helped to bridge the divide between the foundations of microevolution developed by the

population geneticists and the patterns of macroevolution observed by field biologists, with

his 1937 book Genetics and the Origin of Species. Dobzhansky examined the genetic

diversity of wild populations and showed that, contrary to the assumptions of the population

geneticists, these populations had large amounts of genetic diversity, with marked differences

between sub-populations. The book also took the highly mathematical work of the population

geneticists and put it into a more accessible form. Many more biologists were influenced by

population genetics via Dobzhansky than were able to read the highly mathematical works in

the original.

4.0 Conclusion

Students should be able to explain population genetics as we know it today. They should

understand how the present theory arose from the need to reconcile Mendel with Darwin, a

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need which became increasingly urgent as the empirical evidence for Mendelian inheritance

began to pile up.

5.0 Summary

Population genetics is concerned with gene and genotype frequencies, the factors that tend to

keep them constant, and the factors that tend to change them in populations.

6.0 Tutor-Marked Assignment

• What are the principles of population genetics

• Identify keys areas of biological and environmental conservation where a genetic

approach benefits outcomes of management

• Critically review original research in population genetics

7.0 Reference Reading

Postlethwalt, John (2009). Modern Biology. Holt, Rinehart and Winston. pp. 317

Hartl, Daniel (2007). Principles of Population Genetics. Sinauer Associates. p. 95

Michael M. Desai, Daniel S. Fisher (2007). "Beneficial Mutation Selection Balance and

the Effect of Linkage on Positive Selection". Genetics 176 (3): 1759–1798

Provine, W.B., 1971, The Origins of Theoretical Population Genetics, Chicago:

University of Chicago Press.

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UNIT 2: PROCESSES OF POPULATION GENETICS

Contents

1.0 Introduction

2.0 Objectives

3.0 Natural Selection

3.1 Genetic Drift

3.2 Mutation

3.3 Gene flow and transfer

3.4 Reproductive isolation

3.5 Genetic Structure

3.6 Horizontal transfer

3.7 Complications in population genetics

4.0 Conclusion

5.0 Summary

6.0 Tutor-Marked Assignment

7.0 Reference/Further Readings

Unit 2 Processes of Population Genetics

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1.0 Introduction

Population genetics is governed by four fundamental processes. Population genetics is

intimately bound up with the study of evolution and natural selection, and is often regarded as

the theoretical cornerstone of modern Darwinism. The four processes governing population

genetics include; Natural selection, genetic drift, mutation and gene flow and transfer.

2.0 Objectives

• To explain classical transmission genetics and discuss this in the context of genes

• To review the overwhelming scientific evidence for biological evolution

• To explore how selection influences the genetic composition of a population

3.0 Natural Selection

Selection refers to changes in allele frequencies due to the effects of the gene on its host.

Examples would be effects lowering or increasing the death rate of individuals carrying the

gene, or lowering or increasing the number of its surviving offspring. Natural selection is the

fact that some traits make it more likely for an organism to survive and reproduce. Population genetics

describes natural selection by defining fitness as a propensity or probability of survival and

reproduction in a particular environment. The fitness is normally given by the symbol w=1+s where s

is the selection coefficient. Natural selection acts on phenotypes, or the observable characteristics of

organisms, but the genetically heritable basis of any phenotype which gives a reproductive advantage

will become more common in a population. In this way, natural selection converts differences in

fitness into changes in allele frequency in a population over successive generations.

Prior to the advent of population genetics, many biologists doubted that small difference in

fitness was sufficient to make a large difference to evolution. Population geneticists

addressed this concern in part by comparing selection to genetic drift. Selection can

overcome genetic drift when s is greater than 1 divided by the effective population size.

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When this criterion is met, the probability that a new advantageous mutant becomes fixed is

approximately equal to s. The time until fixation of such an allele depends little on genetic

drift, and is approximately proportional to log(sN)/s.

3.1 Genetic Drift

Genetic drift is the result of probabilistic effects due to Mendelism or to the chance effects of

mating and survival in a small population. A carrier of a particular allele may leave no

surviving offspring for reasons which have nothing to do with that allele, for example

accidental death. In general, the number of the surviving offspring of an individual can be

thought of as a random variable, with a mean given by selection, but with still a positive

probability of being zero. An allele that has a selective advantage over others may still be lost

from the population due to random effects.

Genetic drift is referred to as a change in allele frequencies due to random sampling. That is,

the alleles in the offspring are a random sample of those in the parents. Genetic drift may

cause gene variants to disappear completely, and thereby reduce genetic variability. In

contrast to natural selection, which makes gene variants more common or less common

depending on their reproductive success, the changes due to genetic drift are not driven by

environmental or adaptive pressures, and may be beneficial, neutral, or detrimental to

reproductive success.

The effect of genetic drift is larger for alleles present in a smaller number of copies and

smaller when an allele is present in many copies. Vigorous debates wage among scientists

over the relative importance of genetic drift compared with natural selection.

Ronald Fisher held the view that genetic drift plays at the most a minor role in evolution, and

this remained the dominant view for several decades.

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In 1968 Motoo Kimura rekindled the debate with his neutral theory of molecular evolution

which claims that most of the changes in the genetic material are caused by neutral mutations

andd genetic drift. The role of genetic drift by means of sampling error in evolution has been

criticized by John H Gillespie and Will Provine,, who argue that selection on linked sites is a

more important stochastic force.

The population genetics of genetic drift are described using either branching processes or a

diffusion equation describing changes in allele frequency. These approaches are usually

applied to the Wright-Fisher

Fisher and Moran models
models of population genetics. Assuming genetic

drift is the only evolutionary force acting on an allele, after t generations in many replicated

populations, starting with allele frequencies of p and q, the variance in allele frequency across

those populations is

The Wright-Fisher model is an attempt to model these and similar effects. The Wright-Fisher
Wright

model for dioecious populations assumes that the population is rigidly held at N1 males land

N2 females over many generations. At the beginning of each generation, the population

undergoes random-mating to produce a large number offspring. Of these, N1 males and N2

females are chosen at random to adulthood and replace the parents.

3.2 Mutation

Mutation
ion is the ultimate source of genetic variation in the form of new alleles. Mutation can

result in several different types of change in DNA sequences; these can either have no effect,

alter the product of a gene,

gene, or prevent the gene from functioning. Studies in the fly

Drosophila melanogaster suggest that if a mutation changes a protein produced by a gene,

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this will probably be harmful, with about 70 percent of these mutations having damaging

effects, and the remainder being either neutral or weakly beneficial.

Mutations can involve large sections of DNA becoming duplicated, usually through genetic

recombination. These duplications are a major source of raw material for evolving new

genes, with tens to hundreds of genes duplicated in animal genomes every million years.

Most genes belong to larger families of genes of shared ancestry. Novel genes are produced

by several methods, commonly through the duplication and mutation of an ancestral gene, or

by recombining parts of different genes to form new combinations with new functions. Here,

domains act as modules, each with a particular and independent function, that can be mixed

together to produce genes encoding new proteins with novel properties. For example, the

human eye uses four genes to make structures that sense light: three for color vision and one

for night vision; all four arose from a single ancestral gene. Another advantage of duplicating

a gene is that this increases redundancy; this allows one gene in the pair to acquire a new

function while the other copy performs the original function. Other types of mutation

occasionally create new genes from previously noncoding DNA.

In addition to being a major source of variation, mutation may also function as a mechanism

of evolution when there are different probabilities at the molecular level for different

mutations to occur, a process known as mutation bias. If two genotypes, for example one with

the nucleotide G and another with the nucleotide A in the same position, have the same

fitness, but mutation from G to A happens more often than mutation from A to G, then

genotypes with A will tend to evolve. Different insertion vs. deletion mutation biases in

different taxa can lead to the evolution of different genome sizes. Developmental or

mutational biases have also been observed in morphological evolution. For example,

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according to the phenotype-first theory of evolution, mutations can eventually cause the

genetic assimilation of traits that were previously induced by the environment.

Mutation bias effects are superimposed on other processes. If selection would favor either

one out of two mutations, but there is no extra advantage to having both, then the mutation

that occurs the most frequently is the one that is most likely to become fixed in a population.

Mutations leading to the loss of function of a gene are much more common than mutations

that produce a new, fully functional gene. Most loss of function mutations are selected

against. But when selection is weak, mutation bias towards loss of function can affect

evolution. For example, pigments are no longer useful when animals live in the darkness of

caves, and tend to be lost. This kind of loss of function can occur because of mutation bias,

and/or because the function had a cost, and once the benefit of the function disappeared,

natural selection leads to the loss. Loss of sporulation ability in a bacterium during laboratory

evolution appears to have been caused by mutation bias, rather than natural selection against

the cost of maintaining sporulation ability. When there is no selection for loss of function, the

speed at which loss evolves depends more on the mutation rate than it does on the effective

population size, indicating that it is driven more by mutation bias than by genetic drift.

3.3 Gene Flow and Transfer

Gene flow is the exchange of genes between populations, which are usually of the same

species. Examples of gene flow within a species include the migration and then breeding of

organisms, or the exchange of pollen. Gene transfer between species includes the formation

of hybrid organisms and horizontal gene transfer.

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Migration into or out of a population can change allele frequencies, as well as introducing

genetic variation into a population. Immigration may add new genetic material to the

established gene pool of a population. Conversely, emigration may remove genetic material.

3.4 Reproductive isolation

As barriers to reproduction between two diverging populations are required for the

populations to become new species, gene flow may slow this process by spreading genetic

differences between the populations. Gene flow is hindered by mountain ranges, oceans and

deserts or even man-made structures such as the Great Wall of China, which has hindered the

flow of plant genes.

Depending on how far two species have diverged since their most recent common ancestor, it

may still be possible for them to produce offspring, as with horses and donkeys mating to

produce mules. Such hybrids are generally infertile, due to the two different sets of

chromosomes being unable to pair up during meiosis. In this case, closely related species may

regularly interbreed, but hybrids will be selected against and the species will remain distinct.

However, viable hybrids are occasionally formed and these new species can either have

properties intermediate between their parent species, or possess a totally new phenotype. The

importance of hybridization in creating new species of animals is unclear, although cases

have been seen in many types of animals, with the gray tree frog being a particularly well-

studied example.

Hybridization is, however, an important means of speciation in plants, since polyploidy is

tolerated in plants more readily than in animals. Polyploidy is important in hybrids as it

allows reproduction, with the two different sets of chromosomes each being able to pair with

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an identical partner during meiosis. Polyploids also have more genetic diversity, which

allows them to avoid inbreeding depression in small populations.

3.5 Genetic structure

Because of physical barriers to migration, along with limited tendency for individuals to

move or spread, and tendency to remain or come back to natal place, natural populations

rarely all interbreed as convenient in theoretical random models (Buston et al., 2007). There

is usually a geographic range within which individuals are more closely related to one

another than those randomly selected from the general population. This is described as the

extent to which a population is genetically structured (Repaci et al., 2007). Genetic

structuring can be caused by migration due to historical climate change, species range

expansion or current availability of habitat.

3.6 Horizontal Gene Transfer

Horizontal gene transfer is the transfer of genetic material from one organism to another

organism that is not its offspring; this is most common among bacteria. In medicine, this

contributes to the spread of antibiotic resistance, as when one bacteria acquires resistance

genes it can rapidly transfer them to other species. Horizontal transfer of genes from bacteria

to eukaryotes such as the yeast Saccharomyces cerevisiae and the adzuki bean beetle

Callosobruchus chinensis may also have occurred. An example of larger-scale transfers are

the eukaryotic bdelloid rotifers, which appear to have received a range of genes from

bacteria, fungi, and plants. Viruses can also carry DNA between organisms, allowing transfer

of genes even across biological domains. Large-scale gene transfer has also occurred between

the ancestors of eukaryotic cells and prokaryotes, during the acquisition of chloroplasts and

mitochondria.

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3.7 Complications in Population Genetics

Basic models of population genetics consider only one gene locus at a time. In practice,

epistatic and linkage relationships between loci may also be important.

Epistasis

Because of epistasis,, the phenotypic effect of an allele at one locus may depend on which

alleles are present at many other loci. Selection does not act on a single locus, but on a

phenotype that arisess through development from a complete genotype.

According to Lewontin (1974), the theoretical task for population genetics is a process in two

spaces: a "genotypic space" and a "phenotypic space". The challenge of a complete theory of

population genetics is to provide a set of laws that predictably map a population of genotypes

(G1) to a phenotype space (P1), where selection takes place, and another set of laws that map

the resulting population (P2) back to genotype space (G2) where Mendelian genetics can

predict the next generation of genotypes, thus completing the cycle. Even leaving aside for

the moment the non-Mendelian

Mendelian aspects of molecular genetics,, this is clearly a gargantuan

task. Visualizing this transformation schematically:

(Adapted
dapted from Lewontin 1974, p. 12). XD

T1 represents the genetic and epigenetic laws, the aspects of functional biology, or

development,, that transform a genotype into

into phenotype. We will refer to this as the

"genotype-phenotype map".
". T2 is the transformation due to natural selection, T3 are

epigenetic relations that predict genotypes

genotypes based on the selected phenotypes and finally T4 the

rules of Mendelian genetics.

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In practice, there are two bodies of evolutionary theory that exist in parallel, traditional

population genetics operating in the genotype space and the biometric theory used in plant

and animal breeding, operating in phenotype space. The missing part is the mapping between

the genotype and phenotype space. This leads to a "sleight of hand" (as Lewontin terms it)

whereby variables in the equations of one domain, are considered parameters or constants,

where, in a full-treatment they would be transformed themselves by the evolutionary process

and are in reality functions of the state variables in the other domain. The "sleight of hand" is

assuming that we know this mapping. Proceeding as if we do understand it is enough to

analyze many cases of interest. For example, if the phenotype is almost one-to-one with

genotype (sickle-cell disease) or the time-scale is sufficiently short, the "constants" can be

treated as such; however, there are many situations where it is inaccurate.

Linkage

If all genes are in linkage equilibrium, the effect of an allele at one locus can be averaged

across the gene pool at other loci. In reality, one allele is frequently found in linkage

disequilibrium with genes at other loci, especially with genes located nearby on the same

chromosome. Recombination breaks up this linkage disequilibrium too slowly to avoid

genetic hitchhiking, where an allele at one locus rises to high frequency because it is linked to

an allele under selection at a nearby locus. This is a problem for population genetic models

that treat one gene locus at a time. It can, however, be exploited as a method for detecting the

action of natural selection via selective sweeps.

In the extreme case of primarily asexual populations, linkage is complete and different

population genetic equations can be derived and solved, which behave quite differently to the

sexual case. Most microbes, such as bacteria, are asexual. The population genetics of

microorganisms lays the foundations for tracking the origin and evolution of antibiotic

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resistance and deadly infectious pathogens. Population genetics of microorganisms is also an

essential factor for devising strategies for the conservation and better utilization of beneficial

microbes (Xu, 2010).

4.0 Conclusion

At the conclusion of this course, students should be able to; Define population genetics and

applications to other disciplines, Review basic genetic background including genes and

alleles, discuss the four processes in population genetics.

5.0 Summary

Population genetics is a field of biology that studies the genetic composition of biological

populations, and the changes in genetic composition that result from the operation of various

factors, including natural selection. Population geneticists usually define ‘evolution’ as any

change in a population's genetic composition over time. The four factors that can bring about

such a change are: natural selection, mutation, random genetic drift, and migration into or out

of the population.

6.0 Tutor-Marked Assignment

• How do genes act in a population

• What is population genetics

• What are the processes governing population genetics

7.0 Reference/Further Reading

Postlethwalt, John (2009). Modern Biology. Holt, Rinehart and Winston. pp. 317.

Hartl, Daniel (2007). Principles of Population Genetics. Sinauer Associates. p. 95

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Ewens W.J. (2004). Mathematical Population Genetics (2nd Edition). Springer-Verlag,

New York.

Futuyma, Douglas (1998). Evolutionary Biology. Sinauer Associates. p. Glossary.

BS Haldane (1927). "A Mathematical Theory of Natural and Artificial Selection, Part V:

Selection and Mutation". Mathematical Proceedings of the Cambridge Philosophical

Society 23: 838-844.

Hermisson J, Pennings PS (2005). "Soft sweeps: molecular population genetics of

adaptation from standing genetic variation". Genetics 169: 2335-2352

http://bowlingsite.mcf.com/genetics/Genetics.html

Haldane, J.B.S., 1930-1932, ‘A Mathematical Theory of Natural and Artificial Selection’,

Proceedings of the Cambridge Philosophical Society, 26-28, Parts I-IX

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UNIT 3: HARDY-WEINBERG PRINCIPLE

CONTENTS

1.0 Introduction

2.0 Objectives

3.0 Modern theories of evolution

3.1 Examples of the Hardy-Weinberg Principle

3.2 Derivation of the Hardy-Weinberg Principle

4.0 Conclusion

5.0 Summary

6.0 Tutor-Marked Assignment

7.0 Reference/Further Readings

Unit 3 Hardy-Weinberg Principle

1.0 Introduction

Evolution is not only the development of new species from older ones, as most people

assume. It is also the minor changes within a species from generation to generation over long

periods of time that can result in the gradual transition to new species. Evolution has been

defined as the sum total of the genetically inherited changes in the individuals who are the

members of a population's gene pool. It is clear that the effects of evolution are felt by

individuals, but it is the population as a whole that actually evolves.

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2.0 Objectives

At the end of this study, students should be able to:

• Discuss the importance of the Hardy-Weinberg Principle

• Apply the Hardy-Weinberg Law in analyzing population genetics for gene frequency,

sex linkage, equilibrium, and heterozygote frequency.

3.0 Modern Theories of Evolution

Evolution is simply a change in frequencies of alleles in the gene pool of a population. For

instance, let us assume that there is a trait that is determined by the inheritance of a gene with

two alleles--B and b. If the parent generation has 92% B and 8% b and their offspring

collectively have 90% B and 10% b, evolution has occurred between the generations. The

entire population's gene pool has evolved in the direction of a higher frequency of the b

allele--it was not just those individuals who inherited the b allele who evolved. This

definition of evolution was developed largely as a result of independent work in the early

20th century by Godfrey Hardy, an English mathematician, and Wilhelm Weinberg, a

German physician. Through mathematical modelling based on probability, they concluded in

1908 that gene pool frequencies are inherently stable but that evolution should be expected in

all populations virtually all of the time. They resolved this apparent paradox by analyzing the

net effects of potential evolutionary mechanisms.

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 Wilhelm Weinberg
Godfrey Hardy(1877-194) (1862-1937)

Hardy, Weinberg, and the population geneticists who followed them came to understand that

evolution will not occur in a population if seven conditions are met:

• mutation is not occurring

• natural selection is not occurring

• the population is infinitely large

• all members of the population breed

• all mating is totally random

• everyone produces the same number of offspring

• there is no migration in or out of the population

These conditions are the absence of the things that can cause evolution. In other words, if no

mechanisms of evolution are acting on a population, evolution will not occur--the gene pool

frequencies will remain unchanged. However, since it is highly unlikely that any of these

seven conditions, let alone all of them, will happen in the real world, evolution is the

inevitable result.

Godfrey Hardy and Wilhelm Weinberg went on to develop a simple equation that can be used

to discover the probable genotype frequencies in a population and to track their changes from

one generation to another. This has become known as the Hardy-Weinberg equilibrium

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equation. In this equation (p² + 2pq + q² = 1), p is defined as the frequency of the dominant

allele and q as the frequency of the recessive allele for a trait controlled by a pair of alleles (A

and a). In other words, p equals all of the alleles in individuals who are homozygous

dominant (AA) and half of the alleles in people who are heterozygous (Aa) for this trait in a

population. In mathematical terms, this is:

p = AA + ½Aa

Likewise, q equals all of the alleles in individuals who are homozygous recessive (aa) and the

other half of the alleles in people who are heterozygous (Aa).

q = aa + ½Aa

Because there are only two alleles in this case, the frequency of one plus the frequency of the

other must equal 100%, which is to say

p+q=1

Since this is logically true, then the following must also be correct:

p=1-q

There were only a few short steps from this knowledge for Hardy and Weinberg to realize

that the chances of all possible combinations of alleles occurring randomly is

(p + q)² = 1

or more simply

p² + 2pq + q² = 1

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In this equation, p² is the predicted frequency of homozygous dominant (AA) people in a

population, 2pq is the predicted frequency of heterozygous (Aa) people, and q² is the

predicted frequency of homozygous recessive (aa) ones.

From observations of phenotypes, it is usually only possible to know the frequency of

homozygous recessive people, or q² in the equation, since they will not have the dominant

trait. Those who express the trait in their phenotype could be either homozygous dominant

(p²) or heterozygous (2pq). The Hardy-Weinberg equation allows us to predict which ones

they are. Since p = 1 - q and q is known, it is possible to calculate p as well. Knowing p and

q, it is a simple matter to plug these values into the Hardy-Weinberg equation

(p² + 2pq + q² = 1). This then provides the predicted frequencies of all three genotypes for

the selected trait within the population. By comparing genotype frequencies from the next

generation with those of the current generation in a population, one can also learn whether or

not evolution has occurred and in what direction and rate for the selected trait. However, the

Hardy-Weinberg equation cannot determine which of the various possible causes of evolution

were responsible for the changes in gene pool frequencies.

3.1 Examples of the Hardy-Weinberg Principle

The assumptions of the Hardy-Weinberg principle make it easy to calculate the genotype

frequencies for a gene with two alleles (A and a). The frequency of homozygous genotype AA

is the probability of one allele A being in combination with another allele A. The expected

frequency is simply the product of the separate allele frequencies. We will use the term p to

refer to the frequency of allele A:

Frequency of AA = p2 (Homozygote for A) Eqn 1

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The frequency of heterozygous genotype Aa is the probability of allele A being in

combination with allele a. Note that there are two possible ways to get those combinations --

A from Dad and a from Mom, or vice versa (See the figure below).

Frequency of Aa = 2pq (Heterozygote) Eqn 2

The frequency of homozygous genotype aa is the probability of one allele a in combination

with another allele a.

Frequency of aa = q2 (Homozygote for a) Eqn 3

Diagram of Hardy-Weinberg genotype proportions from male (sperm) and female (egg)

contributions. Given a locus with two alleles designated A and a that occur with frequencies p

and q, the chart shows the genotype frequencies (p2, 2pq, and q2) as differently colored areas.

Note that the heterozygotes (blue + yellow = green) can be formed in two different ways.

Example 1 -- calculation of expected genotype frequencies from gene (allele)

frequencies:

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If p = 0.75 and q = 0.25 we can use Eqns 1, 2 and 3 to calculate the expected genotype

frequencies.

AA = p2 = 0.75 * 0.75 = 0.5625

Aa = 2pq = 2 * 0.75 * 0.25 = 0.375

aa = q2 = 0.25 * .025 = 0.0625 Eqns 4.

The values we have just calculated are EXPECTED genotype frequencies IF the Hardy-

Weinberg assumptions hold. We now turn to how we could check that from actual

OBSERVED genotypic data (such as microsatellite data for Wyoming black bears). In order

to calculate allele frequencies all we need are the observed genotype frequencies.

p = p2 + (2pq/2) and q = q2 + (2pq/2) Eqn 5

3.2 Derivation of the Hardy-Weinberg Principle

We can describe empirically and algebraically how genotype frequencies in one generation

are related to genotype frequencies in the next. Let's explore that a bit further. To do so we're

going to use a technique that is broadly useful in population genetics, i.e., we're going to

construct a mating table. A mating table consists of three components:

1. A list of all possible genotype pairings.

2. The frequency with which each genotype pairing occurs.

3. The genotypes produced by each pairing.

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 Offspring genotype

Mating Frequency A1A1 A1A2 A2A2

A1A1 x A1A1 x2 1 0 0
11

A1A2 ½ ½ 0
x11x12

A2A2 1 0
x11x22
0
A1A2 x A1A1 x12x11 ½ ½ 0

A1A2 x 2
¼ ½ ¼
12

A2A2 ½ 1/2
x12x22

A2A2 x A1A1 x22x11 0 1 0

A1A2 x22x12 0 ½ ½

A2A2 x 2 0 0 1
22

In constructing this table we've already made three assumptions about the transmission of

genetic variation from one generation to the next:

2p1 = 2(50)/200 = 0:5, p2 = (2(25) + 50)/200 = 0:5.

Assumption 1 Genotype frequencies are the same in males and females, e.g., x11 is the

frequency of the A1A1 genotype in both males and females.

Assumption 2 Genotypes mate at random with respect to their genotype at this particular

locus.

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Assumption 3 Meiosis is fair. More specifically, we assume that there is no segregation

distortion; no gamete competition; no differences in the developmental ability of eggs, or the

fertilization ability of sperm.

Now that we have this table we can use it to calculate the frequency of each genotype in

newly formed zygotes in the population,5 provided that we're willing to make three

additional assumptions:

Assumption 4 There is no input of new genetic material, i.e., gametes are produced without

mutation, and all offspring are produced from the union of gametes within this population,

i.e., no migration from outside the population.

Assumption 5 The population is of infinite size so that the actual frequency of mating is

equal to their expected frequency and the actual frequency of offspring from each mating is

equal to the Mendelian expectations.

Assumption 6 All matings produce the same number of offspring, on average.

Taking these three assumptions together allows us to conclude that the frequency of a

particular genotype in the pool of newly formed zygotes is

∑ (frequency of mating) (frequency of genotype produce from mating)

So freq. (A1A1 in zygotes) = x211 + 1/2x11 x12 + 1/2x12 x11 + 1/4x212

= x211 + x11x12 + 1/4x212

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 = (x11 + x12/2)2
= p2

freq. (A1A2 in zygotes) = 2pq

freq. (A2A2 in zygotes) = q2

In order to say that these proportions will also be the genotype proportions of adults in the

progeny generation, we have to make two more assumptions:

Assumption 7 Generations do not overlap.

Assumption 8 There are no differences among genotypes in the probability of survival.

4.0 Conclusion

In this unit the student learnt:

• An understanding of evolution depends upon knowledge of population genetics.

• that both allele and genotype frequencies in a population remain constant—that is,

they are in equilibrium—from generation to generation unless specific disturbing

influences are introduced.

• Genetic equilibrium is an ideal state that provides a baseline against which to measure

change.

• Static allele frequencies in a population across generations assume: no mutation, no

migration or emigration, infinitely large population size, and no selective pressure for

or against any genotypes

5.0 Summary

Probably the most important basic concept in population genetics is the Hardy-Weinberg

principle. It provides an expectation for genotypic patterns in populations. Deviations from

the predicted pattern can provide very important insights into processes of genetic and

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evolutionary change. The Hardy-Weinberg principle is a model that relates allele frequencies

to genotype frequencies. Like most models, Hardy-Weinberg is a simplification of real world

complexities.

6.0Tutor-Marked Assignment

• What is the Hardy-Weinberg Principle?

• What is the significance of this principle?

• What are the deviations from the Hardy-Weinberg Principle?

7.0 Reference Reading

Crow, Jf (Jul 1999). "Hardy, Weinberg and language impediments". Genetics 152 (3): 821–5

Hardy, Gh (Jul 1908). "MENDELIAN PROPORTIONS IN A MIXED POPULATION".

Science 28 (706): 49–50

Modern theories of Evolution : Hardy-Weinberg equilibrium model.

http://anthro.palomar.edu/synthetic/Default.htm

R. Ceppellini, M. Siniscalco, and C. A. B. Smith. The estimation of gene frequencies in a

random-mating population. Annals of Human Genetics, 20:97{115, 1955.

A. P. Dempster, N. M. Laird, and D. B. Rubin. Maximum likelihood from incomplete

data. Journal of the Royal Statistical Society Series B, 39:1-38, 1977.

A. E. Gelfand and A. F. M. Smith. Sampling-based approaches to calculating marginal

densities. Journal of the American Statististical Association, 85:398-409, 1990.

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UNIT 4: GENE FREQUENCY/EQUILIBRIUM

Contents

1.0 Introduction

2.0 Objectives

3.0 Genetic Frequency

3.1 Calculation of Genetic frequency

3.2 The effect of mutation

3.3 Population genetics and the Hardy-Weinberg Principle

4.0 Conclusion

5.0 Summary

6.0 Tutor-Marked Assignment

7.0 Reference/Further Readings

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Unit 4 Gene Frequency/Equilibrium

1.0 Introduction

Gene frequency measures the frequency in the population of a particular gene relative to other genes

at its locus. It is expressed as a proportion (between 0 and 1) or percentage (between 0 and 100%). A

genetic equilibrium is at hand for an allele in a gene pool when the frequency of that allele is not

changing. For this to be the case, evolutionary forces acting upon the allele must be equal and

opposite. The only basic requirement is that the population be large enough that the effects of genetic

drift are minimized.

2.0 Objectives

At the end of this course, students should be able to:

• Define genetic frequency

• Significance of genetic frequency

• Relate genetic frequency and the Hardy-Weinberg Principle

3.0 Genetic frequency

Genetic or Allele frequency is the proportion of all copies of a gene that is made up of a

particular gene variant. In other words, it is the number of copies of a particular allele divided

by the number of copies of all alleles at the genetic place in a population. It can be expressed

for example as a percentage. In population genetics, allele frequencies are used to depict the

amount of genetic diversity at the individual, population, and species level. It is also the

relative proportion of all alleles of a gene that are of a designated type.

Given the following:

1. a particular locus on a chromosome and the gene occupying that locus

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 2. a population of N individuals carrying n loci in each of their somatic cells (e.g. two

loci in the cells of diploid species, which contain two sets of chromosomes)

3. different alleles of the gene exist

4. one allele exists in a copies

then the allele frequency is the fraction or percentage of all the occurrences of that locus that

is occupied by a given allele and the frequency of one of the alleles is a/(n*N).For example, if

the frequency of an allele is 20% in a given population, then among population members, one

in five chromosomes will carry that allele. Four out of five will be occupied by other

variant(s) of the gene. Note that for diploid genes the fraction of individuals that carry this

allele may be nearly two in five (36%). The reason for this is that if the allele distributes

randomly, then the binomial theorem will apply: 32% of the population will be heterozygous

for the allele (i.e. carry one copy of that allele and one copy of another in each somatic cell)

and 4% will be homozygous. Together, this means that 36% of diploid individuals would be

expected to carry an allele that has a frequency of 20%. However, alleles distribute randomly

only under certain assumptions, including the absence of selection. When these conditions

apply, a population is said to be in Hardy–Weinberg equilibrium. The frequencies of all the

alleles of a given gene often are graphed together as an allele frequency distribution

histogram, or allele frequency spectrum. Population genetics studies the different "forces"

that might lead to changes in the distribution and frequencies of alleles—in other words, to

evolution. Besides selection, these forces include genetic drift, mutation and migration.

3.1 Calculation of Genetic Frequency

If f(AA), f(Aa), and f(aa) are the frequencies of the three genotypes at a locus with two alleles,

then the frequency p of the A-allele and the frequency q of the a-allele are obtained by

counting alleles. Because each homozygote AA consists only of A-alleles, and because half

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of the alleles of each heterozygote Aa are A-alleles,
A the total frequency p of A-alleles in the

population is calculated as

Similarly, the frequency q of the a allele is given

gi by

It would be expected that p and q sum to 1, since they are the frequencies of the only two

alleles present. Indeed they do:

and from this we get:

q = 1 − p and p = 1 − q

If there are more than two different allelic forms, the frequency for each allele is simply the

frequency of its homozygote plus half the sum of the frequencies for all the heterozygotes in

which it appears. Allele frequency can always be calculated from genotype frequency,
frequency

whereas the reverse requires that the Hardy–Weinberg

Hardy Weinberg conditions of random mating apply.

This is partly due to the three genotype frequencies and the two allele frequencies. It is easier

to reduce from three to two.

In the simplest case, gene frequency is measured by counting the frequencies of each gene in

the population. If a genotype contains two genes, then there are a total of 16 genes per locus

in a population of eight individuals:

Aa AA aa aa AA Aa AA Aa

In the population above,

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Frequency of A = 9/16 = 0.5625

frequency of a = 7/16 = 0.4375.

Algebraically, we can define p as the frequency of A and q as the frequency of a. p and q are

always called 'gene'

ene' frequencies, but in a strict sense they are allele frequencies: they are the

frequencies of the different alleles at one genetic locus.

The gene frequencies can be calculated from the

the genotype frequencies (P, Q, R):
R

p = P + 1/2Q

q = R + 1/2Q

(and p + q = 1). The calculation of gene from genotype frequencies is highly important.

Although the gene frequencies can be calculated from the genotype frequencies, the opposite

is not true: the genotype frequencies cannot be calculated from the gene frequencies (p , q ).

3.2 The effect of mutation

Let ú be the mutation rate from allele A to some other allele a (the probability that a copy of

gene A will become a during the DNA replication preceding meiosis). If pt is the frequency of

the A allele in generation t,, then qt = 1 − pt is the frequency of the a allele in generation t, and

if there are no other causes of gene frequency change (no natural selection, for example), then

the change in allele frequency in one generation is

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where pt − 1 is the frequency of the preceding generation. This tells us that the frequency of A

decreases (and the frequency of a increases) by an amount that is proportional to the mutation
muta

rate ú and to the proportion p of all the genes that are still available to mutate. Thus ∆p gets

smaller as the frequency of p itself decreases, because there are fewer and fewer A alleles to

mutate into a alleles. We can make an approximation that, after n generations of mutation,

3.3 Population
opulation Genetics and the Hardy-Weinberg
Hardy Law

A genetic equilibrium is at hand for an allele in a gene pool when the frequency of that

allele is not changing (i.e. when it is not evolving).

). For this to be the case, evolutionary forces

acting upon the allele must be equal and opposite. The only basic requirement is that the

population be large enough that the effects of genetic drift are minimized.

The Hardy-Weinberg
Weinberg formulas allow scientists to determine whether evolution has occurred.

Any changes in the gene frequencies in the population over time

time can be detected. The law

essentially states that if no evolution is occurring, then an equilibrium of allele frequencies

will remain in effect in each succeeding generation of sexually reproducing individuals. In

order for equilibrium to remain in effect

effect (i.e. that no evolution is occurring) then the

following five conditions must be met:

1. No mutations must occur so that new alleles do not enter the population.

2. No gene flow can occur (i.e. no migration of individuals into, or out of, the

population).

3. Random mating must occur (i.e. individuals must pair by chance)

4. The population must be large so that no genetic drift (random chance) can cause the

allele frequencies to change.

5. No selection can occur so that certain alleles are not selected for, or against.
agai

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Obviously, the Hardy-Weinberg equilibrium cannot exist in real life. Some or all of these

types of forces all act on living populations at various times and evolution at some level

occurs in all living organisms. The Hardy-Weinberg formulas allow us to detect some allele

frequencies that change from generation to generation, thus allowing a simplified method of

determining that evolution is occurring. There are two formulas that must be memorized:

p2 + 2pq + q2 = 1 and p + q = 1

p = frequency of the dominant allele in the population

q = frequency of the recessive allele in the population

p2 = percentage of homozygous dominant individuals

q2 = percentage of homozygous recessive individuals

2pq = percentage of heterozygous individuals

Despite the fact that evolution is a common occurrence in natural populations, allele

frequencies will remain unaltered indefinitely unless evolutionary mechanisms such as

mutation and natural selection cause them to change. Before Hardy and Weinberg, it was

thought that dominant alleles must, over time, inevitably swamp recessive alleles out of

existence. This incorrect theory was called "genophagy" (literally "gene eating"). According

to this wrong idea, dominant alleles always increase in frequency from generation to

generation. Hardy and Weinberg were able to demonstrate with their equation that dominant

alleles can just as easily decrease in frequency.

4.0 Conclusion

At the end of this study, the student has learnt:

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 • Gene frequency measures the frequency in the population of a particular gene relative

to other genes at its locus.

• The significance of genetic frequency to the process of evolution

• The relationship between gene frequency and the Hardy-Weinberg Principle

5.0 Summary

A population is a group of individuals of the same species in a given area whose members

can interbreed. Because the individuals of a population can interbreed, they share a common

group of genes known as the gene pool. Each gene pool contains all the alleles for all the

traits of all the population. For evolution to occur in real populations, some of the gene

frequencies must change with time. The gene frequency of an allele is the number of times an

allele for a particular trait occurs compared to the total number of alleles for that trait. The

Hardy-Weinberg principle is a model that relates genetic frequencies to genotype frequencies

and the possible range for an allele frequency or genotype frequency therefore lies between

zero and one,

Gene frequency = the number of a specific type of allele / the total number of alleles in the

gene pool. An important way of discovering why real populations change with time is to

construct a model of a population that does not change. This is just what Hardy and Weinberg

did. Their principle describes a hypothetical situation in which there is no change in the gene

pool (frequencies of alleles), hence no evolution.

6.0 Tutor-Marked Assignment

• What do you understand by the term ‘Genetic Frequency’?

• What is the importance of genetic frequency?

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 • What is the relationship between genetic frequency and the Hardy-Weinberg

Principle?

7.0 Reference Reading

Cheung, KH; Osier MV, Kidd JR, Pakstis AJ, Miller PL, Kidd KK (2000). "ALFRED: an

allele frequency database for diverse populations and DNA polymorphisms". Nucleic Acids

Research 28 (1): 361–3.

Crow, Jf (Jul 1999). "Hardy, Weinberg and language impediments". Genetics 152 (3): 821–5

Emigh, T.H. (1980). "A comparison of tests for Hardy–Weinberg equilibrium". Biometrics 36

(4): 627–642

Guo, Sw; Thompson, Ea (Jun 1992). "Performing the exact test of Hardy-Weinberg

proportion for multiple alleles". Biometrics (Biometrics, Vol. 48, No. 2) 48 (2): 361–72

Middleton, D; Menchaca L, Rood H, Komerofsky R (2002). "New allele frequency database:

http://www.allelefrequencies.net". Tissue Antigens 61 (5): 403–7.

Allele Frequency http://www.ehstrafd.org/

Population Gene Frequencies. http://www.animalgenome.org/edu/genetics/main.html

Evolution. http://www.blackwellpublishing.com/ridley/

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MODULE 3: POLYMORPHISM

Unit 1: Ecology

Unit 2: Introduction to Polymorphism

Unit 3: Examples of Polymorphism

Unit 1 Ecology

Contents

1.0 Introduction

2.0 Objectives

3.0 The Science of Ecology

3.1 Population Ecology

3.1.1 Deterministic Models

3.1.2 Stochastic Models

3.2 Community Ecology

3.3 Ecosystem Ecology

3.4 Food web

3.5 Trophic Level

3.6 Ecology and Evolution

3.6.1 Behavioural Ecology

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3.6.2 Social Ecology

3.6.3 C0evolution

3.6.4 Biogeography

3.6.5 r/K-Selection Theory

3.6.6 Molecular Ecology

3.6.7 Human Ecology

4.0 Conclusion

5.0 Summary

6.0 Tutor-Marked Assignment

7.0 Reference/Further Readings

Unit 1: Ecology

1.0 Introduction

In biology, polymorphism takes place when two or more different phenotypes exist in the

same population of a species. This means the occurrence of more than one morph or form. In

order to be regarded as such, morphs must occupy the same habitat at the same time and

belong to a panmictic population, which refers to a population with random mating.

Polymorphism is related to biodiversity, genetic variation and adaptation and is common in

nature. It functions to retain variety of form in a population living in a varied environment.

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The most common example is sexual dimorphism, which occurs in many organisms. Other

examples are mimetic forms of butterflies, and human haemoglobin and blood types.

Polymorphism results from evolutionary processes, as does any aspect of a species. It is

heritable and is modified by natural selection.

2.0 Objectives

At the end of this study, students should be able to;

• Define the Ecology and discuss its significance to Evolution

• Differentiate the types of Ecology
• Discuss Ecological Models

3.0 The Science of Ecology

The term “ecology” was coined by the German zoologist, Ernst Haeckel, in 1866 to describe

the “economies” of living forms. The theoretical practice of ecology consists, by and large, of

the construction of models of the interaction of living systems with their environment that

include other living systems. These models are then tested in the laboratory and the field.

Theory in ecology consists of the heuristics—or principles—used to construct models. Unlike

evolutionary theory, ecology has no generally accepted global principles such as Mendel's

and other rules of genetic inheritance. Contemporary ecology consists of a patchwork of sub-

disciplines including population ecology, community ecology, conservation ecology,

ecosystem ecology, metapopulation ecology, metacommunity ecology, spatial ecology,

landscape ecology, physiological ecology, evolutionary ecology, functional ecology, and

behavioral ecology. What is common to all these fields is the view that:

(i) different biota interact in ways that can be described with sufficient precision and

generality to permit their scientific study;

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 (ii) (ii) ecological interactions set the stage for evolution to occur primarily because

they provide the external component of an entity's fitness. The latter aspect makes

ecology a central part of biology. As van Valen once put it: “evolution is the

control of development by ecology

3.1 Population Ecology

The golden age of theoretical ecology (1920-1940)—to borrow the title of a book edited by

Scudo and Ziegler—consisted primarily of population ecology. The next generation saw a

shift of theoretical interest to community ecology. In recent years, interest has reverted to

population ecology, sometimes in the form of metapopulation models, which consist of a set

of populations with migration between them. Models in population ecology are based on

representing an ecological system as the set of populations, which are usually of the same or

different species it consists of. Each population, in turn, consists of potentially interacting

individuals of a species. Populations may be characterized by their state variables -

parameters representing properties of the population as a whole, for instance, size, density,

growth-rate, etc, or by individual variables, that is, the properties of the individuals in them

for example, individual fecundity, interactions, etc. Classical population ecology was

restricted to the study of state-based models primarily because of the requirement that models

be tractable, so as to permit predictions and explanations. Classical population ecology is the

part of ecology that is theoretically the most developed. The central issue of interest in

population ecology is the change in the size of populations over time. Population ecology

considers both deterministic and stochastic models. Much of philosophical writing on

population ecology has been restricted to deterministic population models and this relatively

large body of work will only be very briefly summarized. More attention will be paid to

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stochastic models which raise much more interesting philosophical issues that have not been

adequately explored.

3.1.1 Deterministic Models

If population sizes are large, they can be studied using deterministic models, that is,

fluctuations in populations sizes due to chance factors (such as accidental births and deaths)

can be ignored. Usually a model considers members of a single or a very few interacting

species, for instance, a few predator and a prey species. A typical result, based on the Lotka-

Volterra (coupled differential equations) model, is that predator-prey interactions lead to

population cycles, with the predator population cycle temporally tracking the prey population

cycle. The explanation of this phenomenon is straightforward: as prey populations increase,

the increased availability of resources allows a rise in predator populations a little later in

time. But the increase of predators leads to an increase of prey consumption and,

consequently, a decrease in prey populations. But, now, the lack of resources leads to a

decline of predator populations. As predator populations decline, prey populations increase

initiating the cycle once again. See the figure below:

Figure 1: Predator-Prey Population Cycles

The model is due to Volterra 1978. There are two species, a predator species with a

population, N2, which only feeds on a single prey species with population, N1. The model

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incorporates demographic stochasticity which, nevertheless, does not stamp out the basic

cyclic pattern. (t is a measure of time.)

The Lotka-Volterra model mathematically predicts these cycles. As such, it exemplifies the

explanatory ideal of ecology: not only is there a predictively accurate quantitative model, but

the mechanisms incorporated in the model have a perspicuous biological interpretation.

Unfortunately, in ecology, because of the formalization and interpretation indeterminacy

problems, the last condition is rarely satisfied.

For the simpler case of single species, two standard models are that of exponential and

logistic growth. The exponential growth model is supposed to capture the behaviour of a

population when there is no resource limitation; the logistic growth model is one of the

simplest ways to try to capture the self-regulation of population sizes when there is such a

limitation. See Examples 1.1 and 1.2.

Example1.1 Exponential Growth Model

Let a population consist of n individuals at time t. Suppose that, in an infinitesimal time

interval between t and t+dt,

a fraction b/n of individuals give birth and a fraction d/n die.

Let the change in the size of the population be dn.

Then

dn/dt = (b − d).

Let r = b − d. Then the population dynamics is described by the growth equation:

dn/dt = m.

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This is the exponential growth model. It assumes that no resource limitation constrains the

"intrinsic growth rate", r. It can be solved to give:

n(t) = n0ert,

where n0 is the size of the population at t0.

Example 1.2 Logistic Growth Model

One way to modify the exponential growth model to incorporate resource limitation is to

replace the growth equation of the exponential model by that of the logistic growth model:

dn/dt = m(1 − n/K),

where K is called the "carrying capacity" of the environment; this parameter is supposed to

incorporate how resource limitation affects population growth by regulating it.

When n = K, the growth rate,

dn/dt = 0

and the population does not grow any further. Moreover, when there is no resource limitation;

that is K → ∞, this model reduces to the exponential growth model. Figure 2b shows how a

population governed by the logistic equation grows in size. At the level of individual

behaviour, this model does not have the kind of justification that the exponential growth

model does in the sense that the logistic equation cannot be plausibly derived from the

properties of individuals. In this sense it is a purely "phenomenological" model. The

exponential growth model appeals to only one essentially ecological parameter, the intrinsic

growth rate (r) of a population, interpreted as the rate at which the population would grow if

there were no external factor limiting growth; the logistic model also appeals to the carrying

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capacity (K), interpreted as the maximum size of the population that can persist in a given

environment. See Figures 2a and 2b:

2a

2b

Figures 2a and 2b: The Logistic Growth Model

The figure on the top shows theoretical curves. “Geometric increase” represents the

exponential growth model discussed in the text; “saturating population” refers to the carrying

capacity (see example 1.2). The figure on the bottom shows an example of an empirical

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growth curve obtained in the laboratory. If the curve is fitted to a logistic curve (to which it

shows similarity), then K = 375 is the estimated carrying capacity.

In general, biological experience suggests that all populations regulate their sizes, that is, they

show self-regulation. Theoretical exploration of models has made it clear that a wide variety

of mechanisms can lead to such self-regulation but it is usually unclear which models are

more plausible than others thanks to the typical formalization indeterminacy of the field.

Moreover, the precise mechanisms that are playing regulative roles in individual cases are

often very hard to determine in the field, a classic case of partial observability. Even

parameters such as the intrinsic growth rate and carrying capacity are unusually difficult to

estimate precisely.

The last mentioned difficulties are perhaps most famously illustrated by the 10-year cycle of

snowshoe hares, muskrats and their predators in the North American boreal forests and,

especially, the 4-year cycle of lemmings and, possibly, other microtines in the arctic tundra of

Eurasia and North America. In spite of almost seventy-five years of continuous research on

these well-documented cycles the mechanisms driving them remain unresolved. Models

producing such cycles abound, but the structural uncertainty of most of these models, coupled

with partial observability of many of the parameters in the field have precluded resolution of

the debate.

The models discussed so far are continuous-time models, that is, the temporal or dynamic

parameter is assumed to be a continuous variable. However, discrete-time models have also

been used to study population processes. A discrete analog of the logistic growth model was

one of the first systems in which chaotic dynamic phenomena were discovered. Over the

years there has been considerable debate over the question whether ecological systems with

chaotic dynamics exist in nature; the current consensus is that they have not yet been found.

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3.1.2 Stochastic Models

If population sizes are small, then models should be stochastic: the effects of fluctuations due

of population size must be explicitly analyzed. Stochastic models in ecology are among the

most mathematically complex models in science. Nevertheless they have begun to be

systematically studied because of their relevance to biological conservation—see the entry on

conservation biology. They also raise philosophically interesting questions because they

underscore the extent to which the nature of randomness and uncertainty remains poorly

explored in biological contexts.

What has, by and large, become the standard classification of stochasticity goes back to a

1978 dissertation by Shaffer. The context of that dissertation provides a striking exemplar of

the social determination of science. The United States National Forest Management Act of

1976 required the Forest Service to “provide for diversity of plant and animal communities

based on the suitability and capability of the specific land area.” In 1979 the planning

regulations developed to implement this provision required the Forest Service to “maintain

viable populations of existing native and desired non-native vertebrate species in the planning

area.” A viable population was defined as “one which has the estimated numbers and

distribution of reproductive individuals to insure its continued existence in the planning

area.” For large populations, falling within the domain of deterministic models, establishing

viability is relatively trivial: all that must be ensured is that, on the average, a population is

not declining in size. For small populations, even if it is increasing in size on the average, a

chance fluctuation can result in extinction. Stochastic models are necessary to predict

parameters such as the probability of extinction within a specified time period or the expected

time to extinction.

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In his dissertation, Shaffer attempted such an analysis for the grizzly bears (Ursus arctos) of

Yellowstone which were believed to face the prospect of stochastic extinction. Shaffer

distinguished four sources of uncertainty that can contribute to random extinction:

1. demographic stochasticity which arises from the chance events in the survival and

reproductive success of a finite number of individuals…

2. environmental stochasticity due to temporal variation of birth and death rates,

carrying capacity, and the population of competitors, predators, parasites, and

diseases…

3. natural catastrophes such as floods, fires, droughts, etc.…

4. genetic stochasticity resulting from changes in gene frequencies due to founder effect,

random fixation, or inbreeding.”

Shaffer went on to argue that all these factors increase in importance as the population size

decreases—a claim that will be questioned below—and, therefore, that their effects are hard

to distinguish. Finally, he defined a minimum viable population (MVP): “A minimum viable

population for any given species in any given habitat is the smallest population having at

least a 95% chance of remaining extant for 100 years despite the foreseeable effects of

demographic, environmental, and genetic stochasticity, and natural catastrophes.”Both

numbers (95% and 100 years) are conventional, and to be determined by social choice, rather

than by biological factors, a point that Shaffer explicitly recognized.

In the 1980s, techniques to determine MVPs came to be called “population viability analysis”

and the enthusiasm for the new framework was captured in the much-worn slogan: “MVP is

the product, PVA the process.” By the late 1980s, however, it became clear that the concept

of a MVP was at best of very limited use. Leaving aside the conventional elements of the

definition given above, even for the same species, populations in marginally different habitat

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patches often show highly variable demographic trends resulting in highly variable MVP

estimates for them, with each estimate depending critically on the local context. Moreover, as

will be illustrated below for stochastic population models in general, the determination of

MVPs suffers from irremediable structural uncertainty. This should not come as a surprise:

what would have been more surprising is if legislative fiat had identified a scientifically

valuable parameter. After the demise of the concept of the MVP, PVA began to be performed

largely to estimate other parameters, especially the expected time to extinction of a

population the estimation of which does not require any conventional choices—see the entry

on conservation biology.

Within the context of PVA, Shaffer's classification—though usually with “random

catastrophe” replacing “natural catastrophe”—became canonical within both ecology and

conservation biology. However, the philosophical question remains as to whether it makes

sense—classification, as many philosophers have pointed out, is not innocent of substantive

theoretical assumptions. The first point to note is that genetic stochasticity is not even the

same type of mechanism as the other three: its presence makes Shaffer's classification oddly

heterogeneous. The reason for this is that genetic stochasticity is a consequence of

demographic stochasticity: in small populations, a particular allele may reach fixation purely

by chance reproductive events. It is even possible that stochasticity increases the rate at

which a beneficial allele may go to fixation in a small population provided that the initial

frequency of that allele is already high.

3.2 Community Ecology

Community ecology consists of models of interacting species, forming an ecological

“community,” in which each species is treated as a unit. The appropriate definition of

“community” has been widely debated among ecologists and philosophers; what is being

138
given here is an interactive definition. Alternative options include defining community by

mere geographical association of species at one extreme, or by requiring a good deal of

structure in the interactions at the other, making the community analogous to an organism.

The interactive definition given above is attractive for two reasons: (a) mere association

leaves little of theoretical or practical interest to study, while requiring some specified

elevated levels of interaction introduces an unnecessary arbitrariness in a definition of

community; and (b) the former would make any association of species a community whereas

the latter would typically introduce so much structure that virtually no association would

constitute a community.

Community models can be conveniently represented as loop, diagrams generalized graphs

that have each species as a vertex and edges connecting these vertices when the species

interact. The edges indicate whether the relevant species benefit or are harmed by the

interaction, that is, whether they tend to increase or decrease in abundance, by an interaction.

See Figure 3:

Figure 3: Structure of an Ecological Community

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This is the loop diagram of a community of three species (from Diamond [1975a], p. 435).

Species X1 and X2 both prey upon the resource species X3. There is resource coupling and and

competitive exclusion.

As with population ecology, what is of most interest is are the changes in a community over

time. This brings us to one of the most interesting—and one of the most vexed—questions of

ecology: the relationship between diversity and stability. A deeply rooted intuition among

ecologists has been that diversity begets stability. If this claim is true, it has significant

consequences for biodiversity conservation

What confuses this question from the very beginning, is the multiplicity of possible

definitions of “diversity” and “stability.” There are probably no better instances of

formalization indeterminacy in any scientific context. For instance, a reasonable first attempt

to define diversity would be to equate the diversity of a community to the number of species

in it, that is, its species “richness.” The trouble is that there is ample reason to doubt that

richness captures all that is relevant about diversity, whether or not we are interested in only

its relationship to stability. Consider two communities, the first consisting of 50% species A

and 50% species B, and a second consisting of 99.9 % species A and 0.1% species B. Both

communities have the same richness because they both have two species; however, there is a

clear sense in which the first is more diverse—or less homogeneous—than the second.

Moreover, the difference is likely to be relevant. If diversity does beget stability in these

communities, then that stability must be a result some interaction between the two species. If

species B comprises only 0.1% of the community, the scope for such interaction is typically

much less than if it comprises 50%. Diversity must mean more than richness. There have

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been several attempts to define and quantify diversity beyond richness; one of them is

described in example 2 below.

Example2. Measures of Diversity

Ecologists often distinguish between three concepts of biodiversity, usually using species as

the appropriate unit to measure diversity: (i) “α-diversity”, the diversity within a

community/place (MacArthur 1965); (ii) “β-diversity”, the diversity between

communities/places (Whittaker 1972, 1975); and (iii) “γ-diversity”, the diversity between

regions, that is, β-diversity on a larger spatial scale (Whittaker 1972). Though many measures

of α-diversity have been proposed over the years, MacArthur's (1965) proposal to use the

Shannon measure of information content in a communication process (Shannon 1948) has

remained the most popular (though not universally accepted).

According to this measure, the α-diversity of a community with n species is given by

n
α=− ∑ pi ln pi
i=1

Where pi is the frequency of the i-th species. This is a measure of the diversity of a

community in the same way that the Shannon measure of information content is a measure of

the variety in a signal.

Turning to the two communities discussed in the text, a simple calculation shows that the

diversity of the first is given by α = 0.693, while the diversity of the second is given by α =

0.008, verifying the intuition that the first is more diverse than the second.

3.3 Ecosystem Ecology

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The term “ecosystem” was coined in 1935 by Tansley who defined it as “the whole system (in

the sense of physics) including not only the organism-complex [that is, the community], but

also the whole complex of physical factors forming what we call the environment of the

biome—the habitat factors in the widest sense.” Tansley went on to argue that ecosystems

“are the basic units of nature on the face of the earth.” For Tansley, using the term

“ecosystem” implied a physical description of a community in its habitat. Even though that

perspective still illuminates ecosystem studies (see below), it is no longer a necessary or even

common connotation of the term “ecosystem.” However, independent of the use of

“ecosystem,” ecosystem ecology, in contrast to other ecological sub-disciplines, and in

continuity with its history, does retain an emphasis on physical processes. Should ecosystem

ecology, then, be regarded as an instance of the unification of the physical and biological

sciences? There has been so little philosophical attention to ecology that this question does

not appear ever to have been broached.

The introduction and rapidly growing popularity of the term “ecosystem,” especially during

the late 1950s and 1960s, was marked by two major cognitive and one sociological shift in

the practice of ecology: (a) coming at the end of the so-called golden age of theoretical

population ecology of the late 1920s and 1930s, turning to ecosystems helped shift emphasis

from populations with interacting individuals to much larger and more inclusive systems. In

this sense it was a deliberate anti-“reductionist” move. Ecosystem enthusiasts follow a long

holistic tradition in natural history that tends to deify complexity and deny the possibility of

explaining wholes in terms of their parts. “Systems thinking” was supposed to replace

reductionism, the decomposition of wholes into parts for the sake of analysis; (b) a second

cognitive shift is that ecosystem studies involve models based at least partly on non-

biological variables. For instance, instead of tracking individuals or even species in

communities, models may track energy or matter flow in food webs as a whole; and (c) at the

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sociological level, the expansion of ecosystem studies led to what one historian has called the

invention of “big biology” in the 1960s, chiefly in the US. These studies, for instance the

massive Hubbard Brook Ecosystem Study, required more than just many biologists working

together. They also demanded that other specialists, including geochemists and soil scientists,

be brought in so that all the relevant physical parameters of ecosystems, besides the

biological ones, could be tracked simultaneously. This study constituted the biologists'

attempt to engage in publicly-funded Big Science, initiated by the physicists during the

Manhattan Project, and subsequently profitably exploited by social scientists since the 1950s.

3.4 Food Webs

A food web is the archetypal ecological network. Plants capture and convert solar energy into

the biomolecular bonds of simple sugars during photosynthesis. This food energy is

transferred through a series of organisms starting with those that feed on plants and are

themselves consumed. The simplified linear feeding pathways that move from a basal trophic

species to a top consumer is called the food chain. The larger interlocking pattern of food

chains in an ecological community creates a complex food web. Food webs are a type of

concept map or a heuristic device that is used illustrate and study pathways of energy and

material flows.

Generalized food web of waterbirds from Chesapeake Bay

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Food webs are often limited relative to the real world. Complete empirical measurements are

generally restricted to a specific habitat, such as a cave or a pond. Principles gleaned from

food web microcosm studies are used to extrapolate smaller dynamic concepts to larger

systems. Feeding relations require extensive investigations into the gut contents of organisms,

which can be very difficult to decipher, or stable isotopes can be used to trace the flow of

nutrient diets and energy through a food web. While food webs often give an incomplete

measure of ecosystems, they are nonetheless a valuable tool in understanding community

ecosystems.

Food-webs exhibit principals of ecological emergence through the nature of trophic

entanglement, where some species have many weak feeding links (e.g., omnivores) while

some are more specialized with fewer stronger feeding links (e.g., primary predators).

Theoretical and empirical studies identify non-random emergent patterns of few strong and

many weak linkages that serve to explain how ecological communities remain stable over

time. Food-webs have compartments, where the many strong interactions create subgroups

among some members in a community and the few weak interactions occur between these

subgroups. These compartments increase the stability of food-webs.

As plants grow, they accumulate carbohydrates and are eaten by grazing herbivores. Step by

step lines or relations are drawn until a web of life is illustrated.

3.5 Trophic Level

The Greek root of the word troph, τροφή, trophē, means food or feeding. Links in food-webs

primarily connect feeding relations or trophism among species. Biodiversity within

ecosystems can be organized into vertical and horizontal dimensions. The vertical dimension

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represents feeding relations that become further removed from the base of the food chain up

toward top predators. A trophic level is defined as "a group of organisms acquiring a

considerable majority of its energy from the adjacent level nearer the abiotic source." The

horizontal dimension represents the abundance or biomass at each level. When the relative

abundance or biomass of each functional feeding group is stacked into their respective

trophic levels they naturally sort into a 'pyramid of numbers'.

Functional groups are broadly categorized as autotrophs (or primary producers), heterotrophs

(or consumers), and detrivores (or decomposers). Autotrophs are organisms that can produce

their own food (production is greater than respiration) and are usually plants or cyanobacteria

that are capable of photosynthesis but can also be other organisms such as bacteria near ocean

vents that are capable of chemosynthesis. Heterotrophs are organisms that must feed on

others for nourishment and energy (respiration exceeds production). Heterotrophs can be

further sub-divided into different functional groups, including: primary consumers (strict

herbivores), secondary consumers (carnivorous predators that feed exclusively on herbivores)

and tertiary consumers (predators that feed on a mix of herbivores and predators). Omnivores

do not fit neatly into a functional category because they eat both plant and animal tissues. It

has been suggested that omnivores have a greater functional influence as predators because

relative to herbivores they are comparatively inefficient at grazing.

Trophic levels are part of the holistic or complex systems view of ecosystems. Each trophic

level contains unrelated species that grouped together because they share common ecological

functions. Grouping functionally similar species into a trophic system gives a macroscopic

image of the larger functional design. While the notion of trophic levels provides insight into

energy flow and top-down control within food webs, it is troubled by the prevalence of

omnivory in real ecosystems. This has lead some ecologists to "reiterate that the notion that

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species clearly aggregate into discrete, homogeneous trophic levels is fiction." Nonetheless,

recent studies have shown that real trophic levels do exist, but "above the herbivore trophic

level, food webs are better characterized as a tangled web of omnivores.

A trophic pyramid (a) and a food-web (b) illustrating ecological relationships among
creatures that are typical of a northern Boreal terrestrial ecosystem. The trophic pyramid
roughly represents the biomass (usually measured as total dry-weight) at each level. Plants
generally have the greatest biomass. Names of trophic categories are shown to the right of the
pyramid. Some ecosystems, such as many wetlands, do not organize as a strict pyramid,
because aquatic plants are not as productive as long-lived terrestrial plants such as trees.
Ecological trophic pyramids are typically one of three kinds: 1) pyramid of numbers, 2)
pyramid of biomass, or 3) pyramid of energy

3.6 Ecology and Evolution

Ecology and evolution are considered sister disciplines of the life sciences. Natural selection,

life history, development, adaptation, populations, and inheritance are examples of concepts

that thread equally into ecological and evolutionary theory. Morphological, behavioral and/or

genetic traits, for example, can be mapped onto evolutionary trees to study the historical

development of a species in relation to their functions and roles in different ecological

circumstances. In this framework, the analytical tools of ecologists and evolutionists overlap

as they organize, classify and investigate life through common systematic principals, such as

phylogenetics or the Linnaean system of taxonomy. The two disciplines often appear

together, such as in the title of the journal Trends in Ecology and Evolution. There is no sharp

boundary separating ecology from evolution and they differ more in their areas of applied

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focus. Both disciplines discover and explain emergent and unique properties and processes

operating across different spatial or temporal scales of organization. While the boundary

between ecology and evolution is not always clear, it is understood that ecologists study the

abiotic and biotic factors that influence the evolutionary process.

3.6.1 Behavioural Ecology

All organisms are motile to some extent. Even plants express complex behavior, including

memory and communication. Behavioral ecology is the study of ethology and its ecological

and evolutionary implications. Ethology is the study of observable movement or behavior in

nature. This could include investigations of motile sperm of plants, mobile phytoplankton,

zooplankton swimming toward the female egg, the cultivation of fungi by weevils, the mating

dance of a salamander, or social gatherings of amoeba.

Adaptation is the central unifying concept in behavioral ecology. Behaviors can be recorded

as traits and inherited in much the same way that eye and hair color can. Behaviors evolve

and become adapted to the ecosystem because they are subject to the forces of natural

selection. Hence, behaviors can be adaptive, meaning that they evolve functional utilities that

increases reproductive success for the individuals that inherit such traits. This is also the

technical definition for fitness in biology, which is a measure of reproductive success over

successive generations.

Predator-prey interactions are an introductory concept into food-web studies as well as

behavioral ecology. Prey species can exhibit different kinds of behavioral adaptations to

predators, such as avoid, flee or defend. Many prey species are faced with multiple predators

that differ in the degree of danger posed. To be adapted to their environment and face

predatory threats, organisms must balance their energy budgets as they invest in different

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aspects of their life history, such as growth, feeding, mating, socializing, or modifying their

habitat. Hypotheses posited in behavioral ecology are generally based on adaptive principals

of conservation, optimization or efficiency. For example,

"The threat-sensitive predator avoidance hypothesis predicts that prey should assess the

degree of threat posed by different predators and match their behavior according to current

levels of risk."[

"The optimal flight initiation distance occurs where expected postencounter fitness is

maximized, which depends on the prey's initial fitness, benefits obtainable by not fleeing,

energetic escape costs, and expected fitness loss due to predation risk."

Social display and color variation in differently adapted species of chameleons (Bradypodion
spp.). Chameleons change their skin color to match their background as a behavioral defense
mechanism and also use color to communicate with other members of their species, such as
dominant (left) versus submissive (right) patterns shown in the three species (A-C) above.

Elaborate sexual displays and posturing are encountered in the behavioral ecology of animals.

The birds of paradise, for example, display elaborate ornaments and song during courtship.

These displays serve a dual purpose of signaling healthy or well-adapted individuals and

desirable genes. The elaborate displays are driven by sexual selection as an advertisement of

quality of traits among male suitors.

3.6.2 Social Ecology

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Social ecological behaviors are notable in the social insects, slime moulds, social spiders,

human society, and naked mole rats where eusocialism has evolved. Social behaviors include

reciprocally beneficial behaviors among kin and nest mates. Social behaviors evolve from kin

and group selection. Kin selection explains altruism through genetic relationships, whereby

an altruistic behavior leading to death is rewarded by the survival of genetic copies

distributed among surviving relatives. The social insects, including ants, bees and wasps are

most famously studied for this type of relationship because the male drones are clones that

share the same genetic make-up as every other male in the colony. In contrast, group

selectionists find examples of altruism among non-genetic relatives and explain this through

selection acting on the group, whereby it becomes selectively advantageous for groups if their

members express altruistic behaviors to one another. Groups that are predominantly altruists

beat groups that are predominantly selfish.

Symbiosis: Leafhoppers (Eurymela fenestrata) are protected by ants (Iridomyrmex

purpureus) in a symbiotic relationship. The ants protect the leafhoppers from predators and in
return the leafhoppers feeding on plants exude honeydew from their anus that provides
energy and nutrients to tending ants.

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3.6.3 Coevolution

Ecological interactions can be divided into host and associate relationships. A host is any

entity that harbors another that is called the associate. Host and associate relationships among

species that are mutually or reciprocally beneficial are called mutualisms. If the host and

associate are physically connected, the relationship is called symbiosis. Approximately 60%

of all plants, for example, have a symbiotic relationship with arbuscular mycorrhizal fungi.

Symbiotic plants and fungi exchange carbohydrates for mineral nutrients. Symbiosis differs

from indirect mutualisms where the organisms live apart. For example, tropical rainforests

regulate the Earth's atmosphere. Trees living in the equatorial regions of the planet supply

oxygen into the atmosphere that sustains species living in distant polar regions of the planet.

This relationship is called commensalism because many other host species receive the

benefits of clean air at no cost or harm to the associate tree species supplying the oxygen. The

host and associate relationship is called parasitism if one species benefits while the other

suffers. Competition among species or among members of the same species is defined as

reciprocal antagonism, such as grasses competing for growth space. Popular ecological study

systems for mutualism include, fungus-growing ants employing agricultural symbiosis,

bacteria living in the guts of insects and other organisms, the fig wasp and yucca moth

pollination complex, lichens with fungi and photosynthetic algae, and corals with

photosynthetic algae. Nevertheless, many organisms exploit host rewards without

reciprocating and thus have been branded with a myriad of not-very-flattering names such as

'cheaters', 'exploiters', 'robbers', and 'thieves'. Although cheaters impose several host cots

(e.g., via damage to their reproductive organs or propagules, denying the services of a

beneficial partner), their net effect on host fitness is not necessarily negative and, thus,

becomes difficult to forecast.

3.6.4 Biogeography

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The word biogeography is an amalgamation of biology and geography. Biogeography is the

comparative study of the geographic distribution of organisms and the corresponding

evolution of their traits in space and time. The Journal of Biogeography was established in

1974. Biogeography and ecology share many of their disciplinary roots. For example, the

theory of island biogeography, published by the mathematician Robert MacArthur and

ecologist Edward O. Wilson in 1967is considered one of the fundamentals of ecological

theory.

Biogeography has a long history in the natural sciences where questions arise concerning the

spatial distribution of plants and animals. Ecology and evolution provide the explanatory

context for biogeographical studies. Biogeographical patterns result from ecological

processes that influence range distributions, such as migration and dispersal. and from

historical processes that split populations or species into different areas. The biogeographic

processes that result in the natural splitting of species explains much of the modern

distribution of the Earth's biota. The splitting of lineages in a species is called vicariance

biogeography and it is a sub-discipline of biogeography. There are also practical applications

in the field of biogeography concerning ecological systems and processes. For example, the

range and distribution of biodiversity and invasive species responding to climate change is a

serious concern and active area of research in context of global warming

3.6.5 r/K-Selection theory

A population ecology concept (introduced in MacArthur and Wilson's (1967) book, The

Theory of Island Biogeography) is r/K selection theory, one of the first predictive models in

ecology used to explain life-history evolution. The premise behind the r/K selection model is

that natural selection pressures change according to population density. For example, when

an island is first colonized, density of individuals is low. The initial increase in population

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size is not limited by competition, leaving an abundance of available resources for rapid

population growth. These early phases of population growth experience density-independent

forces of natural selection, which is called r-selection. As the population becomes more

crowded, it approaches the island's carrying capacity, thus forcing individuals to compete

more heavily for fewer available resources. Under crowded conditions the population

experiences density-dependent forces of natural selection, called K-selection.

In the r/K-selection model, the first variable r is the intrinsic rate of natural increase in

population size and the second variable K is the carrying capacity of a population. Different

species evolve different life-history strategies spanning a continuum between these two

selective forces. An r-selected species is one that has high birth rates, low levels of parental

investment, and high rates of mortality before individuals reach maturity. Evolution favors

high rates of fecundity in r-selected species. Many kinds of insects and invasive species

exhibit r-selected characteristics. In contrast, a K-selected species has low rates of fecundity,

high levels of parental investment in the young, and low rates of mortality as individuals

mature. Humans and elephants are examples of species exhibiting K-selected characteristics,

including longevity and efficiency in the conversion of more resources into fewer offspring.

3.6.6 Molecular ecology

The important relationship between ecology and genetic inheritance predates modern

techniques for molecular analysis. Molecular ecological research became more feasible with

the development of rapid and accessible genetic technologies, such as the polymerase chain

reaction (PCR). The rise of molecular technologies and influx of research questions into this

new ecological field resulted in the publication Molecular Ecology in 1992. Molecular

ecology uses various analytical techniques to study genes in an evolutionary and ecological

context. In 1994, John Avise also played a leading role in this area of science with the

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publication of his book, Molecular Markers, Natural History and Evolution. Newer

technologies opened a wave of genetic analysis into organisms once difficult to study from an

ecological or evolutionary standpoint, such as bacteria, fungi and nematodes. Molecular

ecology engendered a new research paradigm for investigating ecological questions

considered otherwise intractable. Molecular investigations revealed previously obscured

details in the tiny intricacies of nature and improved resolution into probing questions about

behavioral and biogeographical ecology. For example, molecular ecology revealed

promiscuous sexual behavior and multiple male partners in tree swallows previously thought

to be socially monogamous. In a biogeographical context, the marriage between genetics,

ecology and evolution resulted in a new sub-discipline called phylogeography.

3.6.7 Human Ecology

Human ecology is the interdisciplinary investigation into the ecology of our species. "Human

ecology may be defined: (1) from a bio-ecological standpoint as the study of man as the

ecological dominant in plant and animal communities and systems; (2) from a bio-ecological

standpoint as simply another animal affecting and being affected by his physical

environment; and (3) as a human being, somehow different from animal life in general,

interacting with physical and modified environments in a distinctive and creative way. A

truly interdisciplinary human ecology will most likely address itself to all three." The term

human ecology was formally introduced in 1921, but many sociologists, geographers,

psychologists, and other disciplines were interested in human relations to natural systems

centuries prior, especially in the late 19th century. Some authors have identified a new

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unifying science in coupled human and natural systems that builds upon, but moves beyond

the field human ecology. Ecology is as much a biological science as it is a human science.

"Perhaps the most important implication involves our view of human society. Homo sapiens

is not an external disturbance, it is a keystone species within the system. In the long term, it

may not be the magnitude of extracted goods and services that will determine sustainability.

It may well be our disruption of ecological recovery and stability mechanisms that determines

system collapse."

4.0 Conclusion

The student has learnt the following

• The concept of ecology

• The significance of ecology to evolution

• Different types of ecology

• Ecological models

5.0 Summary

The science of ecology studies interactions between individual organisms and their

environments, including interactions with both conspecifics and members of other species.

Though ecology emerged in the 19th century much of its theoretical structure only emerged

in the twentieth century. Though ecology includes a wide variety of sub-fields, philosophical

analysis of ecology has so far been restricted to population, community, and ecosystem

ecology. Central philosophical problems include explication of relevant notions of ecological

diversity and stability the relation between diversity and stability. Other debated questions are

the nature of laws and theories in ecology, strategies of model-building, and reductionism.

Contemporary ecology is undergoing a conceptual upheaval because of increased

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computational power. The recent emphasis on individual-based models, which embrace

methodological individualism, should be viewed as a return of reductionism in ecology.

Other important developments include widespread interest in spatially explicit models and

the advent of Geographical Information Systems.

6.0 Tutor-Marked Assignment

• What do you understand by the term ecology

• State the different types of ecology

• Explain one model in ecology

7.0 Reference/Further Reading

Aerts, R. and Chapin III, F. S. 2000. “The Mineral Nutrition of Wild Plants Revisited: A Re-

Evaluation of Processes and Patterns.” Advances in Ecological Research 30: 1-67.

Beissinger, S. R. 2002. “Population Viability Analysis: Past, Present, Future.” In Beissinger,

S. R. and McCullough, D. R. Ed. Population Viability Analysis. Chicago: University of

Chicago Press, pp. 5-17.

Beissinger, S. R. and Westphal, M. I. 1998. “On the Use of Demographic Models of

Population Viability in Endangered Species Management.” Journal of Wildlife Management

62: 821 –841.

Connor, E. F. and McCoy, E. D. 1979. “The Statistics and Biology of the Species-Area

Relationship.” American Naturalist 113: 791-833.

Cooper, G. J. 2004. The Science of the Struggle for Existence: On the Foundations of

Ecology. New York: Cambridge University Press.

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Cuddington, K. 2001. “The ‘Balance of Nature’ Metaphor and Equilibrium in Population

Ecology.” Biology and Philosophy 16: 463-479.

UNIT 2: INTRODUCTION TO POLYMORPHISM

Content

1.0 Introduction

2.0 Objective

3.0 Terminology

3.1 Nomenclature

3.2 Ecology

3.3 Polymorphism and Niche Diversity

3.4 The Switch

3.5 Investigative Methods

3.6 Genetic Polymorphism

3.7 Mechanism of Balancing Selection

3.8 Pleiotropism

3.9 Epistasis

4.0 Origin of Supergenes

5.0 Conclusion

6.0 Summary

7.0 Tutor-Marked Assignment

8.0 Reference/Further Readings

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1.0 Introduction

Polymorphism in biology occurs when two or more clearly different phenotypes exist in the

same population of a species — in other words, the occurrence of more than one form or

morph. In order to be classified as such, morphs must occupy the same habitat at the same

time and belong to a panmictic population (one with random mating).

Polymorphism is common in nature; it is related to biodiversity, genetic variation and

adaptation; it usually functions to retain variety of form in a population living in a varied

environment. The most common example is sexual dimorphism, which occurs in many

organisms. Other examples are mimetic forms of butterflies (see mimicry), and human

haemoglobin and blood types.

Polymorphism results from evolutionary processes, as does any aspect of a species. It is

heritable and is modified by natural selection. In polyphenism, an individual's genetic make-

up allows for different morphs, and the switch mechanism that determines which morph is

shown is environmental. In genetic polymorphism, the genetic make-up determines the

morph. Ants exhibit both types in a single population.

2.0 Objectives

At the end of this unit, the student should be able to:

• Define polymorphism

• State and discuss types of polymorphism

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3.0 Terminology

Although in general use polymorphism is quite a broad term, in biology it has been given a

specific meaning.

• The term omits characters showing continuous variation (such as weight), even

though this has a heritable component. Polymorphism deals with forms in which the

variation is discrete (discontinuous) or strongly bimodal or polymodal.

• Morphs must occupy the same habitat at the same time: this excludes geographical

races and seasonal forms. The use of the words morph or polymorphism for what is a

visibly different geographical race or variant is common, but incorrect. The

significance of geographical variation is in that it may lead to allopatric speciation,

whereas true polymorphism takes place in panmictic populations.

• The term was first used to describe visible forms, but nowadays it has been extended

to include cryptic morphs, for instance blood types, which can be revealed by a test.

• Rare variations are not classified as polymorphisms; and mutations by themselves do

not constitute polymorphisms. To qualify as a polymorphism there has to be some

kind of balance between morphs underpinned by inheritance. The criterion is that the

frequency of the least common morph is too high simply to be the result of new

mutations or, as a rough guide, that it is greater than 1 percent (though that is far

higher than any normal mutation rate for a single allele)

3.1 Nomenclature

Polymorphism crosses several discipline boundaries, including ecology and genetics,

evolution theory, taxonomy, cytology and biochemistry. Different disciplines may give the

same concept different names, and different concepts may be given the same name. For

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example, there are the terms established in ecological genetics by E.B. Ford (1975) and for

classical genetics by John Maynard Smith (1998).The shorter term morphism may be more

accurate than polymorphism, but is not often used. It was the preferred term of the

evolutionary biologist Julian Huxley (1955).

Various synonymous terms exist for the various polymorphic forms of an organism. The most

common are morph and morpha, while a more formal term is morphotype. Form and phase

are sometimes also used, but are easily confused in zoology with, respectively, "form" in a

population of animals, and "phase" as a color or other change in an organism due to

environmental conditions (temperature, humidity, etc.). Phenotypic traits and characteristics

are also possible descriptions, though that would imply just a limited aspect of the body.

In the taxonomic nomenclature of zoology, the word "morpha" plus a Latin name for the

morph can be added to a binomial or trinomial name. However, this invites confusion with

geographically-variant ring species or subspecies, especially if polytypic. Morphs have no

formal standing in the ICZN. In botanical taxonomy, the concept of morphs is represented

with the terms "variety", "subvariety" and "form", which are formally regulated by the ICBN.

Horticulturalists sometimes confuse this usage of "variety" both with cultivar ("variety" in

viticultural usage, rice agriculture jargon, and informal gardening lingo) and with the legal

concept "plant variety" (protection of a cultivar as a form of intellectual property)

3.2 Ecology

Selection, whether natural or artificial, changes the frequency of morphs within a population;

this occurs when morphs reproduce with different degrees of success. A genetic (or balanced)

polymorphism usually persists over many generations, maintained by two or more opposed

and powerful selection pressures. Diver (1929) found banding morphs in Cepaea nemoralis

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could be seen in pre-fossil shells going back to the Mesolithic Holocene. Apes have similar

blood groups to humans; this suggests rather strongly that this kind of polymorphism is quite

ancient, at least as far back as the last common ancestor of the apes and man, and possibly

even further.

The relative proportions of the morphs may vary; the actual values are determined by the

effective fitness of the morphs at a particular time and place. The mechanism of heterozygote

advantage assures the population of some alternative alleles at the locus or loci involved.

Only if competing selection disappears will an allele disappear. However, heterozygote

advantage is not the only way a polymorphism can be maintained. Apostatic selection,

whereby a predator consumes a common morph whilst overlooking rarer morphs is possible

and does occur. This would tend to preserve rarer morphs from extinction.

A polymorphic population does not initiate speciation; nor does it prevent speciation. It has

little or nothing to do with species splitting. However, it has a lot to do with the adaptation of

a species to its environment, which may vary in colour, food supply, predation and in many

other ways. Polymorphism is one good way the opportunities get to be used; it has survival

value, and the selection of modifier genes may reinforce the polymorphism.

3.3 Polymorphism and Niche Diversity

G. Evelyn Hutchinson, a founder of niche research, commented "It is very likely from an

ecological point of view that all species, or at least all common species, consist of

populations adapted to more than one niche". He gave as examples sexual size dimorphism

and mimicry. In many cases where the male is short-lived and smaller than the female, he

does not compete with her during her late pre-adult and adult life. Size difference may permit

both sexes to exploit different niches. In elaborate cases of mimicry, such as the African

butterfly Papilio dardanus, female morphs mimic a range of distasteful models, often in the

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same region. The fitness of each type of mimic decreases as it becomes more common, so the

polymorphism is maintained by frequency-dependent selection. Thus the efficiency of the

mimicry is maintained in a much increased total population.

3.4 The switch

The mechanism which decides which of several morphs an individual displays is called the

switch. This switch may be genetic, or it may be environmental. Taking sex determination as

the example, in humans the determination is genetic, by the XY sex-determination system. In

Hymenoptera (ants, bees and wasps), sex determination is by haplo-diploidy: the females are

all diploid, the males are haploid. However, in some animals an environmental trigger

determines the sex: alligators are a famous case in point. In ants the distinction between

workers and guards is environmental, by the feeding of the grubs. Polymorphism with an

environmental trigger is called polyphenism.

The polyphenic system does have a degree of environmental flexibility not present in the

genetic polymorphism. However, such environmental triggers are the less common of the two

methods.

3.5 Investigative Methods

Investigation of polymorphism requires a coming together of field and laboratory technique.

In the field:

• detailed survey of occurrence, habits and predation

• selection of an ecological area or areas, with well-defined boundaries

• capture, mark, release, recapture data (see Mark and recapture)

• relative numbers and distribution of morphs

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 • estimation of population sizes

And in the laboratory:

• genetic data from crosses

• population cages

• chromosome cytology if possible

• use of chromatography or similar techniques if morphs are cryptic (for example,

biochemical)

Both types of work are equally important. Without proper field-work the significance of the

polymorphism to the species is uncertain; without laboratory breeding the genetic basis is

obscure. Even with insects the work may take many years; examples of Batesian mimicry

noted in the nineteenth century are still being researched.

3.6 Genetic Polymorphism

Since all polymorphism has a genetic basis, genetic polymorphism has a particular meaning:

• Genetic polymorphism is the simultaneous occurrence in the same locality of two or

more discontinuous forms in such proportions that the rarest of them cannot be

maintained just by recurrent mutation or immigration.

The definition has three parts: a) sympatry: one interbreeding population; b) discrete forms;

and c) not maintained just by mutation.

Genetic polymorphism is actively and steadily maintained in populations by natural selection,

in contrast to transient polymorphisms where a form is progressively replaced by another. By

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definition, genetic polymorphism relates to a balance or equilibrium between morphs. The

mechanisms that conserve it are types of balancing selection.

3.7 Mechanism of Balancing Selection

• Heterosis (or heterozygote advantage): "Heterosis: the heterozygote at a locus is fitter

than either homozygote".

• Frequency dependent selection: The fitness of a particular phenotype is dependent on

its frequency relative to other phenotypes in a given population. Example: prey

switching, where rare morphs of prey are actually fitter due to predators concentrating

on the more frequent morphs.

• Fitness varies in time and space. Fitness of a genotype may vary greatly between

larval and adult stages, or between parts of a habitat range.

• Selection acts differently at different levels. The fitness of a genotype may depend on

the fitness of other genotypes in the population: this covers many natural situations

where the best thing to do (from the point of view of survival and reproduction)

depends on what other members of the population are doing at the time.

3.8 Pleiotropism

Most genes have more than one effect on the phenotype of an organism (pleiotropism). Some

of these effects may be visible, and others cryptic, so it is often important to look beyond the

most obvious effects of a gene to identify other effects. Cases occur where a gene affects an

unimportant visible character, yet a change in fitness is recorded. In such cases the gene's

other (cryptic or 'physiological') effects may be responsible for the change in fitness.

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 "If a neutral trait is pleiotropically linked to an advantageous one, it may emerge

because of a process of natural selection. It was selected but this doesn't mean it is an

adaptation. The reason is that, although it was selected, there was no selection for that

trait.

3.9 Epistasis

Epistasis occurs when the expression of one gene is modified by another gene. For example,

gene A only shows its effect when allele B1 (at another Locus) is present, but not if it is

absent. This is one of the ways in which two or more genes may combine to produce a

coordinated change in more than one characteristic (for instance, in mimicry). Unlike the

supergene, epistatic genes do not need to be closely linked or even on the same chromosome.

Both pleiotropism and epistasis show that a gene need not relate to a character in the simple

manner that was once supposed.

4.0 Origin of supergenes

Although a polymorphism can be controlled by alleles at a single locus (e.g. human ABO

blood groups), the more complex forms are controlled by supergenes consisting of several

tightly linked genes on a single chromosome. Batesian mimicry in butterflies and heterostyly

in angiosperms are good examples. There is a long-standing debate as to how this situation

could have arisen, and the question is not yet resolved.

Whereas a gene family (several tighly linked genes performing similar or identical functions)

arises by duplication of a single original gene, this is usually not the case with supergenes. In

a supergene some of the constituent genes have quite distinct functions, so they must have

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come together under selection. This process might involve suppression of crossing-over,

translocation of chromosome fragments and possibly occasional cistron duplication. That

crossing-over can be suppressed by selection has been known for many years.

Debate has centred round the question of whether the component genes in a super-gene could

have started off on separate chromosomes, with subsequent reorganization, or if it is

necessary for them to start on the same chromosome. Originally, it was held that chromosome

rearrangement would play an important role. This explanation was accepted by E. B. Ford

and incorporated into his accounts of ecological genetics.

However, today many believe it more likely that the genes start on the same chromosome.

They argue that supergenes arose in situ. This is known as Turner's sieve hypothesis. John

Maynard Smith agreed with this view in his authoritative textbook but the question is still not

definitively settled.

5.0 Conclusion

In this unit the student learnt the following:

• Definition of polymorphism

• Nomenclature associated with polymorphism

• Ecology

• Genetics and polymorphism

6.0 Summary

Polymorphism, in biology, a discontinuous genetic variation resulting in the occurrence of

several different forms or types of individuals among the members of a single species. A

discontinuous genetic variation divides the individuals of a population into two or more

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sharply distinct forms. The most obvious example of this is the separation of most higher

organisms into male and female sexes.

7.0 Tutor-Marked Assignment

• Define polymorphism

• Explain polymorphism and niche diversity

• Discuss mechanism of balancing selection

• What is Epistatsis

8.0 Reference/ Further Reading

Ford E.B. 1965. Genetic polymorphism. Faber & Faber, London

Dobzhansky, Theodosius. 1970. Genetics of the Evolutionary Process

Clark, W. C. (1976). "The Environment and the Genotype in Polymorphism". Zoological

Journal of the Linnaean Society 58 (3): 255–262.

Ford, E. B. 1975. Ecological Genetics (4th ed.). London: Chapman & Hall

Cain, Arthur J. 1971. "Colour and Banding Morphs in Subfossil Samples of the Snail

Cepaea". In R. Creed (ed.), Ecological genetics and Evolution: Essays in Honour of E.B.

Ford. Oxford: Blackwell.

Begon, Townsend, Harper. 2006. Ecology: from individuals to ecosystems. 4th ed, Blackwell,

Oxford. ISBN 978-1405111171

Charlesworth D., Charlesworth B. (1975). "Theoretical Genetics of Batesian Mimicry". "I.

Single-locus Models". Journal of Theoretical Biology, 55:283–303. "II. Evolution of

166
Supergenes". J. Theoret. Biol., 55:305–324. "III. Evolution of Dominance"". J. Theoret. Biol.

55: 325–337.

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UNIT 3: EXAMPLES OF POLYMORPHISM

Contents

1.0 Introduction

2.0 Objective

3.0 Sexual Dimorphism

3.1 Human Polymorphism

3.1.1 Human Blood Groups

3.1.2 Sickle-Cell Anaemia

3.1.3 Duffy System

3.1.4 G6PD

3.1.5 Cystic Fibrosis

3.1.6 Human Taste Morphisms

3.1.7 Lactose Tolerance/Intolerance

3.1.8 MHC Molecules

4.0 Polymorphism in Lower Organisms

4.1 The Cuckoo

4.2 Hover Fly Polymorphism

4.3 Scarlet Tiger Moth

4.4 Peppered Moth

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4.5 Chromosome Polymorphism in Drosophila

5.0 Conclusion

6.0 Summary

7.0 Tutor-Marked Assignment

8.0 Reference/Further Reading

1.0 INTRODUCTION

Polymorphism results from evolutionary processes, as does any aspect of a species. It is

heritable and is modified by natural selection. In polyphenism, an individual's genetic make-

up allows for different morphs, and the switch mechanism that determines which morph is

shown is environmental. In genetic polymorphism, the genetic make-up determines the

morph. Ants exhibit both types in a single population

2.0 Objective

In this unit the student will learn the following:

• Sexual dimorphism

• Human polymorphism

• Polymorphism in lower organisms

3.0 Sexual dimorphism

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We meet genetic polymorphism daily, since our species uses sexual reproduction, and of

course, the sexes are differentiated. However, even if the sexes were identical in superficial

appearance, the division into two sexes is a dimorphism, albeit cryptic. This is because the

phenotype of an organism includes its sexual organs and its chromosomes, and all the

behaviour associated with reproduction. So research into sexual dimorphism has addressed

two issues: first, the advantage of sex in evolutionary terms; second, the role of visible sexual

differentiation.

The system is relatively stable and heritable, usually by means of sex chromosomes. Every

aspect of this everyday phenomenon bristles with questions for the theoretical biologist. Why

is the ratio ~50/50? How could the evolution of sex occur from an original situation of

asexual reproduction, which has the advantage that every member of a species could

reproduce? Why the visible differences between the sexes? These questions have engaged the

attentions of biologists such as Charles Darwin, August Weismann, Ronald Fisher, George C.

Williams, John Maynard Smith and W. D. Hamilton, with varied success.

Of the many issues involved, there is widespread agreement on the following: the advantage

of sexual and hermaphroditic reproduction over asexual reproduction lies in the way

recombination increases the genetic diversity of the ensuing population. The advantage of

sexual reproduction over hermaphroditic is not so clear. In forms that have two separate

sexes, same sex combinations are excluded from mating which decreases the amount of

diversity compared with hermaphrodites by at least twice. So, why are almost all progressive

species bi-sexual, considering the asexual process is more efficient and simple, whilst

hermaphrodites produce a more diversified progeny? It has been suggested that

differentiation into two sexes has evolutionary advantages allowing changes to concentrate in

the male part of the population and at the same time preserving the existing genotype

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distribution in the females. This enables the population to better meet the challenges of

infection, parasitism, predation and other hazards of the varied environment.

3.1 Human polymorphism

3.1.1 Human blood groups

All the common blood types, such as the ABO blood group system, are genetic

polymorphisms. Here we see a system where there are more than two morphs: the phenotypes

are A, B, AB and O are present in all human populations, but vary in proportion in different

parts of the world. The phenotypes are controlled by multiple alleles at one locus. These

polymorphisms are seemingly never eliminated by natural selection; the reason came from a

study of disease statistics.

Statistical research has shown that the various phenotypes are more, or less, likely to suffer a

variety of diseases. For example, an individual's susceptibility to cholera (and other diarrheal

infections) is correlated with their blood type: those with type O blood are the most

susceptible, while those with type AB are the most resistant. Between these two extremes are

the A and B blood types, with type A being more resistant than type B. This suggests that the

pleiotropic effects of the genes set up opposing selective forces, thus maintaining a balance.

Geographical distribution of blood groups is broadly consistent with the classification of

"races" developed by early anthropologists on the basis of visible features.

3.1.2 Sickle-cell anaemia

Such a balance is seen more simply in sickle-cell anaemia, which is found mostly in tropical

populations in Africa and India. An individual homozygous for the recessive sickle

haemoglobin, HgbS, has a short expectancy of life, whereas the life expectancy of the

standard haemoglobin (HgbA) homozygote and also the heterozygote is normal (though
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heterozygote individuals will suffer periodic problems). The sickle-cell variant survives in the

population because the heterozygote is resistant to malaria and the malaria parasite kills a

huge number of people each year. This is balancing selection or genetic polymorphism,

balanced between fierce selection against homozygous sickle-cell sufferers, and selection

against the standard HgbA homozygotes by malaria. The heterozygote has a permanent

advantage (a higher fitness) so long as malaria exists; and it has existed as a human parasite

for a long time. Because the heterozygote survives, so does the HgbS allele survive at a rate

much higher than the mutation rate.

3.1.3 Duffy system

The Duffy antigen is a protein located on the surface of red blood cells, encoded by the FY

(DARC) gene. The protein encoded by this gene is a non-specific receptor for several

chemokines, and is the known entry-point for the human malarial parasites Plasmodium

vivax and Plasmodium knowlesi. Polymorphisms in this gene are the basis of the Duffy blood

group system. In humans, a mutant variant at a single site in the FY cis-regulatory region

abolishes all expression of the gene in erythrocyte precursors. As a result, homozygous

mutants are strongly protected from infection by P. vivax, and a lower level of protection is

conferred on heterozygotes. The variant has apparently arisen twice in geographically distinct

human populations, in Africa and Papua New Guinea. It has been driven to high frequencies

on at least two haplotypic backgrounds within Africa. Recent work indicates a similar, but

not identical, pattern exists in baboons (Papio cynocephalus), which suffer a mosquito-carried

malaria-like pathogen, Hepatocystis kochi. Researchers interpret this as a case of convergent

evolution.

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3.1.4 G6PD

G6PD (Glucose-6-phosphate dehydrogenase) human polymorphism is also implicated in

malarial resistance. G6PD alleles with reduced activity are maintained at a high level in

endemic malarial regions, despite reduced general viability. Variant A (with 85% activity)

reaches 40% in sub-Saharan Africa, but is generally less than 1% outside Africa and the

Middle East.

3.1.5 Cystic fibrosis

Cystic fibrosis, a congenital disorder which affects about one in 2000 children, is caused by a

mutant form of the CF transmembrane regulator gene, CFTR. The transmission is Mendelian:

the normal gene is dominant, so all heterozygotes are healthy, but those who inherit two

mutated genes have the condition. The mutated allele is present in about 1:25 of the

population (mostly heterozygotes), which is much higher than expected from the rate of

mutation alone. Sufferers from this disease have shortened life expectancy (and males are

usually sterile if they survive), and the disease was effectively lethal in pre-modern societies.

The incidence of the disease varies greatly between ethnic groups, but is highest in Caucasian

populations.

Although over 1500 mutations are known in the CFTR gene, by far the most common mutant

is DF508. This mutant is being kept at a high level in the population despite the lethal or

near-lethal effects of the mutant homozygote. It seems that some kind of heterozygote

advantage is operating. Early theories that the heterozygotes might enjoy increased fertility

have not been borne out. Present indications are that the bacterium which causes typhoid

fever enters cells using CFTR, and experiments with mice suggest that heterozygotes are

resistant to the disease. If the same were true in humans, then heterozygotes would have had

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an advantage during typhoid epidemics. Cystic fibrosis is a prime target for gene therapy

research.

3.1.6 Human taste morphisms

A famous puzzle in human genetics is the genetic ability to taste phenylthiocarbamide

(phenylthiourea or PTC), a morphism which was discovered in 1931. This substance, which

to some of us is bitter, and to others tasteless, is of no great significance in itself, yet it is a

genetic dimorphism. Because of its high frequency (which varies in different ethnic groups) it

must be connected to some function of selective value. The ability to taste PTC itself is

correlated with the ability to taste other bitter substances, many of which are toxic. Indeed,

PTC itself is toxic, though not at the level of tasting it on litmus. Variation in PTC perception

may reflect variation in dietary preferences throughout human evolution, and might correlate

with susceptibility to diet-related diseases in modern populations. There is a statistical

correlation between PTC tasting and liability to thyroid disease.

Fisher, Ford and Huxley tested orangutans and chimpanzees for PTC perception with positive

results, thus demonstrating the long-standing existence of this dimorphism.[48] The recently

identified PTC gene, which accounts for 85% of the tasting variance, has now been analysed

for sequence variation with results which suggest selection is maintaining the morphism.

3.1.7 Lactose tolerance/intolerance

The ability to metabolize lactose, a sugar found in milk and other dairy products, is a

prominent dimorphism that has been linked to recent human evolution.

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3.1.8 MHC molecules

The genes of the major histocompatibility complex (MHC) are highly polymorphic, and this

diversity plays a very important role in resistance to pathogens. This is true for other species

as well.

4.0 Polymorphism in lower organisms

4.1 The Cuckoo

Over fifty species in this family of birds practise brood parasitism; the details are best seen in

the British or European cuckoo (Cuculus canorus). The female lays 15–20 eggs in a season,

but only one in each nest of another bird. She removes some or all of the host's clutch of

eggs, and lays an egg which closely matches the host eggs. Although, in Britain, the hosts are

always smaller than the cuckoo itself, the eggs she lays are small, and coloured to match the

host clutch but thick-shelled. This latter is a defence which protects the egg if the host detects

the fraud.

The intruded egg develops exceptionally quickly; when the newly-hatched cuckoo is only ten

hours old, and still blind, it exhibits an urge to eject the other eggs or nestlings. It rolls them

into a special depression on its back and heaves them out of the nest. The cuckoo nestling is

apparently able to pressure the host adults for feeding by mimicking the cries of the host

nestlings. The diversity of the cuckoo's eggs is extraordinary, the forms resembling those of

its most usual hosts. In Britain these are:

• Meadow pipit (Anthus pratensis): brown eggs speckled with darker brown.

• European robin (Erithacus rubecula): whitish-grey eggs speckled with bright red.

• Reed warbler (Acrocephalus scirpensis): light dull green eggs blotched with olive.

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 • Redstart (Phoenicurus phoenicurus): clear blue eggs.

• Hedge sparrow (Prunella modularis): clear blue eggs, unmarked, not mimicked. This

bird is an uncritical fosterer; it tolerates in its nest eggs that do not resemble its own.

Each female cuckoo lays one type only; the same type laid by her mother. In this way female

cuckoos are divided into groups (known as gentes, singular gens), each parasitises the host to

which it is adapted. The male cuckoo has its own territory, and mates with females from any

gens; thus the population (all gentes) is interbreeding.

The standard explanation of how the inheritance of gens works is as follows. The egg colour

is inherited by sex chromosome. In birds sex determination is ZZ/ZW, and unlike mammals,

the heterogametic sex is the female. The determining gene (or super-gene) for the inheritance

of egg colour is believed to be carried on the W chromosome, which is directly transmitted in

the female line. The female behaviour in choosing the host species is set by imprinting after

birth, a common mechanism in bird behaviour.

Ecologically, the system of multiple hosts protects host species from a critical reduction in

numbers, and maximises the egg-laying capacity of the population of cuckoos. It also extends

the range of habitats where the cuckoo eggs may be raised successfully. Detailed work on the

Cuckoo started with E. Chance in 1922, and continues to the present day; in particular, the

inheritance of gens is still a live issue.

4.2 Hover fly polymorphism

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Xanthogramma pedissiquum, Volucella zonaria, a large Mallota sp., a bumblebee

a wasp mimic bumblebee mimic mimic

Hoverfly mimics can be seen in almost any garden in the temperate zone. The Syrphidae are

a large (5600+ species) family of flies; their imagos feed on nectar and pollen, and are well

known for their mimicry of social hymenoptera. The mimicry is Batesian in nature: hoverflies

are palatable but hymenoptera are generally unpalatable and may also be protected by stings

and/or armour.

Many social wasp (Vespidae) species exhibit Müllerian mimicry, where a group of

unpalatable species benefit from sharing the same kind of warning (aposematic) colouration.

Wasps are decidedly noxious: nasty-tasting and with a painful sting. They form a Mullerian

'ring' of similarly coloured models; the wasps are often accompanied by clusters of hover-fly

mimics, who tend to arrive at the flowers at a similar time of day, and whose flight pattern is

passably similar to wasp flight.

Observers in a garden can see for themselves that hoverfly mimics are quite common, usually

many times more common than the models, and are relatively poor mimics, often easy to

177
distinguish from real wasps. However, it has been established in other cases that imperfect

mimicry can confer significant advantage to the mimic, especially if the model is really

noxious. Also, not only is polymorphism absent from these mimics, it is absent in the wasps

also: these facts are presumably connected.

The situation with bumblebees (Bombus) is rather different. They too are unpalatable, in the

sense of being difficult to eat: their body is covered with setae and is armoured; they are

sometimes described as being 'non-food'. Mostler in 1935 carried out tests of their

palatability: with the exception of specialist bee-eaters, adults of 19 species of birds ate only

2% of 646 bumblebees presented to them. After various trials, Mostler attributed their

avoidance mainly to mechanical difficulties in handling: one young bird took 18 minutes to

subdue, kill and eat a bumblebee.

Bumblebees form Mullerian rings of species, and they do often exhibit polymorphism. The

hoverfly species mimicking bumblebees are generally accurate mimics, and many of their

species are polymorphic. Many of the polymorphisms are different between the sexes, for

example by the mimicry being limited to one sex only.

The question is, how can the differences between social wasp mimics and bumblebee mimics

be explained? Evidently if model species are common, and have overlapping distributions,

they are less likely to be polymorphic. Their mimics are widespread and develop a kind of

rough and ready jack-of-all-trades mimicry. But if model species are less common and have

patchy distribution they develop polymorphism; and their mimics match them more exactly

and are polymorphic also. The issues are currently being investigated.

4.3 Scarlet tiger moth

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The scarlet tiger moth Callimorpha (Panaxia) dominula (family Arctiidae)
Arctiidae occurs in

continental Europe, western

rn Asia and southern England. It is a day-flying
day flying moth, noxious-
noxious

tasting, with brilliant warning colour in flight, but cryptic at rest. The moth is colonial in

habit, and prefers marshy ground or hedgerows. The preferred food of the larvae is the herb

Comfrey (Symphytum
Symphytum officinale).
officinale). In England it has one generation per year.

Callimorpha dominula morpha typica with spread wings. The red with black rear wings,

revealed in flight, warn of its noxious

noxious taste. The front wings are cryptic, covering the rear

wings at rest. Here the moth is resting but alert, and has jinked the front wings forward to

reveal the warning flash.

The moth is known to be polymorphic in its colony at Cothill,, about five miles (8 km) from

Oxford,, with three forms: the typical homozygote;; the rare homozygote (bimacula)
( and the

heterozygote (medionigra).
). It was studied there by Ford and later by Sheppard and their co-

workers over many years. Data is available from 1939 to the present day, got by the usual

field method of capture-mark

mark-release-recapture
recapture and by genetic analysis from breeding in

captivity. The records cover gene frequency and population-size

population for much
uch of the twentieth

century.

In this instance the genetics appears to be simple: two alleles at a single locus,
locus producing the

three phenotypes.. Total captures over 26 years 1939-64

1939 64 came to 15,784 homozygous

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dominula (i.e. typica), 1,221 heterozygous medionigra and 28 homozygous bimacula. Now,

assuming equal viability of the genotypes 1,209 heterozygotes would be expected, so the

field results do not suggest any heterozygous advantage. It was Sheppard who found that the

polymorphism is maintained by selective mating: each genotype preferentially mates with

other morphs. This is sufficient to maintain the system despite the fact that in this case the

heterozygote has slightly lower viability.

4.4 Peppered moth

The peppered moth, Biston betularia, is justly famous as an example of a population

responding in a heritable way to a significant change in their ecological circumstances. E.B.

Ford described peppered moth evolution as "one of the most striking, though not the most

profound, evolutionary changes ever actually witnessed in nature".

Although the moths are cryptically camouflaged and rest during the day in unexposed

positions on trees, they are predated by birds hunting by sight. The original camouflage (or

crypsis) seems near-perfect against a background of lichen growing on trees. The sudden

growth of industrial pollution in the nineteenth century changed the effectiveness of the

moths' camouflage: the trees became blackened by soot, and the lichen died off. In 1848 a

dark version of this moth was found in the Manchester area. By 1895 98% of the Peppered

Moths in this area were black. This was a rapid change for a species that has only one

generation a year.

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Biston betularia morpha typica,
typica the standard light-coloured
coloured Peppered Moth.

Biston betularia morpha carbonaria,

carbonaria the melanic Peppered Moth.

In Europe, there are three morphs: the typical white morph (betularia
(betularia or typica), and

carbonaria,, the melanic black morph. They are controlled by alleles at one locus, with the

carbonaria being dominant.. There is also an intermediate or semi-melanic

semi melanic morph insularia,

controlled by other alleles (see Majerus 1998).

A key fact, not realised initially, is the advantage of the heterozygotes, which survive better

than
an either of the homozygotes. This affects the caterpillars as well as the moths, in spite of

the caterpillars being monomorphic in appearance (they are twig mimics). In practice

heterozygote advantage puts a limit to the effect of selection, since neither homozygote can

reach 100% of the population. For this reason, it is likely that the carbonaria allele was in the

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population originally, pre-industrialisation, at a low level. With the recent reduction in

pollution, the balance between the forms has already shifted back significantly.

Another interesting feature is that the carbonaria had noticeably darkened after about a

century. This was seen quite clearly when specimens collected about 1880 were compared

with specimens collected more recently: clearly the dark morph has been adjusted by the

strong selection acting on the gene complex. This might happen if a more extreme allele was

available at the same locus; or genes at other loci might act as modifiers. We do not, of

course, know anything about the genetics of the original melanics from the nineteenth

century.

This type of industrial melanism has only affected such moths as obtain protection from

insect-eating birds by resting on trees where they are concealed by an accurate resemblance

to their background (over 100 species of moth in Britain with melanic forms were known by

1980). No species which hide during the day, for instance, among dead leaves, is affected,

nor has the melanic change been observed among butterflies.

This is, as shown in many textbooks, "evolution in action". Much of the early work was done

by Bernard Kettlewell, whose methods came under scrutiny later on. The entomologist

Michael Majerus discussed criticisms made of Kettlewell's experimental methods in his 1998

book Melanism: Evolution in Action. This book was misrepresented in some reviews, and the

story picked up by creationist campaigners. Judith Hooper, in her controversial book Of

Moths and Men (2002), implied that Kettlewell's work was fraudulent or incompetent.

Careful studies of Kettlewell's surviving papers by Rudge (2005) and Young (2004) found

that Hooper's accusation of fraud was unjustified, and that "Hooper does not provide one

shred of evidence to support this serious allegation”. Majerus himself described Of Moths and

Men as "littered with errors, misrepresentations, misinterpretations and falsehoods".A

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suitably restrained 2004 summary of opinion mostly favoured predation as the main selective

force. Starting in 2000, Majerus conducted a detailed seven year study of moths,

experimenting to assess the various criticisms. He concluded that that differential bird

predation was a major factor responsible for the decline in carbonaria frequency compared to

typica in Cambridge during the study period, and described his results as a complete

vindication of the peppered moth story. He said, "If the rise and fall of the peppered moth is

one of the most visually impacting and easily understood examples of Darwinian evolution in

action, it should be taught. It provides after all the proof of evolution."

Current interpretation of the available evidence is that the peppered moth is in fact a valid

example of natural selection and adaptation. It illustrates a polymorphic species maintaining

adaptation to a varied and sometimes changing environment.

4.5 Chromosome polymorphism in Drosophila

In the 1930s Dobzhansky and his co-workers collected Drosophila pseudoobscura and D.

persimilis from wild populations in California and neighbouring states. Using Painter's

technique they studied the polytene chromosomes and discovered that the wild populations

were polymorphic for chromosomal inversions. All the flies look alike whatever inversions

they carry: this is an example of a cryptic polymorphism. Accordingly, Dobzhansky favoured

the idea that the morphs became fixed in the population by means of Sewall Wright's drift.

However, evidence rapidly accumulated to show that natural selection was responsible:

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Drosophila polytene chromosome

1. Values for heterozygote inversions of the third chromosome were often much higher than

they should be under the null assumption: if no advantage for any form the number of

heterozygotes should conform to Ns (number in sample) = p2+2pq+q2 where 2pq is the

number of heterozygotes (see Hardy-Weinberg equilibrium).

2. Using a method
thod invented by l'Heretier and Teissier, Dobzhansky bred populations in

population cages,, which enabled feeding, breeding and sampling whilst preventing escape.

This had the benefit of eliminating migration as a possible explanation of the results. Stocks

containing inversions at a known initial frequency can be maintained in controlled conditions.

It was found that the various chromosome types do not fluctuate at random, as they would if

selectively neutral, but adjust to certain frequencies at which they become stabilised. With D.

persimilis he found that the caged population followed the values expected on the Hardy-
Hardy

Weinberg equilibrium when conditions were optimal (which disproved

disproved any idea of non-
non

random mating), but with a restricted food supply heterozygotes had a distinct advantage.

3. Different proportions of chromosome morphs were found in different areas. There is, for

example, a polymorph-ratio
ratio cline in D. robusta along an 18-mile
mile (29 km) transect near

Gatlinburg, TN passing from 1,000 feet (300 m) to 4,000 feet. Also, the same areas sampled

at different times of year yielded significant differences

differences in the proportions of forms. This

indicates a regular cycle of changes which adjust the population to the seasonal conditions.

For these results selection is by far the most likely explanation.

4. Lastly, morphs cannot be maintained at the high levels found simply by mutation, nor is

drift a possible explanation when population numbers are high.

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By the time Dobzhansky published the third edition of his book in 1951, he was persuaded

that the chromosome morphs were being maintained in the population by the selective

advantage of the heterozygotes, as with most polymorphisms. Later he made yet another

interesting discovery. One of the inversions, known as PP, was quite rare up to 1946, but by

1958 its proportion had risen to 8%. Not only that, but the proportion was similar over an

area of some 200,000 square miles (520,000 km2) in California. This cannot have happened

by migration of PP morphs from, say, Mexico (where the inversion is common) because the

rate of dispersal (at less than 2 km/year) is of the wrong order. The change therefore reflected

a change in prevailing selection whose basis was not yet known.

5.0 Conclusion

In this unit the student learnt the following:

• Sexual polymorphism

• Human polymorphism

• Polymorphism in lower organisms

6.0 Summary

Polymorphism is a condition in which a population possesses more than one allele at a locus.

Sometimes it is defined as the condition of having more than one allele with a frequency of

over 5% in the population.

There may be several causes of polymorphism:

• Polymorphism can be maintained by a balance between variation created by new mutations

and natural selection (see mutational load).

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• Genetic variation may be caused by frequency-dependent selection.

• Multiple niche polymorphism exists when different genotypes should have different

fitnesses in different niches.

• Heterozygous advantage may maintain alleles which would otherwise be selected against.

• If selection is operating, migration can introduce polymorphism into a population.

These are all sources of polymorphism which make use of the mechanisms of natural

selection. Genetic drift is also a possible source of genetic variation.

7.0 Reference/Further Reading

Gillespie J.G. 2004. Population genetics: a concise guide. 2nd ed, Johns Hopkins University

Press, Baltimore.

Geodakyan V. A. (2000). "Evolutionary chromosomes and evolutionary sex dimorphism".

Biology Bulletin 27: 99–113.

Fisher, Ronald. 1930. The Genetical Theory of Natural Selection

Hamilton, W. D. 2002. Narrow Roads of Gene Land, Vol. 2: Evolution of Sex. Oxford:

Oxford U. Pr.

Smith, John Maynard. 1978. The Evolution of Sex. Cambridge: Cambridge U. Pr.

Cooke G. S., Hill A. V. S. (2001). "Genetics of susceptibility to human infectious disease".

Nat. Rev. Genet 2 (12): 967–977. doi:10.1038/35103577. PMID 11733749.

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Sykes, B. 1999. The human inheritance: genes, language and evolution. Oxford: Oxford U.

Pr.

Clarke, Cyril A. 1964. Genetics for the Clinician. Oxford: Blackwell

Polymorphism. http://www.blackwellpublishing.com/ridley/

MODULE 4: VARIATION; TYPES AND CAUSES

UNIT 1: EVOLUTION AND VARIATION

1.0 Introduction

Evolution is the cornerstone of modern biology. It unites all the fields of biology under one

theoretical umbrella. It is not a difficult concept, but very few people -- the majority of

biologists included -- have a satisfactory grasp of it. One common mistake is believing that

species can be arranged on an evolutionary ladder from bacteria through "lower" animals, to

"higher" animals and, finally, up to man. Mistakes permeate popular science expositions of

evolutionary biology. Mistakes even filter into biology journals and texts. For example,

Lodish, et. al., in their cell biology text, proclaim, "It was Charles Darwin's great insight that

organisms are all related in a great chain of being..." In fact, the idea of a great chain of

being, which traces to Linnaeus, was overturned by Darwin's idea of common descent.

Misunderstandings about evolution are damaging to the study of evolution and biology as a

whole. People who have a general interest in science are likely to dismiss evolution as a soft

science after absorbing the pop science nonsense that abounds. The impression of it being a

soft science is reinforced when biologists in unrelated fields speculate publicly about

evolution. Evolution is a change in the gene pool of a population over time. A gene is a

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hereditary unit that can be passed on unaltered for many generations. The gene pool is the set

of all genes in a species or population.

The English moth, Biston betularia, is a frequently cited example of observed evolution.

[evolution: a change in the gene pool] In this moth there are two color morphs, light and dark.

H. B. D. Kettlewell found that dark moths constituted less than 2% of the population prior to

1848. The frequency of the dark morph increased in the years following. By 1898, the 95% of

the moths in Manchester and other highly industrialized areas were of the dark type. Their

frequency was less in rural areas. The moth population changed from mostly light colored

moths to mostly dark colored moths. The moths' color was primarily determined by a single

gene. So, the change in frequency of dark colored moths represented a change in the gene

pool. This change was, by definition, evolution.

The increase in relative abundance of the dark type was due to natural selection. The late

eighteen hundreds was the time of England's industrial revolution. Soot from factories

darkened the birch trees the moths landed on. Against a sooty background, birds could see the

lighter colored moths better and ate more of them. As a result, more dark moths survived

until reproductive age and left offspring. The greater number of offspring left by dark moths

is what caused their increase in frequency. This is an example of natural selection.

Populations evolve. In order to understand evolution, it is necessary to view populations as a

collection of individuals, each harboring a different set of traits. A single organism is never

typical of an entire population unless there is no variation within that population. Individual

organisms do not evolve, they retain the same genes throughout their life. When a population

is evolving, the ratio of different genetic types is changing -- each individual organism within

a population does not change. For example, in the previous example, the frequency of black

moths increased; the moths did not turn from light to gray to dark in concert. The process of

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evolution can be summarized in three sentences: Genes mutate. Individuals are selected.

Populations evolve.

Evolution can be divided into microevolution and macroevolution. The kind of evolution

documented above is microevolution. Larger changes, such as when a new species is formed,

are called macroevolution. Some biologists feel the mechanisms of macroevolution are

different from those of microevolutionary change. Others think the distinction between the

two is arbitrary -- macroevolution is cumulative microevolution.

The word evolution has a variety of meanings. The fact that all organisms are linked via

descent to a common ancestor is often called evolution. The theory of how the first living

organisms appeared is often called evolution. This should be called abiogenesis. And

frequently, people use the word evolution when they really mean natural selection -- one of

the many mechanisms of evolution.

2.0 0bjectives

At the end of this unit, the students should be able to:

• Understand the basis for variation: Evolution

• Describe variation

• Highlight the importance of natural selection

3.0 Natural Selection

In elephants, as in cod, many individuals die between egg and adult; they both have excess

fecundity. This excess fecundity exists because the world does not contain enough resources

to support all the eggs that are laid and all the young that are born. The world contains only

limited amounts of food and space. A population may expand to some extent, but logically

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there will come a point beyond which the food supply must limit its further expansion. As

resources are used up, the death rate in the population increases, and when the death rate

equals the birth rate the population will stop growing. Organisms, therefore, in an ecological

sense compete to survive and reproduce a both directly, for example by defending territories,

and indirectly, for example by eating food that could otherwise be eaten by another

individual. The actual competitive factors limiting the sizes of real populations make up a

major area of ecological study. Various factors have been shown to operate. What matters

here, however, is the general point that the members of a population, and members of

different species, compete in order to survive. This competition follows from the conditions

of limited resources and excess fecundity. Darwin referred to this ecological competition as

the “struggle for existence.” The expression is metaphorical: it does not imply a physical

fight to survive, though fights do sometimes happen. The struggle for existence takes place

within a web of ecological relations. Above an organism in the ecological food chain there

will be predators and parasites, seeking to feed off it. Below it are the food resources it must

in turn consume in order to stay alive. At the same level in the chain are competitors that may

be competing for the same limited resources of food, or space.

An organism competes most closely with other members of its own species, because they

have the most similar ecological needs to its own. Other species, in decreasing order of

ecological similarity, also compete and exert a negative influence on the organism’s chance

of survival. Only the successful competitors will reproduce themselves. An organism

competes most closely with other members of its own species, because they have the most

similar ecological needs to its own. Other species, in decreasing order of ecological

similarity, also compete and exert a negative influence on the organism’s chance of survival.

Only the successful competitors will reproduce themselves.

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3.1 Variation

An individual organism's phenotype results from both its genotype and the influence from the

environment it has lived in. A substantial part of the variation in phenotypes in a population

is caused by the differences between their genotypes. The modern evolutionary synthesis

defines evolution as the change over time in this genetic variation. The frequency of one

particular allele will become more or less prevalent relative to other forms of that gene.

Variation disappears when a new allele reaches the point of fixation — when it either

disappears from the population or replaces the ancestral allele entirely.

Natural selection will only cause evolution if there is enough genetic variation in a

population. Before the discovery of Mendelian genetics, one common hypothesis was

blending inheritance. But with blending inheritance, genetic variance would be rapidly lost,

making evolution by natural selection implausible. The Hardy-Weinberg principle provides

the solution to how variation is maintained in a population with Mendelian inheritance. The

frequencies of alleles (variations in a gene) will remain constant in the absence of selection,

mutation, migration and genetic drift.

Variation comes from mutations in genetic material, reshuffling of genes through sexual

reproduction and migration between populations (gene flow). Despite the constant

introduction of new variation through mutation and gene flow, most of the genome of a

species is identical in all individuals of that species. However, even relatively small

differences in genotype can lead to dramatic differences in phenotype: for example,

chimpanzees and humans differ in only about 5% of their genomes.

3.2 Types of variation

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How much, and with respect to what characters, do natural populations show variation and, in

particular, variation in fitness? Let us consider biological variation through a series of levels

of organization, beginning with the organism’s morphology, and working down to more

microscopic levels. The purpose of this section is to give examples of variation, to show how

variation can be seen in almost all the properties of living things, and to introduce some of the

methods (particularly molecular methods) that we shall meet again and that are used to study

variation.

3.2.1 Genetic Variation

Evolution requires genetic variation. If there were no dark moths, the population could not

have evolved from mostly light to mostly dark. In order for continuing evolution there must

be mechanisms to increase or create genetic variation and mechanisms to decrease it.

Mutation is a change in a gene. These changes are the source of new genetic variation.

Natural selection operates on this variation.

3.2.2 Morphological Level

At the morphological level, the individuals of a natural population will be found to vary for

almost any character we may measure. In some characters, like body size, every individual

differs from every other individual; this is called continuous variation. Other morphological

characters show discrete variation as they fall into a limited number of categories. Sex, or

gender, is an obvious example, with some individuals of a population being female, others

male. This kind of categorical variation is found in other characters too. A population that

contains more than one recognizable form is polymorphic (the condition is called

polymorphism). There can be any number of forms in real cases, and they can have any set of

relative frequencies. With sex, there are usually two forms. In the peppered moth (Biston

betularia), two main color forms are often distinguished, though real populations may contain

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three or more As the number of forms in the population increases, the polymorphic,

categorical kind of variation blurs into the continuous kind of variation.

3.2.3 Cellular Level

Variation is not confined to morphological characters. If we descend to a cellular character,

such as the number and structure of the chromosomes, we again find variation. In the fruitfly

Drosophila melanogaster, the chromosomes exist in giant forms in the larval salivary glands

and they can be studied with a light microscope. They turn out to have characteristic banding

patterns, and chromosomes from different individuals in a population have subtly varying

banding patterns. One type of variant is called an inversion, in which the banding pattern a

and therefore the order of genes a of a region of the chromosome is inverted. A population of

fruitflies may be polymorphic for a number of different inversions. Chromosomal variation is

less easy to study in species that lack giant chromosomal forms, but it is still known to exist.

Populations of the Australian grasshopper Keyacris scurra, for example, may contain two

(normal and inverted) forms for each of two chromosomes; that makes nine kinds of

grasshopper in all because an individual may be homozygous or heterozygous for any of the

four chromosomal types. The nine differ in size and viability Chromosomes can vary in other

respects too. Individuals may vary in their number of chromosomes, for example. In many

species, some individuals have one or more extra chromosomes, in addition to the normal

number for the species. These “supernumerary”chromosomes, which are often called B

chromosomes, have been particularly studied in maize and in grasshoppers. In the

grasshopper Atractomorpha australis, normal individuals have 18 autosomes, but individuals

have been found with from one to six supernumary chromosomes. The population is

polymorphic with respect to chromosome number. Inversions and B chromosomes are just

two kinds of chromosomal variation. There are other kinds too; but these are enough to make

the point that individuals vary at the subcellular, as well as the morphological level.

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3.2.4 Biochemical Level

The story is the same at the biochemical level, such as for proteins. Proteins are molecules

made up of sequences of amino acid units. A particular protein, like human hemoglobin, has

a particular characteristic sequence, which in turn determines the molecule’s shape and

properties. But do all humans have exactly the same sequence for hemoglobin, or any other

protein? In theory, we could find out by taking the protein from several individuals and then

working out the sequence in each of them; but it would be excessively laborious to do so. Gel

electrophoresis is a much faster method. Gel electrophoresis works because different amino

acids carry different electric charges. Different proteins and different variants of the same

protein a have different net electric charges, because they have different amino acid

compositions. If we place a sample of proteins (with the same molecular weight) in an

electric field, those with the largest electric charges will move fastest. For the student of

biological variation, the importance of the method is that it can reveal different variants of a

particular type of protein. A good example is provided by a less well known protein than

hemoglobin a the enzyme called alcohol dehydrogenase, in the fruitfly. Fruitflies, as their

name suggests, lay their eggs in, and feed on, decaying fruit. They are attracted to rotting fruit

because of the yeast it contains. Fruitflies can be collected almost anywhere in the world by

leaving out rotting fruit as a lure; and drowned fruitflies are usually found in a glass of wine

left out overnight after a garden party in the late summer. As fruit rots, it forms a number of

chemicals, including alcohol, which is both a poison and a potential energy source. Fruitflies

cope with alcohol by means of an enzyme called alcohol dehydrogenase. The enzyme is

crucial. If the alcohol dehydrogenase gene is deleted from fruitflies, and those flies are then

fed on mere 5% alcohol, “they have difficulty flying and walking, and finally, cannot stay on

their feet” (quoted in Ashburner 1998). Gel electrophoresis reveals that, in most populations

of the fruitfly Drosophila melanogaster, alcohol dehydrogenase comes in two main forms.

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The two forms show up as different bands on the gel after the sample has been put on it, an

electric current put across it for a few hours, and the position of the enzyme has been exposed

by a specific stain. The two variants are called slow (Adh-s) or fast (Adh-f ) according to how

far they have moved in the time. The multiple bands show that the protein is polymorphic.

The enzyme called alcohol dehydrogenase is actually a class of two polypeptides with

slightly different amino acid sequences. Gel electrophoresis has been applied to a large

number of proteins in a large number of species and different proteins show different degrees

of variability. But the point for now is that many of these proteins have been found to be

variable a extensive variation exists in proteins in natural

populations.

3.2.5 DNA Level

If variation is found in every organ, at every level, among the individuals of a population,

variation will almost inevitably also be found at the DNA level too. The inversion

polymorphisms of chromosomes that we met above, for example, are due to inversions of the

DNA sequence. However, the most direct method of studying DNA variation is to sequence

the DNA itself. Let us stay with alcohol dehydrogenase in the fruitfly. Kreitman (1983)

isolated the DNA encoding alcohol dehydrogenase from 11 independent lines of D.

melanogaster and individually sequenced them all. Some of the 11 had Adh-f, others Adh-s,

and the difference between Adh-f and Adh-s was always due to a single amino acid difference

(Thr or Lys at codon 192). The amino acid difference appears as a base difference in the

DNA, but this was not the only source of variation at the DNA level. The DNA is even more

variable than the protein study suggests. At the protein level, only the two main variants were

found in the sample of 11 genes, but at the DNA level there were 11 different sequences with

43 different variable sites. The amount of variation that we find is therefore highest at the

DNA level. At the level of gross morphology, a Drosophila with two Adh-f genes is

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indistinguishable from one with two Adh-s genes; gel electrophoresis resolves two classes of

fly; but at the DNA level, the two classes decompose into innumerable individual

variants. Restriction enzymes provide another method of studying DNA variation. Restriction

enzymes exist naturally in bacteria, and a large number a over 2,300 a of restriction enzymes

are known. Any one restriction enzyme cuts a DNA strand wherever it has a particular

sequence, usually of about 4–8 base pairs. The restriction enzyme called EcoR1, for instance,

which is found in the bacterium Escherichia coli, recognizes the base sequence ...GAATTC...

and cuts it between the initial G and the first A. In the bacterium, the enzymes help to protect

against viral invasion by cleaving foreign DNA, but the enzymes can be isolated in the

laboratory and used to investigate DNA sequences. Suppose the DNA of two individuals

differs, and that one has the sequence GAATTC at a certain site whereas the other individual

has another sequence such as GTATT. If the DNA of each individual is put with EcoR1, only

that of the first individual will be cleaved. The difference can be detected in the length of the

DNA fragments: the pattern of fragment lengths will differ for the two individuals. The

variation is called restriction fragment length polymorphism and has been found in all

populations that have been studied.

4.0 Conclusion

The student has learnt the following:

• Background history on the importance of evolution

• Variation

• Types of variation

5.0 Summary

Evolution has been called the cornerstone of biology, and for good reasons. It is possible to

do research in biology with little or no knowledge of evolution. Most biologists do. But,

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without evolution biology becomes a disparate set of fields. Evolutionary explanations

pervade all fields in biology and brings them together under one theoretical umbrella.

We know that natural selection should optimize the existing genetic variation in a population

to maximize reproductive success. This provides a framework for interpreting a variety of

biological traits and their relative importance. For example, a signal intended to attract a mate

could be intercepted by predators. Natural selection has caused a trade- off between attracting

mates and getting preyed upon. If you assume something other than reproductive success is

optimized, many things in biology would make little sense. Without the theory of evolution,

life history strategies would be poorly understood.

Organisms are modified over time by cumulative natural selection. The numerous examples

of jury- rigged design in nature are a direct result of this. The distribution of genetically based

traits across groups is explained by splitting of lineages and the continued production of new

traits by mutation. The traits are restricted to the lineages they arise in.

Details of the past also hold explanatory power in biology. Plants obtain their carbon by

joining carbon dioxide gas to an organic molecule within their cells. This is called carbon

fixation. The enzyme that fixes carbon is RuBP carboxlyase. Plants using C3 photosynthesis

lose 1/3 to 1/2 of the carbon dioxide they originally fix. RuBP carboxlyase works well in the

absence of oxygen, but poorly in its presence. This is because photosynthesis evolved when

there was little gaseous oxygen present. Later, when oxygen became more abundant, the

efficiency of photosynthesis decreased. Photosynthetic organisms compensated by making

more of the enzyme. RuBP carboxylase is the most abundant protein on the planet partially

because it is one of the least efficient.

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Ecosystems, species, organisms and their genes all have long histories. A complete

explanation of any biological trait must have two components. First, a proximal explanation -

- how does it work? And second, an ultimate explanation -- what was it modified from? For

centuries humans have asked, "Why are we here?" The answer to that question lies outside

the realm of science. Biologists, however, can provide an elegant answer to the question,

"How did we get here?"

6.0 Tutor-Marked Assignment

• What do you know about evolution?

• What is variation?

• Discuss natural selection.

7.0 Reference/ Further Readings

Futuyma, Douglas J. (1997). Evolutionary Biology. Sunderland, Mass.: Sinauer Associates.

Ridley, Mark. (2003). Evolution. Boston: Blackwell Scientific.

Hartl, Daniel L. & Andrew G. Clark. (1997). Principles of Population Genetics. Sunderland,

Mass.: Sinauer Associates.

Crow, James F. & Motoo Kimura. (1970). Introduction to Population Genetics Theory.
Edina,

Minn.: Burgess Publishing Company.

Graur, Dan & Wen-Hsiung Li. (2000). Fundamentals of Molecular Evolution. Sunderland,

Mass.: Sinauer Associates.

Lewontin, Richard C. (1974). The Genetic Basis of Evolutionary Change. New York:
Columbia

Univ. Press.

Gillespie, John H. (1997). The Causes of Molecular Evolution. New York: Oxford Univ.
Press.

Golding, Brian, ed. (1994). Non-Neutral Evolution. Boston: Chapman and Hall.

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Kimura, Motoo. (1983). The Neutral Theory of Molecular Evolution. Cambridge, U.K.:

Cambridge Univ. Press.

Endler, John A. (1986). Natural Selection in the Wild. Princeton, N.J.: Princeton Univ. Press.

UNIT 2: GENETIC VARIATION

1.0 Introduction

In order for continuing evolution there must be mechanisms to increase or create genetic

variation and mechanisms to decrease it. The mechanisms of evolution are mutation, natural

selection, genetic drift, recombination and gene flow. I have grouped them into two classes --

those that decrease genetic variation and those that increase it.

2.0 Objective

At the end of this unit, the student should be able to:

• Discuss on mechanisms that affect genetic variation

• Discuss on conditions for natural selection

• Have an understanding of Mutation, alleles, recombination and Gene flow.

3.0 Mechanisms that Decrease Genetic Variation

3.1.1 Genetic variation has two components: allelic diversity and non- random associations

of alleles. Alleles are different versions of the same gene. For example, humans can have A,

B or O alleles that determine one aspect of their blood type. Most animals, including humans,

are diploid -- they contain two alleles for every gene at every locus, one inherited from their

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mother and one inherited from their father. Locus is the location of a gene on a chromosome.

Humans can be AA, AB, AO, BB, BO or OO at the blood group locus. If the two alleles at a

locus are the same type (for instance two A alleles) the individual would be called

homozygous. An individual with two different alleles at a locus (for example, an AB

individual) is called heterozygous. At any locus there can be many different alleles in a

population, more alleles than any single organism can possess. For example, no single human

can have an A, B and an O allele.

Considerable variation is present in natural populations. At 45 percent of loci in plants there

is more than one allele in the gene pool. Any given plant is likely to be heterozygous at about

15 percent of its loci. Levels of genetic variation in animals range from roughly 15% of loci

having more than one allele (polymorphic) in birds, to over 50% of loci being polymorphic in

insects. Mammals and reptiles are polymorphic at about 20% of their loci - - amphibians and

fish are polymorphic at around 30% of their loci. In most populations, there are enough loci

and enough different alleles that every individual, identical twins excepted, has a unique

combination of alleles.

Linkage disequilibrium is a measure of association between alleles of two different genes. If

two alleles were found together in organisms more often than would be expected, the alleles

are in linkage disequilibrium. If there two loci in an organism (A and B) and two alleles at

each of these loci (A1, A2, B1 and B2) linkage disequilibrium (D) is calculated as D =

f(A1B1) * f(A2B2) - f(A1B2) * f(A2B1) (where f(X) is the frequency of X in the

population). [Loci (plural of locus): location of a gene on a chromosome] D varies between -

1/4 and 1/4; the greater the deviation from zero, the greater the linkage. The sign is simply a

consequence of how the alleles are numbered. Linkage disequilibrium can be the result of

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physical proximity of the genes. Or, it can be maintained by natural selection if some

combinations of alleles work better as a team.

Natural selection maintains the linkage disequilibrium between color and pattern alleles in

Papilio memnon. [linkage disequilibrium: association between alleles at different loci] In this

moth species, there is a gene that determines wing morphology. One allele at this locus leads

to a moth that has a tail; the other allele codes for a untailed moth. There is another gene that

determines if the wing is brightly or darkly colored. There are thus four possible types of

moths: brightly colored moths with and without tails, and dark moths with and without tails.

All four can be produced when moths are brought into the lab and bred. However, only two

of these types of moths are found in the wild: brightly colored moths with tails and darkly

colored moths without tails. The non-random association is maintained by natural selection.

Bright, tailed moths mimic the pattern of an unpalatable species. The dark morph is cryptic.

The other two combinations are neither mimetic nor cryptic and are quickly eaten by birds.

Assortative mating causes a non-random distribution of alleles at a single locus. [locus:

location of a gene on a chromosome] If there are two alleles (A and a) at a locus with

frequencies p and q, the frequency of the three possible genotypes (AA, Aa and aa) will be p2,

2pq and q2, respectively. For example, if the frequency of A is 0.9 and the frequency of a is

0.1, the frequencies of AA, Aa and aa individuals are: 0.81, 0.18 and 0.01. This distribution is

called the Hardy-Weinberg equilibrium.

Non-random mating results in a deviation from the Hardy-Weinberg distribution. Humans

mate assortatively according to race; we are more likely to mate with someone of own race

than another. In populations that mate this way, fewer heterozygotes are found than would be

predicted under random mating. A decrease in heterozygotes can be the result of mate choice,

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or simply the result of population subdivision. Most organisms have a limited dispersal

capability, so their mate will be chosen from the local population.

3.1.2 Conditions in Natural Selection

The excess fecundity, and consequent competition to survive in every species, provide the

preconditions for the process Darwin called natural selection. Natural selection is easiest to

understand, in the abstract, as a logical argument, leading from premises to conclusion. The

argument, in its most general form, requires four conditions:

1. Reproduction. Entities must reproduce to form a new generation.

2. Heredity. The offspring must tend to resemble their parents: roughly speaking, “like

must produce like.”

3. Variation in individual characters among the members of the population. If we are

studying natural selection on body size, then different individuals in the population

must have different body sizes.

4. Variation in the fitness of organisms according to the state they have for a heritable

character. In evolutionary theory, fitness is a technical term, meaning the average number of

offspring left by an individual relative to the number of offspring left by an average member

of the population. This condition therefore means that individuals in the population with

some characters must be more likely to reproduce (i.e., have higher fitness) than others. (The

evolutionary meaning of the term fitness differs from its athletic meaning.)

If these conditions are met for any property of a species, natural selection automatically

results. And if any are not, it does not. Thus entities, like planets, that do not reproduce,

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cannot evolve by natural selection. Entities that reproduce but in which parental characters

are not inherited by their offspring also cannot evolve by natural selection. But when the four

conditions apply, the entities with the property conferring higher fitness will leave more

offspring, and the frequency of that type of entity will increase in the population. The

evolution of drug resistance in HIV illustrates the process The usual form of HIV has a

reverse transcriptase that binds to drugs called nucleoside inhibitors as well as the proper

constituents of DNA (A, C, G, and T). In particular, one nucleoside inhibitor called 3TC is a

molecular analog of C. When reverse transcriptase places a 3TC molecule, instead of a C, in

a replicating DNA chain, chain elongation is stopped and the reproduction of HIV is also

stopped. In the presence of the drug 3TC, the HIV population in a human body evolves a

discriminating form of reverse transcriptase a a form that does not bind 3TCbut does bind C.

The HIV has then evolved drug resistance. The frequency of the drug-resistant HIV increases

from an undetectably low frequency at the time the drug is first given to the patient up to

100% about 3 weeks later. The increase in the frequency of drug-resistant HIV is almost

certainly driven by natural selection. The virus satisfies all four conditions for natural

selection to operate. The virus reproduces; the ability to resist drugs is inherited (because the

ability is due to a genetic change in the virus); the viral population within one human body

shows genetic variation in drug-resistance ability; and the different forms of HIV have

different fitnesses. In a human AIDS patient who is being treated with a drug such as 3TC,

the HIV with the right change of amino acid in their reverse transcriptase will reproduce

better, produce more offspring virus like themselves, and increase in frequency. Natural

selection favors them.

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3.1.3 Natural selection explains both evolution and adaptation

When the environment of HIV changes, such that the host cell contains nucleoside inhibitors

such as 3TC as well as valuable resources such as C, the population of HIV changes over

time. In other words, the HIV population evolves. Natural selection produces evolution when

the environment changes; it will also produce evolutionary change in a constant environment

if a new form arises that survives better than the current form of the species. The process that

operates in any AIDS patient on drug treatment has been operating in all life for 4,000

million years since life originated, and has driven much larger evolutionary changes over

those long periods of time. Natural selection can not only produce evolutionary change, it can

also cause a population to stay constant. If the environment is constant and no superior form

arises in the population, natural selection will keep the population the way it is. Natural

selection can explain both evolutionary change and the absence of change. Natural selection

also explains adaptation. The drug resistance of HIV is an example of an adaptation The

discriminatory reverse transcriptase enzyme enables HIV to reproduce in an environment

containing nucleoside inhibitors. The new adaptation was needed because of the change in

the environment. In the drug treated AIDS patient, a fast but undiscriminating reverse

transcriptase was no longer adaptive. The action of natural selection to increase the frequency

of the gene coding for a discriminating reverse transcriptase resulted in the HIV becoming

adapted to its environment. Over time, natural selection generates adaptation. The theory of

natural selection therefore passes the key test set by Darwin for a satisfactory theory of

evolution.

3.1.4 Sexual Selection

In many species, males develop prominent secondary sexual characteristics. A few oft cited

examples are the peacock's tail, coloring and patterns in male birds in general, voice calls in

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frogs and flashes in fireflies. Many of these traits are a liability from the standpoint of

survival. Any ostentatious trait or noisy, attention getting behavior will alert predators as well

as potential mates. How then could natural selection favor these traits?

Natural selection can be broken down into many components, of which survival is only one.

Sexual attractiveness is a very important component of selection, so much so that biologists

use the term sexual selection when they talk about this subset of natural selection.

Sexual selection is natural selection operating on factors that contribute to an organism's

mating success. Traits that are a liability to survival can evolve when the sexual attractiveness

of a trait outweighs the liability incurred for survival. A male who lives a short time, but

produces many offspring is much more successful than a long lived one that produces few.

The former's genes will eventually dominate the gene pool of his species. In many species,

especially polygynous species where only a few males monopolize all the females, sexual

selection has caused pronounced sexual dimorphism. In these species males compete against

other males for mates. The competition can be either direct or mediated by female choice. In

species where females choose, males compete by displaying striking phenotypic

characteristics and/or performing elaborate courtship behaviors. The females then mate with

the males that most interest them, usually the ones with the most outlandish displays. There

are many competing theories as to why females are attracted to these displays.

The good genes model states that the display indicates some component of male fitness. A

good genes advocate would say that bright coloring in male birds indicates a lack of parasites.

The females are cueing on some signal that is correlated with some other component of

viability.

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Selection for good genes can be seen in sticklebacks. In these fish, males have red coloration

on their sides. Milinski and Bakker showed that intensity of color was correlated to both

parasite load and sexual attractiveness. Females preferred redder males. The redness

indicated that he was carrying fewer parasites.

Evolution can get stuck in a positive feedback loop. Another model to explain secondary

sexual characteristics is called the runaway sexual selection model. R. A. Fisher proposed

that females may have an innate preference for some male trait before it appears in a

population. Females would then mate with male carriers when the trait appears. The offspring

of these matings have the genes for both the trait and the preference for the trait. As a result,

the process snowballs until natural selection brings it into check. Suppose that female birds

prefer males with longer than average tail feathers. Mutant males with longer than average

feathers will produce more offspring than the short feathered males. In the next generation,

average tail length will increase. As the generations progress, feather length will increase

because females do not prefer a specific length tail, but a longer than average tail. Eventually

tail length will increase to the point were the liability to survival is matched by the sexual

attractiveness of the trait and an equilibrium will be established. Note that in many exotic

birds male plumage is often very showy and many species do in fact have males with greatly

elongated feathers. In some cases these feathers are shed after the breeding season.

None of the above models are mutually exclusive. There are millions of sexually dimorphic

species on this planet and the forms of sexual selection probably vary amongst them.

3.1.5 Genetic Drift

Allele frequencies can change due to chance alone. This is called genetic drift. Drift is a

binomial sampling error of the gene pool. What this means is, the alleles that form the next

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generation's gene pool are a sample of the alleles from the current generation. When sampled

from a population, the frequency of alleles differs slightly due to chance alone.

Alleles can increase or decrease in frequency due to drift. The average expected change in

allele frequency is zero, since increasing or decreasing in frequency is equally probable. A

small percentage of alleles may continually change frequency in a single direction for several

generations just as flipping a fair coin may, on occasion, result in a string of heads or tails. A

very few new mutant alleles can drift to fixation in this manner.

In small populations, the variance in the rate of change of allele frequencies is greater than in

large populations. However, the overall rate of genetic drift (measured in substitutions per

generation) is independent of population size. If the mutation rate is constant, large and small

populations lose alleles to drift at the same rate. This is because large populations will have

more alleles in the gene pool, but they will lose them more slowly. Smaller populations will

have fewer alleles, but these will quickly cycle through. This assumes that mutation is

constantly adding new alleles to the gene pool and selection is not operating on any of these

alleles.

Sharp drops in population size can change allele frequencies substantially. When a population

crashes, the alleles in the surviving sample may not be representative of the precrash gene

pool. This change in the gene pool is called the founder effect, because small populations of

organisms that invade a new territory (founders) are subject to this. Many biologists feel the

genetic changes brought about by founder effects may contribute to isolated populations

developing reproductive isolation from their parent populations. In sufficiently small

populations, genetic drift can counteract selection. Mildly deleterious alleles may drift to

fixation.

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Wright and Fisher disagreed on the importance of drift. Fisher thought populations were

sufficiently large that drift could be neglected. Wright argued that populations were often

divided into smaller subpopulations. Drift could cause allele frequency differences between

subpopulations if gene flow was small enough. If a subpopulation was small enough, the

population could even drift through fitness valleys in the adaptive landscape. Then, the

subpopulation could climb a larger fitness hill. Gene flow out of this subpopulation could

contribute to the population as a whole adapting. This is Wright's Shifting Balance theory of

evolution.

Both natural selection and genetic drift decrease genetic variation. If they were the only

mechanisms of evolution, populations would eventually become homogeneous and further

evolution would be impossible.

3.2 Mechanisms that Increase Genetic Variation

Mutation is any change occurring in the message that a gene carries. Mutations mainly arise

as copy errors when DNA is replicated at mitosis and meiosis. Darwinian evolution requires

a constant supply of variation: much of it is supplied by mutation, and a mutation-selection

balance can maintain a genetic polymorphism. The first major geneticist to study mutation

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was H.J. Muller, who demonstrated it can be induced by X-rays. He also recognized that the

rate of mutation in nature is extremely low, and that they are almost always deleterious to the

fitness of the organism. The accumulation of deleterious mutations places a mutational load

on the population. Mutations can occur at single base level or at chromosomal level. The

effects of mutation can occasionally be very dramatic: some of these fruitflies have suffered

mutations which alter the number of wings that develop.

Mutations are changes in the DNA sequence of a cell's genome. When mutations occur, they

can either have no effect, alter the product of a gene, or prevent the gene from functioning.

Based on studies in the fly Drosophila melanogaster, it has been suggested that if a mutation

changes a protein produced by a gene, this will probably be harmful, with about 70% of these

mutations having damaging effects, and the remainder being either neutral or weakly

beneficial.

Mutations can involve large sections of a chromosome becoming duplicated (usually by

genetic recombination), which can introduce extra copies of a gene into a genome. Extra

copies of genes are a major source of the raw material needed for new genes to evolve. This

is important because most new genes evolve within gene families from pre-existing genes

that share common ancestors. For example, the human eye uses four genes to make structures

that sense light: three for colour vision and one for night vision; all four are descended from a

single ancestral gene.

New genes can be generated from an ancestral gene when a duplicate copy mutates and

acquires a new function. This process is easier once a gene has been duplicated because it

increases the redundancy of the system; one gene in the pair can acquire a new function while

the other copy continues to perform its original function. Other types of mutations can even

generate entirely new genes from previously noncoding DNA.

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The generation of new genes can also involve small parts of several genes being duplicated,

with these fragments then recombining to form new combinations with new functions. When

new genes are assembled from shuffling pre-existing parts, domains act as modules with

simple independent functions, which can be mixed together to produce new combinations

with new and complex functions. For example, polyketide synthases are large enzymes that

make antibiotics; they contain up to one hundred independent domains that each catalyze one

step in the overall process, like a step in an assembly line. Mutation limits the rate of

evolution. The rate of evolution can be expressed in terms of nucleotide substitutions in a

lineage per generation. Substitution is the replacement of an allele by another in a population.

This is a two step process: First a mutation occurs in an individual, creating a new allele. This

allele subsequently increases in frequency to fixation in the population. The rate of evolution

is k = 2Nvu (in diploids) where k is nucleotide substitutions, N is the effective population

size, v is the rate of mutation and u is the proportion of mutants that eventually fix in the

population.

Mutation need not be limiting over short time spans. The rate of evolution expressed above is

given as a steady state equation; it assumes the system is at equilibrium. Given the time

frames for a single mutant to fix, it is unclear if populations are ever at equilibrium. A change

in environment can cause previously neutral alleles to have selective values; in the short term

evolution can run on "stored" variation and thus is independent of mutation rate. Other

mechanisms can also contribute selectable variation. Recombination creates new

combinations of alleles (or new alleles) by joining sequences with separate microevolutionary

histories within a population. Gene flow can also supply the gene pool with variants. Of

course, the ultimate source of these variants is mutation.

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3.2.1 The Fate of Mutant Alleles

Mutation creates new alleles. Each new allele enters the gene pool as a single copy amongst

many. Most are lost from the gene pool, the organism carrying them fails to reproduce, or

reproduces but does not pass on that particular allele. A mutant's fate is shared with the

genetic background it appears in. A new allele will initially be linked to other loci in its

genetic background, even loci on other chromosomes. If the allele increases in frequency in

the population, initially it will be paired with other alleles at that locus -- the new allele will

primarily be carried in individuals heterozygous for that locus. The chance of it being paired

with itself is low until it reaches intermediate frequency. If the allele is recessive, its effect

won't be seen in any individual until a homozygote is formed. The eventual fate of the allele

depends on whether it is neutral, deleterious or beneficial.

3.2.2 Neutral alleles

Most neutral alleles are lost soon after they appear. The average time (in generations) until

loss of a neutral allele is 2(Ne/N) ln(2N) where N is the effective population size (the number

of individuals contributing to the next generation's gene pool) and N is the total population

size. Only a small percentage of alleles fix. Fixation is the process of an allele increasing to a

frequency at or near one. The probability of a neutral allele fixing in a population is equal to

its frequency. For a new mutant in a diploid population, this frequency is 1/2N.

If mutations are neutral with respect to fitness, the rate of substitution (k) is equal to the rate

of mutation(v). This does not mean every new mutant eventually reaches fixation. Alleles are

added to the gene pool by mutation at the same rate they are lost to drift. For neutral alleles

that do fix, it takes an average of 4N generations to do so. However, at equilibrium there are

multiple alleles segregating in the population. In small populations, few mutations appear

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each generation. The ones that fix do so quickly relative to large populations. In large

populations, more mutants appear over the generations. But, the ones that fix take much

longer to do so. Thus, the rate of neutral evolution (in substitutions per generation) is

independent of population size.

The rate of mutation determines the level of heterozygosity at a locus according to the neutral

theory. Heterozygosity is simply the proportion of the population that is heterozygous.

Equilibrium heterozygosity is given as H = 4Nv/[4Nv+1] (for diploid populations). H can

vary from a very small number to almost one. In small populations, H is small (because the

equation is approximately a very small number divided by one). In (biologically

unrealistically) large populations, heterozygosity approaches one (because the equation is

approximately a large number divided by itself). Directly testing this model is difficult

because N and v can only be estimated for most natural populations. But, heterozygosities are

believed to be too low to be described by a strictly neutral model. Solutions offered by

neutralists for this discrepancy include hypothesizing that natural populations may not be at

equilibrium.

At equilibrium there should be a few alleles at intermediate frequency and many at very low

frequencies. This is the Ewens- Watterson distribution. New alleles enter a population every

generation, most remain at low frequency until they are lost. A few drift to intermediate

frequencies, a very few drift all the way to fixation. In Drosophila pseudoobscura, the protein

Xanthine dehydrogenase (Xdh) has many variants. In a single population, Keith, et. al., found

that 59 of 96 proteins were of one type, two others were represented ten and nine times and

nine other types were present singly or in low numbers.

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3.2.3 Deleterious alleles

Deleterious mutants are selected against but remain at low frequency in the gene pool. In

diploids, a deleterious recessive mutant may increase in frequency due to drift. Selection

cannot see it when it is masked by a dominant allele. Many disease causing alleles remain at

low frequency for this reason. People who are carriers do not suffer the negative effect of the

allele. Unless they mate with another carrier, the allele may simply continue to be passed on.

Deleterious alleles also remain in populations at a low frequency due to a balance between

recurrent mutation and selection. This is called the mutation load.

3.2.4 Beneficial alleles

Most new mutants are lost, even beneficial ones. Wright calculated that the probability of

fixation of a beneficial allele is 2s. (This assumes a large population size, a small fitness

benefit, and that heterozygotes have an intermediate fitness. A benefit of 2s yields an overall

rate of evolution: k=4Nvs where v is the mutation rate to beneficial alleles) An allele that

conferred a one percent increase in fitness only has a two percent chance of fixing. The

probability of fixation of beneficial type of mutant is boosted by recurrent mutation. The

beneficial mutant may be lost several times, but eventually it will arise and stick in a

population. (Recall that even deleterious mutants recur in a population.)

Directional selection depletes genetic variation at the selected locus as the fitter allele sweeps

to fixation. Sequences linked to the selected allele also increase in frequency due to

hitchhiking. The lower the rate of recombination, the larger the window of sequence that

hitchhikes. Begun and Aquadro compared the level of nucleotide polymorphism within and

between species with the rate of recombination at a locus. Low levels of nucleotide

polymorphism within species coincided with low rates of recombination. This could be

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explained by molecular mechanisms if recombination itself was mutagenic. In this case,

recombination with also be correlated with nucleotide divergence between species. But, the

level of sequence divergence did not correlate with the rate of recombination. Thus, they

inferred that selection was the cause. The correlation between recombination and nucleotide

polymorphism leaves the conclusion that selective sweeps occur often enough to leave an

imprint on the level of genetic variation in natural populations.

One example of a beneficial mutation comes from the mosquito Culex pipiens. In this

organism, a gene that was involved with breaking down organophosphates - common

insecticide ingredients -became duplicated. Progeny of the organism with this mutation

quickly swept across the worldwide mosquito population. There are numerous examples of

insects developing resistance to chemicals, especially DDT which was once heavily used in

this country. And, most importantly, even though "good" mutations happen much less

frequently than "bad" ones, organisms with "good" mutations thrive while organisms with

"bad" ones die out.

If beneficial mutants arise infrequently, the only fitness differences in a population will be

due to new deleterious mutants and the deleterious recessives. Selection will simply be

weeding out unfit variants. Only occasionally will a beneficial allele be sweeping through a

population. The general lack of large fitness differences segregating in natural populations

argues that beneficial mutants do indeed arise infrequently. However, the impact of a

beneficial mutant on the level of variation at a locus can be large and lasting. It takes many

generations for a locus to regain appreciable levels of heterozygosity following a selective

sweep.

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3.2.5 Recombination

Each chromosome in our sperm or egg cells is a mixture of genes from our mother and our

father. Recombination can be thought of as gene shuffling. Most organisms have linear

chromosomes and their genes lie at specific location (loci) along them. Bacteria have circular

chromosomes. In most sexually reproducing organisms, there are two of each chromosome

type in every cell. For instance in humans, every chromosome is paired, one inherited from

the mother, the other inherited from the father. When an organism produces gametes, the

gametes end up with only one of each chromosome per cell. Haploid gametes are produced

from diploid cells by a process called meiosis.

In meiosis, homologous chromosomes line up. The DNA of the chromosome is broken on

both chromosomes in several places and rejoined with the other strand. Later, the two

homologous chromosomes are split into two separate cells that divide and become gametes.

But, because of recombination, both of the chromosomes are a mix of alleles from the mother

and father.

Recombination creates new combinations of alleles. Alleles that arose at different times and

different places can be brought together. Recombination can occur not only between genes,

but within genes as well. Recombination within a gene can form a new allele. Recombination

is a mechanism of evolution because it adds new alleles and combinations of alleles to the

gene pool.

3.2.6 Gene Flow

New organisms may enter a population by migration from another population. If they mate

within the population, they can bring new alleles to the local gene pool. This is called gene

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flow. In some closely related species, fertile hybrids can result from interspecific matings.

These hybrids can vector genes from species to species.

Gene flow between more distantly related species occurs infrequently. This is called

horizontal transfer. One interesting case of this involves genetic elements called P elements.

Margaret Kidwell found that P elements were transferred from some species in the

Drosophila willistoni group to Drosophila melanogaster. These two species of fruit flies are

distantly related and hybrids do not form. Their ranges do, however, overlap. The P elements

were vectored into D. melanogaster via a parasitic mite that targets both these species. This

mite punctures the exoskeleton of the flies and feeds on the "juices". Material, including

DNA, from one fly can be transferred to another when the mite feeds. Since P elements

actively move in the genome (they are themselves parasites of DNA), one incorporated itself

into the genome of a melanogaster fly and subsequently spread through the species.

Laboratory stocks of melanogaster caught prior to the 1940's lack of P elements. All natural

populations today harbor them.

4.0 Conclusion

In this unit the student learnt the following:

• Genetic variation

• Mechanisms that decrease genetic variation

• Natural selection

• Conditions for natural selection

• Sexual selection

• Genetic drift

• Mechanisms that increase genetic variation

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 • Mutation

• Alleles

• Recombination

• Gene flow

5.0 Summary

Evolution is a change in the gene pool of a population over time; it can occur due to several

factors. Three mechanisms add new alleles to the gene pool: mutation, recombination and

gene flow. Two mechanisms remove alleles, genetic drift and natural selection. Drift removes

alleles randomly from the gene pool. Selection removes deleterious alleles from the gene

pool. The amount of genetic variation found in a population is the balance between the

actions of these mechanisms.

Natural selection can also increase the frequency of an allele. Selection that weeds out

harmful alleles is called negative selection. Selection that increases the frequency of helpful

alleles is called positive, or sometimes positive Darwinian, selection. A new allele can also

drift to high frequency. But, since the change in frequency of an allele each generation is

random, nobody speaks of positive or negative drift.

Except in rare cases of high gene flow, new alleles enter the gene pool as a single copy. Most

new alleles added to the gene pool are lost almost immediately due to drift or selection; only

a small percent ever reach a high frequency in the population. Even most moderately

beneficial alleles are lost due to drift when they appear. But, a mutation can reappear

numerous times.

The fate of any new allele depends a great deal on the organism it appears in. This allele will

be linked to the other alleles near it for many generations. A mutant allele can increase in

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frequency simply because it is linked to a beneficial allele at a nearby locus. This can occur

even if the mutant allele is deleterious, although it must not be so deleterious as to offset the

benefit of the other allele. Likewise a potentially beneficial new allele can be eliminated from

the gene pool because it was linked to deleterious alleles when it first arose. An allele "riding

on the coat tails" of a beneficial allele is called a hitchhiker. Eventually, recombination will

bring the two loci to linkage equilibrium. But, the more closely linked two alleles are, the

longer the hitchhiking will last.

The effects of selection and drift are coupled. Drift is intensified as selection pressures

increase. This is because increased selection (i.e. a greater difference in reproductive success

among organisms in a population) reduces the effective population size, the number of

individuals contributing alleles to the next generation.

6.0 Tutor-Marked Assignment

• What is genetic variation?

• What are the mechanisms that affect genetic variation?

7.0 Reference/Further Reading

Eldredge, Niles. (1989). Macroevolutionary Dynamics. New York: McGraw-Hill.

Cowen, Richard. (2004). History of Life. Boston: Blackwell Scientific.

Dawkins, Richard. (1987). The Blind Watchmaker. New York: W.W. Norton.

Kitcher, Philip. (1982). Abusing Science. Cambridge, Mass.: MIT Press.

Wilson, Edward O. (1992). The Diversity of Life. Cambridge, Mass.: Harvard Belknap.

Darwin, Charles. (1859). On the Origin of Species.

Darwin, Charles. (1871). The Descent of Man.

Haldane, J.B.S. (1932). The Causes of Evolution. Princeton, N.J.: Princeton Univ. Press

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(reprinted 1990).

Simpson, George G. (1944). Tempo and Mode in Evolution. New York: Columbia Univ.
Press.

Mayr, Ernst E. (1982). The Growth of Biological Thought. Cambridge, Mass: Harvard
Belknap.

Provine, William B. (2001). The Origins of Theoretical Population Genetics. Chicago: Univ.
of

Chicago Press.

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UNIT 3: RESHUFFLING OF GENES

1.0 Introduction

Genetic recombination is a process by which a molecule of nucleic acid (usually DNA, but

can also be RNA) is broken and then joined to a different one. Recombination can occur

between similar molecules of DNA, as in homologous recombination, or dissimilar

molecules, as in non-homologous end joining. Recombination is a common method of DNA

repair in both bacteria and eukaryotes.

2.0 Objectives

At the end of this unit, students should learn the following

• Genetic recombination

• Chromosomal crossover

• Sexual reproduction

3.0 Genetic Recombination

The shuffling of genes brought about by genetic recombination is thought to have many

advantages, as it is a major engine of genetic variation and also allows sexually reproducing

organisms to avoid Muller's ratchet, in which the genomes of an asexual population

accumulate deleterious mutations in an irreversible manner.

In genetic engineering, recombination can also refer to artificial and deliberate recombination

of disparate pieces of DNA, often from different organisms, creating what is called

recombinant DNA. A prime example of such a use of genetic recombination is gene

targeting, which can be used to add, delete or otherwise change an organism's genes. This

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technique is important to biomedical researchers as it allows them to study the effects of

specific genes. Techniques based on genetic recombination are also applied in protein

engineering to develop new proteins of biological interest.

Genetic recombination is catalyzed by many different enzymes, called recombinases. RecA,

the chief recombinase found in Escherichia coli, is responsible for the repair of DNA double

strand breaks (DSBs). In yeast and other eukaryotic organisms there are two recombinases

required for repairing DSBs. The RAD51 protein is required for mitotic and meiotic

recombination, whereas the DMC1 protein is specific to meiotic recombination.

3.1 Chromosomal Crossover

Chromosomal crossover refers to recombination between the paired chromosomes inherited

from each of one's parents, generally occurring during meiosis. During prophase I the four

available chromatids are in tight formation with one another. While in this formation,

homologous sites on two chromatids can mesh with one another, and may exchange genetic

information.

Because recombination can occur with small probability at any location along chromosome,

the frequency of recombination between two locations depends on their distance. Therefore,

for genes sufficiently distant on the same chromosome the amount of crossover is high

enough to destroy the correlation between alleles.

Tracking the movement of genes during crossovers has proven quite useful to geneticists.

Because two genes that are close together are less likely to become separated than genes that

are farther apart, geneticists can deduce roughly how far apart two genes are on a

chromosome if they know the frequency of the crossovers. Geneticists can also use this

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method to infer the presence of certain genes. Genes that typically stay together during

recombination are said to be linked. One gene in a linked pair can sometimes be used as a

marker to deduce the presence of another gene. This is typically used in order to detect the

presence of a disease-causing gene.

3.2 Sexual Reproduction

In asexual organisms, genes are inherited together, or linked, as they cannot mix with genes

of other organisms during reproduction. In contrast, the offspring of sexual organisms contain

random mixtures of their parents' chromosomes that are produced through independent

assortment. In a related process called homologous recombination, sexual organisms

exchange DNA between two matching chromosomes. Recombination and reassortment do

not alter allele frequencies, but instead change which alleles are associated with each other,

producing offspring with new combinations of alleles. Sex usually increases genetic variation

and may increase the rate of evolution.

Sexual reproduction is the creation of a new organism by combining the genetic material of

two organisms. There are two main processes during sexual reproduction; they are: meiosis,

involving the halving of the number of chromosomes; and fertilization, involving the fusion

of two gametes and the restoration of the original number of chromosomes. During meiosis,

the chromosomes of each pair usually cross over to achieve homologous recombination.

The evolution of sexual reproduction is a major puzzle. The first fossilized evidence of

sexually reproducing organisms is from eukaryotes of the Stenian period, about 1 to 1.2

billion years ago. Sexual reproduction is the primary method of reproduction for the vast

majority of macroscopic organisms, including almost all animals and plants. Bacterial

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conjugation, the transfer of DNA between two bacteria, is often mistakenly confused with

sexual reproduction, because the mechanics are similar.

Evolutionary thought proposes several explanations for why sexual reproduction developed

out of former asexual reproduction. It may be due to selection pressure on the clade itself—

the ability for a population to radiate more rapidly in response to a changing environment

through sexual recombination than parthenogenesis allows. Also, sexual reproduction allows

for the "ratcheting" of evolutionary speed as one clade competes with another for a limited

resource

3.3 Plants

Animals typically produce male gametes called sperm, and emale gametes called eggs and

ova, following immediately after meiosis, with the gametes produced directly by meiosis.

Plants on the other hand have mitosis occurring in spores, which are produced by meiosis.

The spores germinate into the gametophyte phase. The gametophytes of different groups of

plants vary in size; angiosperms have as few as three cells in pollen, and mosses and other so

called primitive plants may have several million cells. Plants have an alternation of

generations where the sporophyte phase is succeeded by the gametophyte phase. The

sporophyte phase produces spores within the sporangium by meiosis.

Flowering plants are the dominant plant form on land and they reproduce by sexual and

asexual means. Often their most distinguishing feature is their reproductive organs,

commonly called flowers. The anther produces male gametophytes, the sperm is produced in

pollen grains, which attach to the stigma on top of a carpel, in which the female

gametophytes (inside ovules) are located. After the pollen tube grows through the carpel's

style, the sex cell nuclei from the pollen grain migrate into the ovule to fertilize the egg cell

and endosperm nuclei within the female gametophyte in a process termed double fertilization.

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The resulting zygote develops into an embryo, while the triploid endosperm (one sperm cell

plus two female cells) and female tissues of the ovule give rise to the surrounding tissues in

the developing seed. The ovary, which produced the female gametophyte(s), then grows into

a fruit, which surrounds the seed(s). Plants may either self-pollinate or cross-pollinate.

Nonflowering plants like ferns, moss and liverworts use other means of sexual reproduction.

Bryophytes, which include liverworts, hornworts and mosses, reproduce both sexually and

vegetatively. They are small plants found growing in moist locations and like ferns, have

motile sperm with flagella and need water to facilitate sexual reproduction. These plants start

as a haploid spore that grows into the dominate form, which is a multicellular haploid body

with leaf-like structures that photosynthesize. Haploid gametes are produced in antherida and

archegonia by mitosis. The sperm released from the antherida respond to chemicals released

by ripe archegonia and swim to them in a film of water and fertilize the egg cells thus

producing a zygote. The zygote divides by mitotic division and grows into a sporophyte that

is diploid. The multicellular diploid sporophyte produces structures called spore capsules,

which are connected by seta to the archegonia. The spore capsules produce spores by meiosis,

when ripe the capsules burst open and the spores are released. Bryophytes show considerable

variation in their breeding structures and the above is a basic outline. Also in some species

each plant is one sex while other species produce both sexes on the same plant.

3.4 Insects

Insect species make up more than two-thirds of all extant animal species, and most insect

species use sex for reproduction, though some species are facultatively parthenogenetic.

Many species have sexual dimorphism, while in others the sexes look nearly identical.

Typically they have two sexes with males producing spermatozoa and females ova. The ova

develop into eggs that have a covering called the chorion, which forms before internal

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fertilization. Insects have very diverse mating and reproductive strategies most often resulting

in the male depositing spermatophore within the female, which stores the sperm until she is

ready for egg fertilization. After fertilization, and the formation of a zygote, and varying

degrees of development; the eggs are deposited outside the female in many species, or in

some, they develop further within the female and live born offspring are produced.

3.5 Mammals

There are three extant kinds of mammals: Monotremes, Placentals and Marsupials, all with

internal fertilization. In placental mammals, offspring are born as juveniles: complete animals

with the sex organs present although not reproductively functional. After several months or

years, the sex organs develop further to maturity and the animal becomes sexually mature.

Most female mammals are only fertile during certain periods during their estrous cycle, at

which point they are ready to mate. Individual male and female mammals meet and carry out

copulation. For most mammals, males and females exchange sexual partners throughout their

adult lives.

Male

The male reproductive system contains two main divisions: the penis, and the testicles, the

latter of which is where sperm are produced. In humans, both of these organs are outside the

abdominal cavity, but they can be primarily housed within the abdomen in other animals (for

instance, in dogs, the penis is internal except when mating). Having the testicles outside the

abdomen best facilitates temperature regulation of the sperm, which require specific

temperatures to survive. Sperm are the smaller of the two gametes and are generally very

short-lived, requiring males to produce them continuously from the time of sexual maturity

until death. Prior to ejaculation the produced sperm are stored in the epididymis. The sperm

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cells are motile and they swim using tail-like flagella to propel themselves towards the ovum.

The sperm follows temperature gradients (thermotaxis) and chemical gradients (chemotaxis)

to locate the ovum.

Female

The female reproductive system likewise contains two main divisions: the vagina and uterus,

which act as the receptacle for the sperm, and the ovaries, which produce the female's ova.

All of these parts are always internal. The vagina is attached to the uterus through the cervix,

while the uterus is attached to the ovaries via the Fallopian tubes. At certain intervals, the

ovaries release an ovum, which passes through the fallopian tube into the uterus.

If, in this transit, it meets with sperm, the egg selects sperm with which to merge; this is

termed fertilization. The fertilization usually occurs in the oviducts, but can happen in the

uterus itself. The zygote then implants itself in the wall of the uterus, where it begins the

processes of embryogenesis and morphogenesis. When developed enough to survive outside

the womb, the cervix dilates and contractions of the uterus propel the fetus through the birth

canal, which is the vagina.

The ova, which are the female sex cells, are much larger than the sperm and are normally

formed within the ovaries of the fetus before its birth. They are mostly fixed in location

within the ovary until their transit to the uterus, and contain nutrients for the later zygote and

embryo. Over a regular interval, in response to hormonal signals, a process of oogenesis

matures one ovum which is released and sent down the Fallopian tube. If not fertilized, this

egg is released through menstruation in humans and other great apes, and reabsorbed in other

mammals in the estrus cycle.

4.0 Conclusion

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In this unit, students have learnt the following:

• Genetic recombination

• Chromosomal crossover

• Sexual reproduction

5.0 Summary

The process of recombination takes place when germ cells are produced, when large segments of

DNA are exchanged between each pair of chromosomes. This kind of genetic shuffling means that

any chromosome inherited is in fact a mosaic of chromosomes she inherited or transferred. This

reshuffling increases the possible number of combinations of genetic variants, which in turn ensures

greater variability of characteristics among individuals.

6.0 Tutor-Marked Assignment

• What is genetic recombination?

• What processes determine gene reshuffling?

• What are the possible outcomes of gene reshuffling?

7.0 Refernce/ Further reading

Radding C (1982). "Homologous pairing and strand exchange in genetic recombination".

Annu. Rev. Genet. 16 (1): 405–37. doi:10.1146/annurev.ge.16.120182.002201.

PMID 6297377.

Agrawal AF (2006). "Evolution of sex: why do organisms shuffle their genotypes?". Curr.

Biol. 16 (17): R696. doi:10.1016/j.cub.2006.07.063. PMID 16950096.

Peters AD, Otto SP (2003). "Liberating genetic variance through sex". Bioessays 25 (6):

533–7. doi:10.1002/bies.10291. PMID 12766942.

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Goddard MR, Godfray HC, Burt A (2005). "Sex increases the efficacy of natural selection in

experimental yeast populations". Nature 434 (7033): 636–40. Bibcode 2005Natur.434..636G.

doi:10.1038/nature03405. PMID 15800622.

N.J. Buttefield (2000). "Bangiomorpha pubescens n. gen., n. sp.: implications for the

evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of

eukaryotes". Paleobiology 26 (3): 386–404. doi:10.1666/0094-

8373(2000)026<0386:BPNGNS>2.0.CO;2.

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UNIT 4: POLYPLOIDY

1.0 Introduction

2.0 Objective

3.0 Types of Polyploidy

3.1 Polyploidy in animals and plants

3.2 Polyploidy in plants

3.3 Origin of polyploidy

3.4 Polyploidy in animals

3.5 Polyploidy in man

4.0 Conclusion

5.0 Summary.

6.0 Tutor-Marked Assignment.

7.0 Reference/Further Readings

Unit 3 Polyploidy

1.0 Introduction

Polyploidy is a term used to describe cells and organisms containing more than two paired

(homologous) sets of chromosomes. Most eukaryotic species are diploid, meaning they have

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two sets of chromosomes — one set inherited from each parent. However polyploidy is found

in some organisms and is especially common in plants. In addition, polyploidy also occurs in

some tissues of animals who are otherwise diploid, such as human muscle tissues. This is

known as endopolyploidy. (Monoploid organisms also occur; a monoploid has only one set of

chromosomes. These include the vast majority of prokaryotes.)

Polyploidy refers to a numerical change in a whole set of chromosomes. Organisms in which

a particular chromosome, or chromosome segment, is under- or overrepresented are said to be

aneuploid (from the Greek words meaning "not," "good," and "fold"). Therefore the

distinction between aneuploidy and polyploidy is that aneuploidy refers to a numerical

change in part of the chromosome set, whereas polyploidy refers to a numerical change in the

whole set of chromosomes

2.0 Objective

At the end of this unit, students should be able to explain the following:

• Polyploidy

• Importance of Polyploidy

• Polyploidy in animals and plants

3.0 Types of polyploidy

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This image shows haploid (single), diploid (double), triploid (triple), and tetraploid
(quadruple) sets of chromosomes. Triploid and tetraploid chromosomes are examples of
polyploidy.

Two main modes of origin of the polyploid condition are recognized somatic doubling in

mitosis, and nonreduction in meiosis (Heilborn, 1934; Grant, 1971). The mechanism of

somatic doubling is exemplified by polyploid Primula kewensis, and nonreduction was the

mode of origin seen in polyploid Rhaphobrassica. It used to be thought most that polyploids

formed by hybridization followed by chromosome doubling.

doubling. However, Harlan and deWet

(1975) argued that unreduced gametes played an important role. While agronomy researchers

took notice of this (e.g. Peloquin, 19XX), textbooks did not change. Recently, a lot of

theoretical modeling (Rodriguez, 1996; Ramsey and

and Schemske, 1998, 2002) and fieldwork

(Husband 1999, 2000) has contributed to the view that unreduced gametes and triploid

bridges are a major source of polyploid formation. This is also a mechanism for how diploid

and polyploid genomes can interact (thus,

(thus, the new polyploid species are not strictly sealed off

from its diploid progenitors).

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During meiosis, homologous chromosomes pair and undergo crossing over resulting in the

exchange of parts of their chromosomes. In diploid hybrids derived from crosses of two

species, chromosomes from the two species may differ or one of the chromosomes may be

absent. This can cause irregularities during meiosis and may result in cell cycle arrest and

subsequent embryo abortion. However, if the chromosome number is doubled in the hybrid,

allotetraploids are formed, which have four sets of chromosomes. This can occur by crossing

autotetraploids of the two species, or more likely in nature, by the fussion of unreduced

gametes. Allotetraploids generally will have pairing and crossing over only within the two

chromosomes of each original parent (the homologous chromosomes AA) and only rarely

between chromosomes from the two original parents (the homeologous chromosomes AA’).

This meiotic behavior assures proper pairing of the chromosomes and the correct assortment

into gametes

Polyploid types are labeled according to the number of chromosome sets in the nucleus:

• triploid (three sets; 3x), for example seedless watermelons, common in the phylum

Tardigrada

• tetraploid (four sets; 4x), for example Salmonidae fish

• pentaploid (five sets; 5x), for example Kenai Birch (Betula papyrifera var. kenaica)

• hexaploid (six sets; 6x), for example wheat, kiwifruit

• octaploid (eight sets; 8x), for example Acipenser (genus of sturgeon fish), dahlias

• decaploid (ten sets; 10x), for example certain strawberries

• dodecaploid (twelve sets; 12x), for example the plant Celosia argentea and the

amphibian Xenopus ruwenzoriensis

• To recognize polyploids, biologists have traditionally counted chromosomes and

guess if taxa were diploid or polyploid with rules of thumb. For example, anything

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with over a certain number of chromosomes, especially if it were multiple of the

number, was assumed to be polyploid (refs/examples). Often, an increase in organ

size (e.g., stomates) was used as a substitute measure for comparing genome size

(Masterson, 1994). Today, biologists use genomic tools (molecular cytogenetics,

genetic maps) to observe a continuum of diploids and polyploids in various states of

genome evolution. Many species, such as Arabidopsis, Zea mays, and yeast (TAGI,

2000; Blanc et al., 2003; Langkjaer et al., 2003) are believed to have undergone a

doubling of their genome in the past but now behave as diploids (Wendel, 2000), .

These ancient polyploids (paleopolyploids) have undergone a multitude of genomic

changes, such as deletions of large fragments of chromosomes, silencing of duplicate

genes, and recombining of homoeologous chromosome segments (Wolfe, 2001; Levy

and Feldman, 2002) some of which may lead the organism to a more diploid-like

state. In some polyploids, chromosomal reorganization is so extensive that the

genome is no longer structured as an allopolyploid. Paradoxically, the more extensive

this process of diploidization, the more difficult it is to discern. For example,

“diploid” Brassica can be considered ancient polyploids when compared to

Arabidopsis, and Arabidopsis itself shows ancient duplications. Since plant genomes

show cycles of polyploidization and diploidization, it can be difficult to determine

whether gene duplication arose by polyploidy or some other mechanism.

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According to Grant (1971, 1981), the phenomena of polyploidy was discovered during the

exploratory phase of plant cytogenetics in the early years of the twentieth century. Winkler

(1916) introduced the term polyploidy, and Winge (1917) proposed that polyploidy occurred

by somatic doubling in species hybrids. Early polyploid studies included those in in Nicotiana

(Clausen and Goodspeed 1925), Raphanus-Brassica (Karpechenko 1927) and Galeopsis

(Muntzing 1930, 1932). The distinctions between autopolyploidy and allopolyploidy were

made by Kihara and Ono (1926) and later elaborated on by Clausen, Keck, and Hiesey (1945)

and Stebbins (1950,1971). Stebbins also proposed the category of segmental allopolyploids ,

which are essentially intermediate forms between auto- and allo- polyploids (Stebbins 1950).

Harlan and deWet (1975) suggested that most polyploids arose through the production of

unreduced gametes as oppossed to somatic doubling. Ramsey and Schemske (2002) review

the controversies surrounding the confusion over whether to classify polyploids by mode of

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origin criteria or by cytological criteria (Ramsey and Schemske, 2002). Using cytological

criteria, allopolyploids display mostly bivalent chromosome pairing (aggregates containing

two chromosomes) while autopolyploids can have higher frequencies of multivalent

chromosome configurations. Here we follow Ramsey and Schemske (2002) and adopt mode

of origin criteria: if the chromosomes of one genome within an organism or species are

simply duplicated, the resulting polyploid is an autopolyploid. However, if genome

duplication occurs during a cross of two different species, the resulting organism is referred

to as an allopolyploid.

Polyploids can acquire variation both through mechanisms of population genetics (gene flow

with diploids and multiple origins of polyploids), and through mechanisms that generate “de

novo variation” such as chromosomal rearrangements and epigenetic phenomena.

Polyploidy has long been considered an important example of instant or sympatric speciation,

since polyploid species are mostly reproductively isolated from their diploid progenitors

(Stebbins 1950, 1971; Levin 1983). An interesting aspect related to allopolyploidization or

hybridization of different species is the question of the “species barrier” when using a

biological species concept. Members of the same biological species are commonly defined as

related individuals of a population that can interbreed and whose offspring are fertile. Thus,

the horse and a donkey are considered separate species because their hybrid offspring are

viable but infertile. In plants, hybridization of different species is quite common and many of

the well-known crop plants are allopolyploids resulting from inter-species hybrids. Such

allopolyploids pose a challenge to phylogenetic species concepts, which define species on

strict monophyletic criteria. Over the last decade this challenge has taken on additional

relevance as “polyploid species” have been found to form repeatedly in close proximity to

one another (Soltis and Soltis, 1993; 1999; 2000). The polyphyly of “polyploid species” calls

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into question the very definition of “species.” Allopolyploids – like other organisms with

reticulate evolutionary histories (e.g., eukaryotes, lichens) – give biologists important

examples when theorizing about evolutionary entities. Aside from philosophical

considerations about species definitions, there are many implications for the multiplicity of

origins for polyploids. Multiple origins of polyploid species have been reported for mosses,

ferns, and many angiosperms (reviewed in Vogel et al., 1999; Soltis and Soltis, 2000).

Allopolyploidy presents a paradox because it is both a diversifying force and a genetic

bottleneck (Stebbins, 1971). However, the genetic bottleneck problem may be solved by the

fact that population-level genetic studies of polyploid plants and animals indicate that

polyploidy is not a rare event leading to unique and uniform genotypes. Rather, the multiple

independent formations of polyploid species from heterozygous diploid progenitors may

provide a significant source of genetic variation (reviewed in Soltis and Soltis, 1993; 1999;

2000).

Many new polyploids also are genetically unstable, and the next section describes

mechanisms that can lead to novel variation.

3.1 Polyploidy in animals and plants

Polyploidy occurs in some animals, such as goldfish, salmon, and salamanders. However,

polyploidy is especially common among ferns and flowering plants, including both wild and

cultivated species. Wheat, for example, after millennia of hybridization and modification by

humans, has strains that are diploid (two sets of chromosomes); tetraploid (four sets of

chromosomes), with the common name of durum or macaroni wheat; and hexaploid (six sets

of chromosomes), with the common name of bread wheat.

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Many agriculturally important plants of the genus Brassica are also tetraploids. This genus,

known as cabbages or mustards, includes turnips, brussels sprouts, cabbage,

cabbage cauliflower,

broccoli,, mustard seed and other important crops. The Triangle of U is a theory, developed by

a Woo Jang-choon,
choon, a Korean botanist who was working in Japan, that says the genomes of

three ancestral species of Brassica combined to create the three common tetraploid species

Brassica juncea (Indian mustard), Brassica napus (Rapeseed, rutabaga), and Brassica

carinata (Ethiopian mustard).

Speciation via polyploidy: A diploid cell undergoes failed meiosis,, producing diploid

gametes, which self-fertilize

fertilize to produce a tetraploid
tet zygote.

Examples in animals are more common in the lower forms such as flatworms,
flatworms leeches, and

brine shrimp.. Polyploid animals are often sterile, so they often reproduce by parthenogenesis,

a form of asexual reproduction.

reproduction Polyploid salamanders and lizards are also quite common and

parthenogenetic. While mammalian liver cells are polyploid, rare instances of polyploid

mammals are known, but most often result in prenatal death.

The only known exception to this rule is an octodontid rodent of Argentina's

Argentina harsh desert

regions, known as the Red Viscacha-Rat

Viscacha (Tympanoctomys barrerae),, discovered by Milton

Gallardo Narcisi.. This rodent is not a rat, but kin to guinea pigs and chinchillas.
chinchillas Its "new"

diploid [2n] number is 102 and so its cells are roughly twice normal size. Its closest living

relation is Octomys mimax,, the Andean Viscacha-Rat

Rat of the same family, whose 2n=56. It is

surmised that an Octomys-like

like ancestor produced tetraploid (i.e., 4n=112) offspring that were,

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by virtue of their doubled chromosomes, reproductively isolated from their parents; but that

these likely survived the ordinarily catastrophic effects of polyploidy in mammals by

shedding (via chromosomal translocation or some similar mechanism) the "extra" set of sex

chromosomes gained at this doubling.

Polyploidy can be induced in cell culture by some chemicals: the best known is colchicine,

which can result in chromosome doubling, though its use may have other less obvious

consequences as well.

3.2 Polyploidy in Plants

Polyploidy is very common in plants, especially in angiosperms. From 30% to 70% of today's

angiosperms are thought to be polyploid. Species of coffee plant with 22, 44, 66, and 88

chromosomes are known. This suggests that the ancestral condition was a plant with a

haploid (n) number of 11 and a diploid (2n) number of 22, from which evolved the different

polyploid descendants.

In fact, the chromosome content of most plant groups suggests that the basic angiosperm

genome consists of the genes on 7–11 chromosomes. Domestic wheat, with its 42

chromosomes, is probably hexaploid (6n), where n (the ancestral haploid number) was 7.

Some other examples:

Plant Probable ancestral Chromosome Ploidy level

haploid number number
Domestic oat 7 42 6n
Peanut 10 40 4n
Sugar cane 10 80 8n
Banana 11 22,33 2n, 3n
White potato 12 48 4n
Tobacco 12 48 4n
Cotton 13 52 4n
Apple 17 34,51 2n, 3n

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Polyploid plants not only have larger cells but the plants themselves are often larger. This has

led to the deliberate creation of polyploid varieties of such plants as watermelons, marigolds,

and snapdragons.

3.3 Origin of Polyploidy

Polyploidy has occurred often in the evolution of plants.

The process can begin if diploid (2n) gametes are formed. These can arise in at least two

ways.

• The gametes may be formed by mitosis instead of meiosis.

• Plants, in contrast to animals, form germ cells (sperm and eggs) from somatic tissues.

If the chromosome content of a precursor somatic cell has accidentally doubled (e.g.,

as a result of passing through S phase of the cell cycle without following up with

mitosis and cytokinesis), then gametes containing 2n chromosomes are formed

Polyploidy also occurs naturally in certain plant tissues.

• As the endosperm (3n) develops in corn (maize) kernels (Zea mays), its cells undergo

successive rounds (as many as 5) of endoreplication producing nuclei that range as

high as 96n.

• When rhizobia infect the roots of their legume host, they induce the infected cells to

undergo endoreplication producing cells that can become 128n

Polyploidy can also be induced in the plant-breeding laboratory by treating dividing cells

with colchicine. This drug disrupts microtubules and thus prevents the formation of a spindle.

Consequently, the duplicated chromosomes fail to separate in mitosis. Onion cells exposed to

colchicine for several days may have over 1000 chromosomes inside.

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When a newly-arisen tetraploid (4n) plant tries to breed with its ancestral species (a

backcross), triploid offspring are formed. These are sterile because they cannot form gametes

with a balanced assortment of chromosomes.

However, the tetraploid plants can breed with each other. So in one generation, a new species

has been formed.

Polyploidy even allows the formation of new species derived from different ancestors.

In 1928, the Russian plant geneticist Karpechenko produced a new species by crossing a

cabbage with a radish. Although belonging to different genera (Brassica and Raphanus

respectively), both parents have a diploid number of 18. Fusion of their respective gametes

(n=9) produced mostly infertile hybrids.

However, a few fertile plants were formed, probably by the spontaneous doubling of the

chromosome number in somatic cells that went on to form gametes (by meiosis). Thus these

contained 18 chromosomes — a complete set of both cabbage (n=9) and radish (n=9)

chromosomes.

Fusion of these gametes produced vigorous, fully-fertile, polyploid plants with 36

chromosomes. (They had the roots of the cabbage and the leaves of the radish.)

These plants could breed with each other but not with either the cabbage or radish ancestors,

so Karpechenko had produced a new species.

The process also occurs in nature. Three species in the mustard family (Brassicaceae) appear

to have arisen by hybridization and polyploidy from three other ancestral species:

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 • B. oleracea (cabbage, broccoli, etc.) hybridized with B. nigra (black mustard) → B.

carinata (Abyssinian mustard).

• B. oleracea x B. campestris (turnips) → B. napus (rutabaga)

• B. nigra x B. campestris → B. juncea (leaf mustard)

Modern wheat and perhaps some of the other plants listed in the table above have probably

evolved in a similar way.

3.4 Polyploidy in animals

Examples in animals are more common in the 'lower' forms such as flatworms, leeches, and

brine shrimp. Polyploid animals are often sterile, so they often reproduce by parthenogenesis.

Polyploid lizards are also quite common and parthenogenetic. Polyploid mole salamanders

(mostly triploids) are all female and reproduce by kleptogenesis, "stealing" spermatophores

from diploid males of related species to trigger egg development but not incorporating the

males' DNA into the offspring. While mammalian liver cells are polyploid, rare instances of

polyploid mammals are known, but most often result in prenatal death.

An octodontid rodent of Argentina's harsh desert regions, known as the Plains Viscacha-Rat

(Tympanoctomys barrerae) has been reported as an exception to this 'rule'. However, careful

analysis using chromosome paints shows that there are only two copies of each chromosome

in T. barrerae not the four expected if it were truly a tetraploid. The rodent is not a rat, but

kin to guinea pigs and chinchillas. Its "new" diploid [2n] number is 102 and so its cells are

roughly twice normal size. Its closest living relation is Octomys mimax, the Andean

Viscacha-Rat of the same family, whose 2n = 56. It was therefore surmised that an Octomys-

like ancestor produced tetraploid (i.e., 4n = 112) offspring that were, by virtue of their

doubled chromosomes, reproductively isolated from their parents.

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Polyploidy is much rarer in animals. It is found in some insects, fishes, amphibians, and

reptiles. Until recently, no polyploid mammal was known. However, the 23 September 1999

issue of Nature reported that a polyploid (tetraploid; 4n = 102) rat has been found in

Argentina.

Polyploid cells are larger than diploid ones; not surprising in view of the increased amount of

DNA in their nucleus. The liver cells of the Argentinian rat are larger than those of its diploid

relatives, and its sperm are huge in comparison. Normal mammalian sperm heads contain

some 3.3 picograms (10-12 g) of DNA; the sperm of the rat contains 9.2 pg.

Although only one mammal is known to have all its cells polyploid, many mammals have

polyploid cells in certain of their organs, e.g, the liver.

3.5 Polyploidy in Man

Polyploidy occurs in some animals, such as goldfish, salmon, and salamanders, but is

especially common among ferns and flowering plants (see Hibiscus rosa-sinensis), including

both wild and cultivated species. Wheat, for example, after millennia of hybridization and

modification by humans, has strains that are diploid (two sets of chromosomes), tetraploid

(four sets of chromosomes) with the common name of durum or macaroni wheat, and

hexaploid (six sets of chromosomes) with the common name of bread wheat. Many

agriculturally important plants of the genus Brassica are also tetraploids. Polyploidization is a

mechanism of sympatric speciation because polyploids are usually unable to interbreed with

their diploid ancestors.

Polyploidy can be induced in plants and cell cultures by some chemicals: the best known is

colchicine, which can result in chromosome doubling, though its use may have other less

obvious consequences as well. Oryzalin also will double the existing chromosome content.

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True polyploidy rarely occurs in humans, although it occurs in some tissues (especially in the

liver). Aneuploidy is more common.

Polyploidy occurs in humans in the form of triploidy, with 69 chromosomes (sometimes

called 69,XXX), and tetraploidy with 92 chromosomes (sometimes called 92,XXXX).

Triploidy, usually due to polyspermy, occurs in about 2–3% of all human pregnancies and

15% of miscarriages. The vast majority of triploid conceptions end as miscarriage and those

that do survive to term typically die shortly after birth. In some cases survival past birth may

occur longer if there is mixoploidy with both a diploid and a triploid cell population present.

Triploidy may be the result of either digyny (the extra haploid set is from the mother) or

diandry (the extra haploid set is from the father). Diandry is mostly caused by reduplication

of the paternal haploid set from a single sperm, but may also be the consequence of dispermic

(two sperm) fertilization of the egg. Digyny is most commonly caused by either failure of one

meiotic division during oogenesis leading to a diploid oocyte or failure to extrude one polar

body from the oocyte. Diandry appears to predominate among early miscarriages while

digyny predominates among triploidy that survives into the fetal period. However, among

early miscarriages, digyny is also more common in those cases <8.5 weeks gestational age or

those in which an embryo is present. There are also two distinct phenotypes in triploid

placentas and fetuses that are dependent on the origin of the extra haploid set. In digyny there

is typically an asymmetric poorly grown fetus, with marked adrenal hypoplasia and a very

small placenta. In diandry, a partial hydatidiform mole develops. These parent-of-origin

effects reflect the effects of genomic imprinting.

Complete tetraploidy is more rarely diagnosed than triploidy, but is observed in 1–2% of

early miscarriages. However, some tetraploid cells are commonly found in chromosome

analysis at prenatal diagnosis and these are generally considered 'harmless'. It is not clear

243
whether these tetraploid cells simply tend to arise during in vitro cell culture or whether they

are also present in placental cells in vivo. There are, at any rate, very few clinical reports of

fetuses/infants diagnosed with tetraploidy mosaicism.

Mixoploidy is quite commonly observed in human preimplantation embryos and includes

haploid/diploid as well as diploid/tetraploid mixed cell populations. It is unknown whether

these embryos fail to implant and are therefore rarely detected in ongoing pregnancies or if

there is simply a selective process favoring the diploid cells.

4.0 Conclusion

At the end of this unit, the student learnt the following:

• Definition of polyploidy

• Polyploidy in animals and plants

• Polyploidy in man

5.0 Summary.

Polyploidy is the condition whereby a biological cell or organism has more than two

homologous sets of chromosomes, with each set essentially coding for all the biological traits

of the organism. A haploid (n) only has one set of chromosomes. A diploid cell (2n) has two

sets of chromosomes. Polyploidy involves three or more times the haploid number of

chromosomes. Polyploid types are termed according to the number of chromosome sets in the

nucleus: triploid (three sets; 3n), tetraploid (four sets; 4n), pentaploid (five sets; 5n),

hexaploid (six sets; 6n), and so on.

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6.0 Tutor-Marked Assignment.

• What is polyploidy?

• Describe polyploidy in animals and plants

7.0 Reference/Further Readings

Parmacek MS, Epstein JA (July 2009). "Cardiomyocyte renewal". N. Engl. J. Med. 361 (1):

86–8. doi:10.1056/NEJMcibr0903347. PMID 19571289.

Griffiths, Anthony J. F. (1999). An Introduction to genetic analysis. San Francisco: W.H.

Freeman. ISBN 0-7167-3520-2.

Ohno S, Muramoto J, Christian L, Atkin NB (1967). "Diploid-tetraploid relationship among

old-world members of the fish family Cyprinidae". Chromosoma 23 (1): 1–9.

doi:10.1007/BF00293307.

Bertolani R (2001). "Evolution of the reproductive mechanisms in Tardigrades: a review".

Zoologischer Anzeiger 240 (3-4): 247–252. doi:10.1078/0044-5231-00032.

The genetic origin of kiwifruit. http://www.actahort.org/books/297/297_5.htm

Bogart JP, Bi K, Fu J, Noble DW, Niedzwiecki J (February 2007). "Unisexual salamanders

(genus Ambystoma) present a new reproductive mode for eukaryotes". Genome 50 (2): 119–

36. doi:10.1139/g06-152. PMID 17546077.

Svartman M, Stone G, Stanyon R (Aprilt 2005). "Molecular cytogenetics discards polyploidy

in mammals". Genomics 85 (4): 425–30. doi:10.1016/j.ygeno.2004.12.004. PMID 15780745.

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MODULE 5: EVOLUTION OF LIFE

Unit 1: Origin of Life

Unit 2: Evidence of evolution, adaptation and Speciation

Unit 3: Classification and phylogeny

Unit 4: Geological periods and epoch

Unit 5: Evolution of the plants

UNIT 1: ORIGIN OF LIFE

CONTENTS

1.0 Introduction

2.0 Objectives

3.0 Main contents

3.1 Origin of life

3.2 Probable stages in the origin of life

3.2.1 First stage (the primitive earth)

3.2.2 Second stage (evolution of small organic molecules)

3.2.3 Third stage (macromolecules)

3.2.4 Fourth stage (the protocell)

3.2.5 Fifth stage (The true cell)

4.0 Conclusion

5.0 Summary

6.0 Tutor-Marked Assignment

7.0 References/Further Readings

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1.0 INTRODUCTION

It is important to understand how life began. The origin of the first cell is an event of low probability,
because a complete series of events would have had to occur- but this length of time is long enough
for an event of low probability to have occurred. Today we do not believe that life arises
spontaneously from nonlife and we say that ‘a life comes from a life’. However, the very first living
thing had to have come from non living chemicals.

2.0 OBJECTIVES

At the end of this unit, student should be able to:

- explain the origin of life

- understand the probable stages in the origin of life

- explain what is organic evolution

3.0 MAIN CONTENT

3.1 Origin of life

The planet earth came into existence 4 and 5 billion years ago. Life evolved on planet earth
about 3.5 billion years ago. At that time it was extremely hot. The existence of life in any
form at that high temperature was not possible.

So, life two questions arise pertaining to

1. How did life originated on earth?

2. How did primitive organisms evolve into new forms resulting in the evolution of
a variety of organism on earth?

Origin of life means the appearance of simplest primordial life from non living matter (Fig.
3.1).

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Fig. 3.1: Origin of first cell (s)

3.2 Probable stages in the origin of life

3.2.1 First stage (the primitive earth)

Theorized early primitive atmosphere consisted mostly of water vapour, nitrogen and carbon
dioxide with small amounts of hydrogen and carbon monoxide with little if any, of free oxygen.

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3.2.2 Second stage (evolution of small organic molecules)

A particular mix of inorganic chemicals could have reacted with one another to produce small organic
molecules (or compound) such as glucose, amino acids and nucleotides. Most chemical reactions take
place in water and the first proto cell undoubtedly arose in the ocean. In 1953, Stanley Miller and
Harold Urey performed an experiment known as the (Miller-Urey experiment) that supports the
hypothesis that small organic molecules were formed at the ocean’s surface (Fig. 3.2). In the early
earth, volcanoes erupted constantly and the first atmospheric gas would have consequently contained
methane (CH4), ammonia (NH3) and hydrogen (H2). These gases could have been washed into the
ocean by the first rains, fierce lightning and unabated ultraviolent radiation would have allowed them
to react and produce the first organic molecules.

Fig 3.2: Miller and Ureys apparatus and experiment.

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To test the hypothesis of chemical evolution, Miller placed the organic chemicals mentioned in a
closed system, heated the mixture and circulated it past an electric spark (simulating lightning). After
a week, the solution contained a variety amino acids and organic acids. This and other similar
experiments support the hypothesis that inorganic chemicals in the absence of oxygen (O2) and in the
presence of a strong energy source can result in organic molecules.

The formation of small organic molecules is thought to be the first step toward the origin

3.2.3 Third stage (macromolecules)

Once formed, the first small organic molecules gave rise to still larger molecules. Then these would
have polymerized into macromolecules. There are three primary hypotheses concerning this stage in
the origin of life.

RNA first- hypothesis: this hypothesis suggests that only the macromolecule RNA (ribonucleic acid)
was needed at this time to progress toward formation of the first cell or cell(s). Such RNA molecules
are called ribozymes since we know that ribozymes exist.

Protein-first hypothesis: this hypothesis suggests that amino acids collected in shallow puddles along
the rocky shore and the heat of the sun caused them to form protenoids, small polypeptides that have
some catalytic properties. When protenoids are returned to water, they form the properties of a cell.
Some of these proteins could have had enzymatic properties.

The third hypothesis is put forth by Graham Cairns-Smith. He believes that clay was especially
helpful in causing the polymerization of both proteins and nucleic acids at the same time. Clay attracts
small organic molecules and contains iron and zinc, which may have served as inorganic catalysts for
polypeptide formation. In addition, clay tends to collect energy from radioactive decay and then
discharge it when the temperature or humidity changes, possibly providing a source of energy for
polymerization. Cairns-Smith suggests that RNA nucleotides and amino acids became associated in
such a way that polypeptides were ordered by, and helped synthesize, RNA.

Chemical reactions likely produced the macromolecules we associate with living things.

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3.2.4 Fourth stage (the protocell)

After macromolecules formed, something akin to a modern plasma membrane was needed to separate
them from the environment. Thus before the first true cell arose, there would likely have been a
protocell (fig. 3.3), which could carry on metabolism but not reproduce, formed when lipids and
microspheres formed a lipid – protein membrane. It has been suggested that the protocell likely was a
heterotrophy, an organism that takes in preformed food.

The Heterotroph Hypothesis has been suggested that the protocell likely was a heterotroph, an
organism that takes in performed food. During the early evolution of life, the ocean contained
abundant nutrition in the form of small organic molecules. This suggests that heterotrophs preceded
autotrophs, organisms that make their own food.

Once the protocell was capable of reproduction, it became a true cell, and biological evolution began

3.2.5 Fifth stage (The true cell)

A true cell is a membrane-bounded structure that can carry on protein synthesis to produce the
enzymes that allow DNA to replicate. The central concept of genetics states that DNA directs protein
synthesis and that information flows from DNA to RNA to protein. It is possible that this sequence
developed in stages. Once the protocells acquired genes that could replicate, they became cells
capable of reproducing, and biological evolution began.

The hypothesis that the origin of life followed a transition from small organic molecules to
macromolecules to protocells to true cells is currently widely favoured by scientists.

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Fig.3.3: Protocell components

4.0 CONCLUSION

In this unit you have leant about the meaning of origin of life and the five probable stages involved in
the origin of life. This knowledge will facilitate the understanding of the subsequent study units in this
module.

5.0 SUMMARY

Chemical reactions are believed to have led to the formation of the first true cell(s). Inorganic
chemicals, probably derived from the primitive atmosphere, reacted to form small organic molecules.
These reactions occurred in the ocean, either on the surface or in the region of hydrothermal vents
deep within.

After small organic molecules such as glucose, amino acids, and nucleotides arose, they polymerised
to form the macromolecules. Amino acids joined to form proteins, and nucleotides joined to form
nucleic acids. Perhaps RNA was the first nucleic acid. The RNA-first hypothesis is supported by the

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discovery of ribozymes, RNA enzymes. The protein-first hypothesis is supported by the observation
that amino acids polymerize abiotically when exposed to dry heat.

Once a plasma membrane developed, the protocell came into being. Eventually, the
DNA→RNA→protein system evolved, and a true cell came into being.

6.0 TUTOR – MARKED ASSIGMENT

1. Explain the origin of life

2. List 5 probable stages involved in the origin of life

3. The RNA- first hypothesis for the origin of cells is supported by the discovery of

----------

7.0 REFERENCES/FURTHER READINGS

Magurran, A. E., and R. M. May. 1999. Evolution of biological diversity. Oxford, U.K., Oxford
University Press. An edited volume covering recent issues in the study of specification, with
contributions from many active evolutionary biologists.

www.mhhe.com/zoology

www.mcgraw.com

UNIT 2: EVIDENCE OF EVOLUTION, ADAPTION AND SPECIATION

CONTENTS

1.0 Introduction

2.0 Objectives

3.0 Main contents

3.1 Evidence of evolution

3.1.1 Fossil evidence

3.1.2 Biogeographical evidence
3.1.3 Anatomical evidence

3.1.4 Biochemical evidence

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 3.2 Adaptation

3.3 Speciation

4.0 Conclusion

5.0 Summary

6.0 Tutor-Marked Assignment

7.0 References/Further Readings

1.0 INTRODUCTION

Evolution is defined as “common descent”. Because of descent with modification, all living
things share the same fundamental characteristics: they are made of cells, take chemicals and energy
from the environment, respond to external stimuli, and reproduce. Living things are diverse because
individual organisms exist in the many environments throughout the Earth, and the features that
enable them to survive in those environments are quite diverse. Many fields of biology provide
evidence that evolution through descent with modification occurred in the past and is still occurring.
Let us look at the various types of evidence for evolution.

Evolution influences every aspect of the form and behavior of organisms. Most prominent are the
specific behavioural and physical adaptation that are the outcome of natural selection. These
adaptations increase fitness by aiding activities such as finding food, avoiding predators or attracting
mates.

2.0 OBJECTIVES

After the completing this lesson, you will be able to:

- give the fossils, anatomy, biochemical and biogeographical evidence

- explain adaptation

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- explain speciation and four mechanisms involved

3.0 MAIN CONTENT

3.1 EVIDENCES OF EVOLUTION

The evidences supporting organic evolution are derived from a number of fields of biology. Those
discuss here are:

1. Fossil evidence 2. Anatomy evidence 3. Biochemical evidence 4. Biogeographical evidence

3.1.1 Fossil Evidence

Fossils are the remains and traces of past life or any other direct evidence of past life. Most fossils
consist only of hard parts of organisms, such as shells, bones, or teeth, because these are usually
preserved after death. The soft parts of a dead organism are often consumed by scavengers or
decomposed by bacteria. Occasionally, however, an organism is buried quickly and in such a way that
decomposition is never completed or is completed so slowly that the soft parts leave an imprint of
their structure. Traces include trails, footprints, burrows, worm casts, or even preserved droppings.

The great majority of fossils are found embedded in sedimentary rock. Sedimentation, a process that
has been going on since Earth formed, can take place on land or in bodies of water. The weathering
and erosion of rocks produces particles that vary in size and are called sediment. As such particles
accumulate, sediment becomes a stratum (pl., strata), a recognizable layer of rock. Any given stratum
is older than the one above it and younger than the one immediately below it, so that the relative age
of fossils can be determined based on their depth.

Palaeontologists are biologists who study the fossils record and from it draw conclusions about the
history of life. Particularly interesting are the fossils that serve as transitional links between groups.
For example, the famous fossils of Archaeopteryx are intermediate between reptiles and birds
(Fig.3.4). The dinosaur-like skeleton of this fossil has reptilian features, including jaws with teeth and
a long, jointed tail, but Archaeopteryx also had feathers and wings, all suggesting that reptiles evolved
from birds. Other transitional links among fossil vertebrates suggest that fishes evolved before
amphibians, which evolved before both birds and mammals in the history of life. As a result of
studying strata, scientists have divided Earth’s history into eras, and then periods and epochs. The
fossil record has helped determine the dates given in the table. There are two ways to date fossils. The

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relative dating method determines the relative order of fossils and strata depending on the layer of
rock in which they were found, but it does not determine the actual date they were formed.

a.

b.

Fig. 3.4 (a&b): Transitional fossils

The absolute dating method relies on radioactive dating techniques to assign an actual date to a fossil.
All radioactive isotopes have a particular half-life, the length of time it takes for half of the
radioactive isotope to change into another stable element. Carbon 14 (14C) is the only radioactive
isotope in organic matter. Using both relative and absolutedating methods, we can learn from fossils
about the various organisms and environments that existed across the planet during any time period.
Fossils

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Table 3.1: The Geological Time Scale: Major Divisions of Geological Time and Same of the Major
Evolutionary Events of Each Time Period

allowed scientists to construct the geological timescale that traces the history of life.

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3.1.2 Biogeographical evidence

Another type of evidence that supports evolution through descent with modification is found in the
field of biogeography, the study of the distribution of species throughout the world.

Different mammals and flowering plants evolved separately in each biogeographical region, and
barriers such as mountain ranges and oceans prevented them from migrating to other regions.

Many of these barriers arose through a process called continental drift. That is, the continents have
never been fixed; rather, their positions and the positions of the oceans have changed over time.

The distribution of many organisms on earth is explainable by knowing when they evolved, either
before or after the continents moved apart

3.1 .3 Anatomical evidence

The fact that anatomical similarities exist among organisms provides further support for evolution via
descent with modification. Vertebrate forelimbs are used for flight (birds and bat), orientation during
swimming (whales and seals). Running (horses), climbing (arboreal lizard), or swinging from tree
branches (monkey). Yet all vertebrate forelimbs contain the same set of bones organized in the same
ways, despite the dissimilar functions. The most plausible explanation for this unity is that the basic
forelimb plan belongs to a common ancestor, and then the plan was modified in the succeeding groups
as each continued along its own evolutionary pathway. Structures that are anatomically similar
because they are inherited from a common ancestor called homologous structure structures. In
contrast, analogous structures serve the same function, but are not constructed similarly nor do they
share a common ancestry. The wings of birds and insect and the eyes of octopi and humans are
analogous structure and are similar due to a common ancestry. The presence of homology, analogy, is
evidence that organisms are related

Vestigial structures are anatomical features that are fully developed in one group of organisms but that
are reduced and may have no functions in similar groups. Most birds, for example , have well-
developed wings for flight. However some species (e.g., ostrich) have greatly reduced wings and do
not fly. Similarly, snakes have no use for hind limbs, and yet some have remnant of hind limbs in a
pelvic girdle and legs. The presence of vestigial structures occur because organisms inherit their
anatomy from their ancestors: they are traces of an organism’s evolutionary history.

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 Fig. 3.5: Significance of homologous structures

The homology shared by vertebrates extends to their embryology development. At some time during
development, all vertebrates have a post anal tail and exhibit paired pharyngeal pouches. In fishes and
amphibian larvae these pouches develop into functioning gills. In humans, the first pair of pouches
becomes the cavity of the middle ear and the auditory tube. The second pair becomes the tonsils,
while the third and fourth pairs become the thymus and parathyroid gland. Why should terrestrial
vertebrates develop and then modify structures like pharyngeal pouches that have lost their original
function? The most likely explanation is that fishes are ancestral to other vertebrate groups.

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 Fig. 3.6: Significance of developmental similarities

Organisms that share homologous structures are closely related and have a common ancestry. Studies
of comparative and embryological development reveal homologous structures.

3.1.4 Biochemical evidence

Almost all living organism use the same basic biochemical molecules, including DNA, ATP
(adenosine triphosphate), and many identical or nearly identical enzymes. Further, organisms use the
same DNA triplet code for the 20 amino acid in their proteins. Since the sequences of DNA bases in

260
genomes of many organisms are now known, it has become clear that humans share a large number of
genes with much

Fig. 3.7: Significance of biochemical differences

simpler organisms. It appears that life’s vast diversity has come about by only a slight difference in
many of same genes. The result has been widely divergent types of bodies. When the degree of
similarity in DNA nucleotide sequences or the degree of similarity in amino acid sequences of
proteins is examined, the more similar the DNA sequences are, generally the more closely related the
organisms are. For example, humans and chimpanzees’ are about 99% similar! Cytochrome c is a
molecule that is used in used in electron transport chain of all the organisms appearing in figure 3.7.
data regarding differences in the amino acid sequence of cytochrome c show that the sequence in a

261
human differs from that in a yeast by 51 amino acids. These data are consistent with other data
regarding the anatomical similarities of these organisms and, therefore, how closely they are related.

Evolution in no longer considered a hypothesis. It is one of the great unifying theories of

biology. In science the word theory is reserved for those conceptual schemes that are supported by a
large number of observation and scientific experiments. The theory of evolution has the same status in
biology that the germ theory of disease has in medicine.

Many line of evidence support the theory of evolution by descent with modification. Recently
biochemical evidence has also been found to support evolution. A hypothesis is strengthened when it
is supported by many different lines of evidence.

3.2 Adaptation

Adaptation is the process that makes organisms better suited to their habitat. Also, the term
adaptation may refer to a trait that is important for an organism's survival. For example, the
adaptation of horses' teeth to the grinding of grass. By using the term adaptation for the
evolutionary process and adaptive trait for the product (the bodily part or function), the two
senses of the word may be distinguished. Adaptations are produced by natural selection. The
following definitions are due to Theodosius Dobzhansky.

Adaptation is the evolutionary process whereby an organism becomes better able to

live in its habitat or habitats.
Adaptedness is the state of being adapted: the degree to which an organism is able to
live and reproduce in a given set of habitats.
An adaptive trait is an aspect of the developmental pattern of the organism which
enables or enhances the probability of that organism surviving and reproducing.
Adaptation may cause either the gain of a new feature, or the loss of an ancestral feature. An
example that shows both types of change is bacterial adaptation to antibiotic selection, with
genetic changes causing antibiotic resistance by both modifying the target of the drug, and
increasing the activity of transporters that pump the drug out of the cell. Other striking examples
are the bacteria Escherichia coli evolving the ability to use citric acid as a nutrient in a long-term
laboratory experiment, Flavobacterium evolving a novel enzyme that allows these bacteria to
grow on the by-products of nylon manufacturing, and the soil bacterium Sphingobium evolving
an entirely new metabolic pathway that degrades the synthetic pesticide pentachlorophenol. An
interesting but still controversial idea is that some adaptations might increase the ability of

262
organisms to generate genetic diversity and adapt by natural selection (increasing organisms'
evolvability).

Fig. 3.8: A baleen whale skeleton, a and b label flipper bones, which were adapted
from front leg bones: while c indicates vestigial leg bones, suggesting an adaptation
from land to sea.

Adaptation occurs through the gradual modification of existing structures. Consequently,

structures with similar internal organization may have different functions in related organisms.
This is the result of a single ancestral structure being adapted to function in different ways. The
bones within bat wings, for example, are very similar to those in mice feet and primate hands, due
to the descent of all these structures from a common mammalian ancestor. However, since all
living organisms are related to some
some extent, even organs that appear to have little or no structural
similarity, such as arthropod,
arthropod, squid and vertebrate eyes, or the limbs and wings of arthropods and
vertebrates, can depend on a common set of homologous genes that control their assembly and
function; this is called deep homology.
homology

During evolution, some structures may lose their original function and become vestigial
structures.. Such structures may have little or no function in a current species, yet have a clear
function in ancestral species, or other closely related species. Examples include pseudogenes, the
non-functional
functional remains of eyes in blind cave-dwelling
cave dwelling fish, wings in flightless birds, and the
presence of hip bones in whales and snakes. Examples of vestigial structures in humans include
wisdom teeth, the coccyx,, the vermiform appendix,, and other behavioural vestiges such as goose
bumps and primitive reflexes.
reflexes

However, many traits that appear to be simple adaptations are in fact exaptations:
exaptations structures
originally adapted for one function, but which coincidentally became somewhat useful for some

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 other function in the process. One example is the African lizard Holaspis guentheri, which
developed an extremely flat head for hiding in crevices, as can be seen by looking at its near
relatives. However, in this species, the head has become so flattened that it assists in gliding from
tree to tree—an exaptation. Within cells, molecular machines such as the bacterial flagella and
protein sorting machinery evolved by the recruitment of several pre-existing proteins that
previously had different functions. Another example is the recruitment of enzymes from
glycolysis and xenobiotic metabolism to serve as structural proteins called crystallins within the
lenses of organisms' eyes.

A critical principle of ecology is that of competitive exclusion: no two species can occupy the
same niche in the same environment for a long time. Consequently, natural selection will tend to
force species to adapt to different ecological niches. This may mean that, for example, two
species of cichlid fish adapt to live in different habitats, which will minimise the competition
between them for food.

An area of current investigation in evolutionary developmental biology is the developmental

basis of adaptations and exaptations. This research addresses the origin and evolution of
embryonic development and how modifications of development and developmental processes
produce novel features. These studies have shown that evolution can alter development to
produce new structures, such as embryonic bone structures that develop into the jaw in other
animals instead forming part of the middle ear in mammals. It is also possible for structures that
have been lost in evolution to reappear due to changes in developmental genes, such as a
mutation in chickens causing embryos to grow teeth similar to those of crocodiles. It is now
becoming clear that most alterations in the form of organisms are due to changes in a small set of
conserved genes.

3.3 Speciation

Speciation is the origin or evolution of new species. Speciation has occurred when one
species gives rise to two species, each of which continues on its own evolutionary pathway. Species is
a latin word meaning "kind" or "appearance" Species is defined as a group of subpopulations that are
capable of inter breeding and are isolated reproductively form other species. The subpopulations of
the same species can exchange genes, but different species do not exchange genes. Species have
traditionally been described on the basis of their physical form or morphology

Speciation occurs in the following ways and is termed accordingly.

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How can we recognize speciation?

Whenever reproductive isolation develops between two formerly interbreeding groups of populations,
speciation has occurred.

Allopatric speciation takes place when a part of the population becomes

geographically separated (geographical isolation) from the parental population.

For example a group of birds lives at the base of the mountain, some members

fly up and get geographically isolated. Variation and natural selection act differently

on the two because the environment in which the two live is different. Gradually

genetic changes render them to be reproductively isolated.

Sympatric speciation

Sometimes a genetic barrier (reproductive barrier) prevents reproduction between

a section of a population of a species with other members. Such a section

of population usually arises in plants because of polyploidy. Polyploidy is a

mutation in which the normal diploid number of chromosomes become doubled

or trebled (2n becomes 3n, 4n, 5n etc) in a section of the population of a

species due to certain irregularities during cell division. The polyploid section

of the population is then unable to interbreed (mate and reproduce) with the

other and becomes a new species.

3.3.1 Two isolation mechanisms

Prezygotic isolation mechanisms are in place before fertilization, and thus reproduction is never
attempted. Postzygotic isolation mechanisms are in place after fertilization, so reproduction may take
place, but it does not produce fertile offspring (Table 3.2).

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 Reproductive Isolating Mechanisms

Isolation Mechanism Example

Prezygotic

Habitat isolation Species at same locale occupy different habitats

Temporal isolation Species reproduce at different seasons or different times of

day.

Behavioural isolation In animals, courtship behaviour differs, or they respond to

different songs, calls, pheromones, or other signals

Mechanical isolation Genitalia unsuitable for one another

Postzygotic

Gamete isolation Sperm cannot reach or fertilize egg

Zygote mortality Fertilization occurs, but zygote does not survive

Hybrid sterility Hybrid survives but is sterile and cannot reproduce

F2 fitness Hybrid is sterile, but F2 hybrid has reduced fitness

3.3.2 Models of speciation

There are two accepted models of speciation that have given rise to the biodiversity

1. Phyletic Gradualism model

Two species from common ancestor gradually become more and more structurally

different acquiring adaptations unique to each (Fig. 1.11b(i)). Darwin also

believed that evolution is a slow and gradual process.

2. Punctuated equilibrium

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A new species arises through major changes in the beginning and then remain

constant for long periods before changing again. (Fig. 3.9b (ii)) This model

was suggested by paleontologists (scientists who study fossils), Niles Eldredge

and Stephen Jay Gould.

Fig. 3.9: Models of speciation (a) Phyletic gradualism (b) Punctuated equilibrum

3.3.3 The four mechanisms of speciation.

Speciation is the process where a species diverges into two or more descendant species. Barriers
to reproduction between two diverging sexual populations are required for the populations to
become new species. Gene flow may slow this process by spreading the new genetic variants also
to the other populations. Depending on how far two species have diverged since their most recent
common ancestor, it may still be possible for them to produce offspring, as with horses and
donkeys mating to produce mules. Such hybrids are generally infertile. In this case, closely
related species may regularly interbreed, but hybrids will be selected against and the species will
remain distinct. However, viable hybrids are occasionally formed and these new species can
either have properties intermediate between their parent species, or possess a totally new
phenotype. The importance of hybridisation in producing new species of animals is unclear,
although cases have been seen in many types of animals, with the gray tree frog being a
particularly well-studied example.

Speciation has been observed multiple times under both controlled laboratory conditions and in
nature. In sexually reproducing organisms, speciation results from reproductive isolation
followed by genealogical divergence. There are four mechanisms for speciation.

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 The most common in animals is allopatric speciation,, which occurs in populations initially
isolated geographically, such as by habitat fragmentation or migration. Selection under these
thes
conditions can produce very rapid changes in the appearance and behaviour of organisms. As
selection and drift act independently on populations isolated from the rest of their species,
separation may eventually produce organisms that cannot interbreed.

Fig. 3.10: The four mechanisms

The second mechanism of speciation is peripatric speciation,, which occurs when small
populations of organisms become isolated in a new environment.
environment. This differs from allopatric
speciation in that the isolated populations are numerically much smaller than the parental population.
Here, the founder effect causes rapid speciation after an increase in inbreeding increases selection on
homozygotes, leading to rapid genetic change.

The third mechanism of speciation is parapatric speciation.. This is similar to peripatric speciation
in that a small population enters a new habitat, but differs in that there is no physical separation
between these two populations. Instead, speciation results from the evolution of mechanisms that
reduce gene flow between the two populations.

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Generally this occurs when there has been a drastic change in the environment within the parental
species' habitat. One example is the grass Anthoxanthum odoratum, which can undergo parapatric
speciation in response to localised metal pollution from mines. Here, plants evolve that have
resistance to high levels of metals in the soil. Selection against interbreeding with the metal-sensitive
parental population produced a gradual change in the flowering time of the metal-resistant plants,
which eventually produced complete reproductive isolation. Selection against hybrids between the
two populations may cause reinforcement, which is the evolution of traits that promote mating within
a species, as well as character displacement, which is when two species become more distinct in
appearance.

Fig. 3.11: Finches from Galapagos Archipelago

Geographical isolation of finches on the Galápagos Islands produced over a dozen new species.

Finally, in sympatric speciation species diverge without geographic isolation or changes in

habitat. This form is rare since even a small amount of gene flow may remove genetic differences
between parts of a population. Generally, sympatric speciation in animals requires the evolution
of both genetic differences and non-random mating, to allow reproductive isolation to evolve.

4.0 Conclusion
In this unit you have learnt about evidence of evolution, adaptation and speciation, this
knowledge will facilitate the understanding of the subsequent study units in this module.

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5.0 Summary

The fossil record and biogeography, as well as studies of comparative anatomy, development, and
biochemistry, all provide evidence of evolution. The fossil record gives clues about the history of life
in general and allows us to trace the descent of a particular group. Biogeography shows that the
distribution of organisms on Earth can be influenced by a combination of evolutionary and geological
processes. Comparing the anatomy and the development of organisms reveals homologous structures
among those that share common ancestry. All organisms have certain biochemical molecules in
common, and these chemical similarities indicate the degree of relatedness. Adaptation is the
evolutionary process whereby an organism becomes better able to live in its habitat or habitats.
Speciation is the origin of new species. This usually requires geographic isolation, followed by
reproductive isolation. The evolution of several species of finches on the Galápagos Islands is an
example of speciation caused by adaptive radiation because each one has a different way of life.
Currently, there are two hypotheses about the pace of speciation. Traditionalists support phyletic
gradualism—slow, steady change leading to speciation. In contrast, a more recent model, called
punctuated equilibrium, proposes that long periods of stasis are interrupted by rapid speciation.

6.0 TUTOR-MARKED ASSIGNMENT

1. List and explain 4 evidences of evolution

2. What is adaptation?

3. Explain two models of speciation

7.0 REFERENCES/FURTHER READINGS

Raff, R. A. 1996. The ahape of life: genes, development and the evolution of animal form. Chicago,
University of Chicago Press. A provocative discussion of the genetic and developmental processes
underlying evolution of animal diversity.

www.mhhe.com/zoology

www.mcgraw.com

270
UNIT 3 : CLASSIFICATION AND PHYLOGENY

CONTENTS

1.0 Introduction
2.0 Objectives
3.0 Main contents

271
 3.1 Classification

3.1.1 Taxonomy categories

3.1.2 Scientific naming of organisms

3.1.3 Prokaryotes and Eukaryotes

3.1.4 The five kingdoms of organisms

3.2 Phylogeny

3.2.1 Phylogenetics

4.0 Conclusion

5.0 Summary

6.0 Tutor-Marked Assignment

7.0 References/Further Readings

1.0 INTRODUCTION

Classification means identifying similarities and differences between different kinds of organism and
then placing similar organisms in one group and different kinds of organisms in different groups.
Taxonomy may thus be defined as the science of classification of organisms into categories,
maintaining certain rules. Early taxonomists classified organisms according to morphological features
only. Once the concept of organic evolution was accepted, taxonomists began to draw evolutionary
relationships between different kinds of organisms. This was termed systematic. Today taxonomy and
systematic are treated as synonymous since for classification, both morphological and biochemical
resemblances and even those of between molecules such as DNA and RNA are studied to establish
evolutionary relationships. Phylogeny is the evolutionary relationship among organisms. Ideally,
classifications reflect phylogeny in that it tells how organisms are related through evolution and
common ancestry. Species in the same genus are more closely related than species in separate genera
and so forth as we proceed from genus to domain.

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2.0 OBJECTIVES

At the end of this unit, students should be able to:

- Define classification
- Justify the need for classification of organisms
- List the bases of classification
- Explain taxonomy and phylogeny

3.0 MAIN CONTENT

3.1 Classification

Classification involves assigning species to a hierarchy of categories: species, genus, family, order,
class, phylum and kingdom. While classifying an organism, it is assigned to categories which show its
evolutionary relationship with other groups of organisms. Each level or category is termed taxon
(plural-taxa). The lowermost category is species. Other categories are arranged above species so that
there is a hierarchy of categories.

3.1.1 Taxonomic categories

The various taxonomic categories are given below:

Species: Group of individuals of one kind which can interbreed to produce fertile offspring.

Genus: Group of species resembling each other in several features indicating common ancestry.

Family: Group of genera (singular-genus) resembling each other. e.g. Felis domestica (the cat) and
Panthera tigris (the tiger), both belong to family Felidae.

Order: Includes families showing similar characteristics.

Class: Includes related orders.

Phylum: Includes related classes.

The various phyla belong to their respective kingdoms. There are five kingdoms

Example.

Kingdom : Animalae (Animals)

Phylum : Chordata (Animals with notochord/ backbone)

Class : Mammalia (Animals that suckle their young ones.)

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Order : Primates (Mammals with larger brains and binocular vision)

Family : Hominidae (Humans and human like ancestors)

Genus : Homo (Fossilmen and modern man)

Species : H.sapiens (Modern man)

3.1.2 Scientific naming of organisms

Different plants and animals have different common names. A cat is called ‘billi’ in Hindi, ‘biral’ in
Bengali, ‘punai’ in Tamil and manjar in Marathi. There are different words for cat in French or
German. There arose the need to give organisms names which could be understood throughout the
world. So, the scientific names were given to organisms. Scientific names of organisms are
understood all over the world.

A simplified system of naming organisms called binomial nomenclature has been the standard for
more than two centuries now. It was proposed by the Swedish biologist, Carolus Linnaeus (1707-
1778). Binomial nomenclature simply means two-name system of naming. The name of every kind of
organism has two parts, that of the genus followed by that of species. The generic name is written
with a capital letter and the specific name with a small letter. e.g. Homo sapiens is the scientific name
of modem man, Mangifera indica is the biological name of mango.

Three main features of biological naming are as follows:

1. A scientific name, by convention, is printed in italics or underlined when hand written.

2. Scientific naming is according to a set of scientific rules of nomenclature.

3. Scientific names are mostly in Greek and Latin. They are understood all over the world and have
made communication about organisms easier.

3.1.3 Prokaryotes and Eukaryotes

The organisms that are most primitive or the first to evolve on earth are the bacteria.

They do not possess a nuclear membrane around their single chromosome. Absence of a well defined
nucleus or in other words a primitive nucleus terms them prokaryotes (pro = primitive, karyon =
nucleus). All bacteria are prokaryotes.

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As a constrast, organisms other than bacteria possessing a well defined nucleus are eukaryotes (eu =
true; karyon = nucleus). There are other differences between them are given in the table 3.3

3.1.4 The Five Kingdoms of Organisms

Till recently there were only two kingdoms for classification - Plantae and

Animalae. Such a two kingdom classification had several drawbacks, e.g. bacteria

and fungi were kept along with plants although they are very different.

R.H. Whittaker in 1969 suggested the five kingdom classification which is based

on 3 criteria:

(i) The presence or absence of a well-defined nucleus.

(ii) Unicellular or multicellular

(iii)Mode of nutrition

Table 3.2 Differences between Prokaryotes and Eukaryotes

Characteristics Prokaryotes Eukaryotes

1. Size 0.1-10 µm 10-100 µm (greater volume)

2. Genetic material
Circular DNA, no linear DNA, Histones present on which DNA
histones associated with DNA, molecule wrapped, well defined
nucleoid form, no nuclear chromosomes, nuclear
membrane membrane present

DNA in cytoplasm DNA inside distinct nucleus

3. Site of Nuclear material
4. Organelles

Non membrane bound Mitochondria, golgi body,

5. Cell wall organelles lysosome present in the cell

Always present, contains None {animals} or made of

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 peptidoglycan cellulose, chitin {plant and
fungi}

By mitochondria
6. Respiration
7. Reproduction Asexual and sexual e.g
By mesosomes
protoctista, fungi, plants animal
Mostly asexual e.g bacterial,
cyanobacterial and blue green
algae

The five kingdom classification of organisms

Name of Nature of Whether Kind of Kingdom nucleus unicells or nutrition multicells

1. MONERA Prokaryotic Unicellular Diverse type of (Blue green algae nutrition and bacteria)

2. PROTOCTISTA Eukaryotic Unicellular Diverse kind of (Algae and nutrition Protozoa)

3. FUNGI Eukaryotic Multicellular Saprophytic (Moulds, etc.) (Feed on dead, decaying matter)

4. PLANTAE Eukaryotic Multicellular Autotrophic (All green plants) (Synthesize food by

photosynthesis)

5. ANIMALAE Eukaryotic Multicellular Heterotrophic (Animals) (Depend on others for food

3.2 Phylogeny

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Life’s history is depicted as a branching tree, called a phylogeny. All forms of life, including many
extinct forms that represent dead branches, will connect to this tree somewhere.

3.2.1 Phylogenetics

Phylogenetics is the modern way in which organisms are classified and arranged in evolutionary trees.
Phylogeneticists arrange species and higher classification categories into clades. Clades may be
represented on a diagram called a cladogram. A clade contains a most recent common ancestor and all
its descendant species—the common ancestor is presumed and not identified. Figure 3.12 depicts a
cladogram for seven groups of vertebrates. Only the lamprey, the so-called “outgroup,” lacks jaws,
but the other six groups of vertebrates are in the same clade because they all have jaws, a derived
characteristic relative to their ancestors. On the other hand, the vertebrates beyond the shark are all in
the same clade because they have lungs, and so forth.

Fig. 3.12: Cladogram

4.0 Conclusion

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In this unit you have leant about the classification of organisms, taxonomy, phylogeny and its
importance. This knowledge will facilitate the understanding of the subsequent study units in this
module.

5.0 Summary
Classification involves assigning species to a hierarchy of categories: kingdom, phylum,
class, order, family, genus, and species, and in this text, domain. The five-kingdom
system of classification recognizes these kingdoms: Monera (the bacteria), Protista (algae,
protozoans), Fungi, Plantae, and Animalia. The more recent which is three-domain
system (Bacteria, Archaea, and Eukarya), based on molecular data, is currently preferred.
Both bacteria and archaea are prokaryotes. Members of the kingdoms Protista, Fungi,
Plantae, and Animalia are eukaryotes.
Phylogeneticists classify and diagram the evolutionary relationships among organisms.
They use as many characteristics as possible to put species in clades, which are
represented on portions of a diagram called a cladogram. A clade contains a most recent
common ancestor and all its descendant species, which share the same derived
characteristics relative to their ancestors.

6.0 Tutor – Marked Assignment

(1) Name the Scientists who proposed:
(a) Binomial nomenclature
(b) Five kingdom classification
(2) Name the categories above order level in a correct sequence.
(3) What is cladogram?

7.0 References/Further Readings

Buss L.W. 1987. The evolution of individuality. Princeton, New Jersey, Princeton
University Press. An original and provocative thesis on the relationship between
development and evolution, with examples drawn from many different animal phyla.

Freeman, S., and J.C. Herron. 1998. Evolutionary analysis. Upper saddle River, New
Jersey, Prentice-Hall. An introductory textbook on evolutionary biology designed for
undergraduate biology majors.

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Gould, S.J. 1989. Wonderful life: the Burgess Shale and the nature of history. New York,
W.W. Norton & Company. An insightful discussion of what fossils tell us about the
nature of life’s evolutionary history.

Hartl, D. L., and A.G. Clark. 1997. Principles of population genetics. Sunderland,
Massachusetts, Sinateur Associates. A current textbook on population genetics.

www.mhhe.com/zoology

www.mcgraw.com

http://www.ucmp.berkeley.edu/help/taxaform.html

http://www.ucmp.berkeley.edu/phyla/metazoamm.html

http://www.ucmp.berkeley.edu/plants/plantaemm.html

http://www.ucmp.berkeley.edu/chromista/chromista.html

http://www.ucmp.berkeley.edu/alllife/eukaryotasy.html

http://www.ucmp.berkeley.edu/fungi/fungi.html

http://www.ucmp.berkeley.edu/alllife/virus.html

http://www.ucmp.berkeley.edu/archaea/archaea.html

http://www.ucmp.berkeley.edu/bacteria/bacteria.html

http://www.mansfield.ohio-state.edu/~sabedon/biol3008.htm

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UNIT 4: GEOLOGICAL TIME AND EPOCH

CONTENTS

1.0 Introduction
2.0 Objectives
3.0 Main contents
3.1 Geological time scale

4.0 Conclusion

5.0 Summary

6.0 Tutor-Marked Assignment

7.0 References/Further Readings

1.0 Introduction

Long before the earth’s age was known, geologists divided its history into a table of succeeding
events based on the ordered layers of sedimentary rock. Geologists found that they needed some
scheme by which to classify time (geological variety). In the 19th Century, fossils were becoming
increasing important for correlating rock units, but they were also useful for determining time.
Organisms evolved and died off. If you could determine their relative ages, you could start to age
(relatively) the rocks that contained them.

2.0 Objectives

At the end of this unit, students should be able to:

- Explain geological time scale

- Explain epoch

3.0 Main content

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3.1 Geological time scale

As a result of studying strata, scientists have divided Earth’s history into eras, and then periods and
epochs (Table 3.1). The largest divisions are Eons. To 19th Century geologists, the rocks could be
broken up into 2 divisions 1) those containing visible signs of life (e.g., fossils) and those devoid of
life (e.g., pre-fossils).; the Phanerozoic (“visible life; 544 Million years to the present) and the
Proterozic (before life; up to 544 Million years). Some Proterozoic rocks did in fact contain primitive
life (bacteria and later on soft-tissued organisms), but not beasties that produced skeletal remains. The
Proterozoic is now defined as a specific interval of time (2.5 billion years to 544 million years). Two
additional Eras have been added to the Geological Time Scale; the Archean (4.0 to 2.5 billion years)
and the Hadean (4.5 to 4.0 billion years).

Table 3. 5: Division of earth’s history

Eon Era Time

Phanerozoic Cenozoic 65 MA to 0 MA

Mesozoic 245 MA to 65 MA

Paleozoic 550 MA to 245 MA

Proterozoic Neoproterozoic 900 MA to 550 Ma

Mesoproterozoic 1.6 GA to 900 MA

Paleoproterozoic 2.5 GA to 1.6 GA

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Archean 3.96 Ga to 2.5 Ga

Hadean 4.6 Ga to 3.96 Ga

Table 3.6: The Geological Time Scale

Era Period Epoch

Cenozoic Quaternary Holocene (0 to 10 Ka)

(0 to 65 Ma) (0 to 2 Ma)

Pleistocene (10 Ka to 2 Ma)

Tertiary Pliocene (2 Ma to 5 Ma)

(2 MA to 65 Ma) Miocene (5 Ma to 24 Ma

Oligocene (24 Ma – 37Ma)

Eocene (37 Ma to 58 Ma)

Paleocene (58 to 65 Ma)

Mesozoic Cretaceous

(65 to 245 Ma) (65 to 144 Ma) Lots of

Epochs in

Jurassic All

(144 to 208 Ma) Periods

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 Triassic

(208 to 245 Ma)

Paleozoic Permian

(245 to 544 Ma) (245 to 286 Ma)

Pennsylvanian

(286 to 320 Ma)

Mississippian

(320 to 362 Ma)

Devonian

(362 to 418 Ma)

Silurian

(418 to 441 Ma)

Ordovician

(441 to 505 Ma)

Cambrian

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 (505 to 550 Ma)

Neoproterozoic Ediacarin

(600 to 550 Ma)

Cryogenian

(850 to 600 Ma)

The use of fossils for dating rocks was of course limited to those rocks which contained

fossils (i.e., mostly the Phanerozoic). Since there were lots of different fossils that came

and went, it seemed logical to break the Phanerozoic up into smaller divisions called

Eras. Three Paleozoic Eras are recognized:

Cenozoic (0 to 65 million years BP)

Mesozoic (65 to 245 million years BP)

Paleozoic (245 to 544 million years BP)

The Eras are further subdivided into smaller Periods and the Periods can be further

subdivided into Epochs. The best way of illustrating this is to show you how these

subdivisions work for the Phanerozoic and the latest portion of the Proterozoic

(neoproterozoic). That occurs on the next page. The names used (e.g., Devonian) come

from specific localities (usually in Europe) where especially well exposed rocks of that

particular division are well exposed. You will also note that there are dates assigned to

each division. These are absolute dates based upon radiometric dating of materials within

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certain rocks. The dates are regularly modified if better radiometric analyses are developed. But the
divisions themselves are fixed. They represent major changes in the fossil record. For example, the
boundary between the Mesozoic and Cenozoic Eras (65 Ma) represents a major extinction event (the
dinosaurs all died off). The boundary between the Paleozoic and Mesozoic (245 Ma) represents an
even bigger extinction. Radiometric dating puts an absolute date on the geological divisions, but the
divisions are largely paleontological in nature.

4.0 Conclusion

In this unit you have leant about the geological time scale. This knowledge will facilitate the
understanding of the subsequent study units in this module.

5.0 Summary

Geological time is unlike normal time, it is broken up into manageable bits. The largest divisions are
Eons. The use of fossils for dating rocks was of course limited to those rocks which contained fossils
(i.e., mostly the Phanerozoic). Since there were lots of different fossils that came and went, it seemed
logical to break the Phanerozoic* up into smaller divisions called Eras. The Eras are further
subdivided into smaller Periods and the Periods can be further subdivided into Epochs.

6.0 TUTOR – MARKED ASSIGMENT

1. What is Eon?
2. List all the division of Era

7.0 REFERENCES/FURTHER READINGS

Buss L.W. 1987. The evolution of individuality. Princeton, New Jersey, Princeton University Press.
An original and provocative thesis on the relationship between development and evolution, with
examples drawn from many different animal phyla.

Freeman, S., and J.C. Herron. 1998. Evolutionary analysis. Upper saddle River, New Jersey, Prentice-
Hall. An introductory textbook on evolutionary biology designed for undergraduate biology majors.

285
Gould, S.J. 1989. Wonderful life: the Burgess Shale and the nature of history. New York, W.W.
Norton & Company. An insightful discussion of what fossils tell us about the nature of life’s
evolutionary history.

www.mhhe.com/zoology

www.mcgraw.com

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UNIT 5: EVOLUTION OF THE PLANTS

CONTENTS

1.0 Introduction
2.0 Objectives
3.0 Main contents
3.1 Plant Evolution
3.2 Multicellular plant
3.2.1 Non vascular plants
3.2.2 The evolution of vascular plants
3.2.3 Tracheophytes: The vascular plants
3.2.4 Seedless vascular plants
3.2.5 Evolution of seed plants
3.2.6 Gymnosperms
3.2.7 Rise of the Angiosperms
3.3 Plant Adaptations of life on land
3.3.1 Mineral Absorption
3.3.2 Water conservation
3.3.3 Reproduction on Land
3.4 Role of Oxygen

4.0 Conclusion

5.0 Summary

6.0 Tutor-Marked Assignment

7.0 References/Further Readings

1.0 Introduction

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 In the history of life on Earth, one of the most revolutionary events was the colonization of land,
first by plants, then by animals. Fossil and biochemical evidence indicates plants are descended
from multicellular green algae. Algae dominated the oceans of the precambrian time over 700
million years ago. The evolution of plants has resulted in increasing levels of complexity, from the
earliest algal mats, through bryophytes, lycopods, ferns to the complex gymnosperms and
angiosperms of today. While the groups which appeared earlier continue to thrive, especially in the
environments in which they evolved, each new grade of organization has eventually become more
"successful" than its predecessors by most measures. Between 500 and 400 million years ago, some
algae made the transition to land, becoming plants by developing a series of adaptations to help
them survive out of the water.

2.0 Objectives

At the end of this unit, student should be able to:

- Explain plant evolution , multicellular development, rise of angiosperms and role of

oxygen
3.0 Main Content

3.1 Plant Evolution

Land plants evolved from chlorophyte algae, perhaps as early as 510 million years ago; some
molecular estimates place their origin even earlier, as much as 630 million years ago. Their closest
living relatives are the charophytes, specifically Charales; assuming that the Charales' habit has
changed little since the divergence of lineages, this means that the land plants evolved from a
branched, filamentous, alga.

Plants were not the first photosynthesisers on land, though: consideration of weathering rates
suggests that organisms were already living on the land 1,200 million years ago.

The first evidence of plants on land comes from spores of Mid-Ordovician age (early Llanvirn, ~470
million years ago). These spores, known as cryptospores, were produced either singly (monads), in
pairs (diads) or groups of four (tetrads), and their microstructure resembles that of modern liverwort
spores, suggesting they share an equivalent grade of organisation.

Four key evolutionary innovations serve to trace the evolution of the plant kingdom

1. Alternation of generations

Plants developed a more dominant diploid phase of the life cycle

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2. Vascular tissue

Transports water and nutrients throughout the plant body, Thus plants were able to grow larger and in
drier conditions

3. Seeds

Protected the embryo, thus allowing plants to dominate their terrestrial environments

4. Flowers and fruits

3.2 Multicellular plant

All seed plants are derived from a single common ancestor. The plant kingdom contains multicellular
phototrophs that usually live on land. The earliest plant fossils are from terrestrial deposits, although
some plants have since returned to the water. All plant cells have a cell wall containing the
carbohydrate cellulose, and often have plastids in their cytoplasm. The plant life cycle has an
alternation between haploid (gametophyte) and diploid (sporophyte) generations. There are more than
300,000 living species of plants known, as well as an extensive fossil record.

Plants divide into two groups: plants lacking lignin-impregnated conducting cells (the
nonvascular plants) and those containing lignin-impregnated conducting cells (the vascular
plants). Living groups of nonvascular plants include the bryophytes: liverworts, hornworts,
and mosses.

There are five living phyla.

Four are gymnosperms, ovules not completely enclosed by sporophyte at time of pollination.

Fifth is angiosperms, ovules completely enclosed by a vessel of

sporophyte tissue, the carpel, at time of pollination

All multicellular plants have a life cycle comprising two generations or phases. One is termed the
gametophyte, has a single set of chromosomes (denoted 1N), and produces gametes (sperm and eggs).
The other is termed the sporophyte, has paired chromosomes (denoted 2N), and produces spores. The
gametophyte and sporophyte may appear identical – homomorphy – or may be very different –
heteromorphy.

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The pattern in plant evolution has been a shift from homomorphy to heteromorphy. All land plants
(i.e. embryophytes) are diplobiontic – that is, both the haploid and diploid stages are multicellular.
Two trends are apparent: bryophytes (liverworts, mosses and hornworts) have developed the
gametophyte, with the sporophyte becoming almost entirely dependent on it; vascular plants have
developed the sporophyte, with the gametophyte being particularly reduced in the seed plants.

There are two competing theories to explain the appearance of a diplobiontic lifecycle.

The interpolation theory (also known as the antithetic or intercalary theory). This theory implies that
the first sporophytes bore a very different morphology that the gametophyte they depended on. This
seems to fit well with what we know of the bryophytes, in which a vegetative thalloid gametophyte is
parasitised by simple sporophytes, which often comprise no more than a sporangium on a stalk.
Increasing complexity of the ancestrally simple sporophyte, including the eventual acquisition of
photosynthetic cells, would free it from its dependence on a gametophyte, as we see in some
hornworts (Anthoceros), and eventually result in the sporophyte developing organs and vascular
tissue, and becoming the dominant phase, as in the tracheophytes (vascular plants). This theory may
be supported by observations that smaller Cooksonia individuals must have been supported by a
gametophyte generation. The observed appearance of larger axial sizes, with room for photosynthetic
tissue and thus self-sustainability, provides a possible route for the development of a self-sufficient
sporophyte phase.

The alternative hypothesis is termed the transformation theory (or homologous theory). This explains
the behaviour of some algae, which produce alternating phases of identical sporophytes and
gametophytes. Subsequent adaption to the desiccating land environment, which makes sexual
reproduction difficult, would result in the simplification of the sexually active gametophyte, and
elaboration of the sporophyte phase to better disperse the waterproof spores. The tissue of sporophytes
and gametophytes preserved in the Rhynie chert is of similar complexity, which is taken to support
this hypothesis.

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Fig.3.13: The evolution of plants

3.2.1 Nonvascular Plants

Only two phyla of living plants lack a vascular system

Liverworts (Phylum Hepaticophyta) (The simplest of all living plants)

Hornworts (Phylum Anthocerophyta)

Mosses (Phylum Bryophyta) were the first plants to evolve strands of specialized conduction cells.
The conducting cells do not have specialized wall thickenings. Thus, a primitive vascular system, at
the most

291
Fig 3.14: Hair-cup moss, Polytrichum

Bryophytes

Bryophytes are small, nonvascular plants that first evolved approximately 500 million years
ago. The earliest land plants were most likely bryophytes. Bryophytes lack vascular tissue
and have life cycles dominated by the gametophyte phase. The lack of conducting cells limits
the size of the plants, generally keeping them under 5 inches high. Roots are absent in
bryophytes, instead there are root-like structures known as rhizoids. Bryophytes include the
hornworts, liverworts, and mosses.

3.2.2 The Evolution of Vascular plant

The first vascular plant appeared approximately 430 million years ago (mya), Early plants became
successful colonizers of land through the development of vascular tissue, efficient water-and food-
conducting system. Vascular plants are the more common plants like pines, ferns, corn, and oaks.

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Fig. 3.15: The vascular system of a leaf

Vascular plants first developed during the Silurian Period, about 400 million years ago. The
earliest vascular plants had no roots, leaves, fruits, or flowers, and reproduced by producing
spores.

Cooksonia, is a typical early vascular plant. It was less than 15 cm tall, with stems that
dichotomously branched. Dichotomous branching (where the stem divides into two ewqual
branches) appears a primitive or ancestral trait in vascular plants. Some branches terminated
in sporangia that produced a single size of spore.

Many scientists now consider "Cooksonia" an evolutionary grade rather than a true
monophyletic taxon. Their main argument is that not all stems of Cooksonia-type plants have
vascular tissue. The evolutionary situation of a grade would have some members of the group
having the trait, others not. The shapes of sporangia on various specimens of Cooksonia also
vary considerably.

Rhynia, is another early vascular plant. Like Cooksonia, it lacked leaves and roots. One of the
species formerly assigned to this genus, R. major, has since been reclassified as Aglaophyton
major. Some paleobotanists consider A. major a bryophyte, however, it does have a separate
free-living sporophyte that is more prominent than the sporophyte, but appears to lack
lignified conducting cells. The remaining species, R. gwynne-vaughanii is an undoubted
vascular plant.

Devonian plant lines included the trimerophytes and zosterophyllophytes, which have been
interpreted as related to ferns and lycophytes.

The Psilophytes

The Division Psilophyta consists of Psilotum nudum, a living plant that resembling what
paleobotanists believe Cooksonia to have been: a naked, photosynthetic stem bearing
sporangia. Also in the group is Tmesipteris, which resembles Psilotum except for its
possession of smallo vascularized leaves arising on opposite sides of the stem. However,
most paleobotanists doubt that Psilotum is a direct descendant of Cooksonia. Molecular
studies suggest an affiliation with ferns for Psilotum. Psilotum also has three fused sporangia,

293
termed a synangium, located on the sides of the stems (instead of the tips of stems as in
Cooksonia).

The Lycophytes

The next group, the Division Lycophyta, have their sporangia organized into strobili
(singular: strobilus). A strobilus is a series of sporangia and modified leaves closely grouped
on a stem tip. The leaves in strobili are soft and fleshy as opposed to the hard, modified
leaves in cones.

Leaves that contained vascular tissue are another major advance for this group.The leaves in
lycophytes, both living and fossil forms, are known as microphylls. This term does not imply
any size constraint, but rather refers to the absence of a leaf gap in the vascular supply of the
stem at the point where the leaf vascular trace departs. Ferns and other plants have
megaphylls, leaves that produce this leaf gap.

Today there are fewer genera of lycophytes than during the group's heyday, the Paleozoic
Era. Major living lycophytes include Lycopodium (commonly called the club moss, although
it is NOT a moss), Isoetes, and Selaginella (the so-called resurrection plant). Lycopodium
produces isospores that germinate in the soil and produce a bisexual gametophyte. These
spores are all approximately the same size. Selaginella and Isoetes are heterosporous, and
thus produce two sizes of spores: small spores (termed microspores) that germinate to
produce the male gametophyte; and larger spores (megaspores) that germinate to produce the
female gametophyte. The production of two sizes of spores, and also making separate
unisexual gametophytes, is thought an important step toward the seed. Modern lycophytes are
small, herbaceous plants. Many of the prominent fossil members of this group produced large
amounts of wood and were significant trees in the Carboniferous-aged coal swamps.

Selaginella is a heterosporous member of the lycophytes. Some species of this genus are able
to withstand drying out by going dormant until they are rehydrated. For this reason these
forms of the genus are commonly called resurrection plants.

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Fossil Lycophytes: Baragwanathia and Drepanophycus

Baragwanathia, is an undoubted lycophyte from the middle Silurian deposits of Australia. It

has microphyllous leaves spirally attached to the stem, and sporangia clustered in some areas
of the plant, although not in terminal strobili as in modern lycophytes.

Drepanophycus is a middle Devonian lycophyte from the Northern Hemisphere. Its features
are very similar to modern lycophytes.

Lepidodendron and Sigillaria

The Lycophytes became significant elements of the world's flora during the Carboniferous
time (the Mississippian and Pennsylvanian are terms used for this time span in the United
States). These non-seed plants evolved into trees placed in the fossil genera Lepidodendron
and Sigillaria, with heights reaching up to 40 meters and 20-30 meters respectively.
Lepidodendron stems are composed of less wood (secondary xylem) that usually is found in
gymnosperm and angiosperm trees.

We know much about the anatomy of these coal-age lycopods because of an odd type of
preservation known as a coal ball. Coal balls can be peeled and the plants that are
anatomically preserved within them laboriously studied to learn the details of cell structure of
these coal age plants. Additionally, we have some exceptional petrifactions and compressions
that reveal different layers of the plants' structure. Estimates place the bulk, up to 70%, of
coal material as being derived from lycophytes.

Lepidodendron, was a heterosporous lycophyte tree common in coal swamps of the

Carboniferous time. As with many large plant fossils, one rarely if ever finds the entire tree
preserved intact. Consequently there are a number of fossil plant genera that are "organ taxa"
and represent only the leaves (such as Lepidophylloides), reproductive structures
(Lepidostrobus), stem (Lepidodendron), spores (Lycospora), and roots (Stigmaria).
Lepidodendron had leaves borne spirally on branches that dichotomously forked, with roots
also arising spirally from the stigmarian axes, and both small (microspores) and large
(megaspores) formed in strobili (a loose type of soft cone). Lepidodendron may have attained
heigths of nearly 40 meters, with trunks nearly 2 meters in diameter. The trees branched

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extensively and produced a large number of leaves. When these leaves fell from the branches,
they left behind them the leaf scars characteristic of the genus.

Sigillaria was another arborescent lycopod, and is also common in coal-age deposits. In
contrast to the spirally borne leaves of Lepidodendron, Sigillaria had leaved arranged in
vertical rows along the stem.

The Sphenophyta

The Division Sphenophyta contains once dominant plants (both arborescent as well as
herbaceous) in Paleozoic forests, equisetophytes are today relegated to minor roles as
herbaceous plants. Today only a single genus, Equisetum, survives. The group is defined by
their jointed stems, with many leaves being produced at a node, production of isospores in
cones borne at the tips of stems, and spores bearing elaters (devices to aid in spore dispersal).
The gametophyte is small, bisexual, photosynthetic, and free-living. Silica concentrated in the
stems give this group one of their common names: scouring rushes. These plants were
reportedly used by American pioneers to scour the pots and pans. The fossil members of this
group are often encountered in coal deposits of Carboniferous age in North America and
Europe.

The Ferns

Ferns reproduce by spores from which the free-living bisexual gametophyte generation
develops. There are 12,000 species of ferns today, placed in the Division Pteridophyta. The
fossil history of ferns shows them to have been a dominant plant group during the Paleozoic
Era. Most ferns have pinnate leaves, exhibiting small leaflets on a frond, Ferns have
megaphyllous leaves, which cause a leaf gap in the vascular cylinder of the stem/rhizome.
The first ferns also appear by the end of the Devonian. Some anatomical similarities suggest
that ferns and sphenophytes may have shared a common ancestor within the trimerophytes.

3.2.3 Tracheophytes: The Vascular Plants

The vascular plants have specialized transporting cells xylem (for transporting water and
mineral nutrients) and phloem (for transporting sugars from leaves to the rest of the plant).

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When we think of plants we invariably picture vascular plants. Vascular plants tend to be
larger and more complex than bryophytes, and have a life cycle where the sporophyte is more
prominent than the gametophyte. Vascular plants also demonstrate increased levels of
organization by having organs and organ systems. The novel features oif the vascular plants
are summarized in Table 3.7

Table 3.7: Major evolutionary advances of the vascular plants

Advance Green Algae Bryophytes Tracheophytes

early vascular plants

nonvascularized body no vascular system are naked, rootless
Development of
(thallus) that may be vascularized stems
the root-stem-
leaflike structures are
variously shaped
leaf vascular
present, but lack any later vascular plants
system
no levaes, shoots, or roots vascular tissue develop vascularized
leaves, then roots

progressive reduction
in size and complexity
of the gametoiphyte
sporophyte generation generation, leading to
dependant on its complete
Reduction in the wide range of life cycles,
gametophyte dependance on the
size of the some gametophyte
generation for food; sporophyte for food
gametophyte dominant, others
gametophyte is free-
generation sporophyte dominant
living and in angiosperms, 3

photosynthetic celled male

gametophyte and a
(usually) 8 celled
female gametophyte

Development of seed plants retain the

seeds in some no seeds no seeds female gametophyte on
vascular plants the sporophyte

Spores/Pollen spores for Spores that germinate Spores that germinate into the

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 resisting into the gametophyte gametophyte generation or spores
environmental generation that have the gametophyte
degradation generation develop within
themselves

3.2.4 Seedless Vascular Plants

Two phyla of modern-day vascular plants lack seeds

Ferns (Phylum Pterophyta)

Club mosses (Phylum Lycophyta)

Both have free-swimming sperm that require free water for fertilization By far, the largest group are
ferns

~ 12,000 living species

3.2.5 Evolution of Seed Plants

Seeds are embryo covers that protect the embryonic plant at its most vulnerable stage.

Seed plants produce two kinds of gametophytes

1. Male gametophytes called pollen grains arise from microspores

2. Female gametophytes contains the egg develops from a megaspore produced within
an ovule

Pollination is the transfer of pollen by insects, winds Thus; there is no need for free water for
fertilization.

A seed has three parts

1. A sporophyte plant embryo

2. A source of food for the embryo called endosperm

3. A drought-resistant protective cover

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Fig. 3.16: (a) Corn and (b) Bean

Seeds have greatly improved the adaptations of plants to living on land

1. Dispersal: Facilitate migration dispersal

2. Dormancy: Postpone development until conditions are favourable

3. Germination: Permit embryonic development to be synchronized with habitat

4. Nourishment : Offer an energy source of young plants

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Fig. 3.17: Cycad

3.2.6 Gymnosperms

Gymnosperms are non flowering seed plants, they include four phyla

Conifers (Coniferophyta)

Cycads (Cycadophyta)

Gnetophytes (Gnetophyta)

Ginkgo (Ginkgophyta)

3.2.6 .1 Conifers

The most common (and familiar) of the gymnosperms include Pine, spruce, cedar, redwood and fir
trees, conifers are trees that produce their seeds in cones Seeds (ovules) develop on scales within
cones and are exposed at the time of pollination.

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Fig. 3. 18: Conifers

3.2.6.2 Cycads

Have short stems and palmlike leaves, The predominant land plant in the Jurassic Period

Fig. 3.19: Cycad

3.2.6.3 Gnetophytes

The most closely related to angiosperms, only three types of plants; all unusual, Have flagellated
sperm

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Fig. 3.20: Gnetophytes

3.2.6.4 Ginkgo

Only one living species exists; The maidenhair tree, Ginkgo biloba

Resistant to air pollution, reproductive structures found on different trees and have flagellated sperm.

Fig. 3.20: Ginkgo

3.2.7 Rise of the Angiosperms

Angiosperms comprise 90% of all living plants > 300,000 species, virtually all our food is derived,
directly or indirectly from them

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In gymnosperm reproduction, pollen grains are carried passively by the wind

Angiosperms have evolved more direct way of transferring pollen

Induce animals to carry it for them

Flowers are the reproductive organs of angiosperms , A flower employs bright colors to attract insects
and nectar, to induce the insects to enter the flower, there they are coated with pollen grains, which
they carry with them to other flowers

Fig. 3.22: flower (a and b)

3.2.7.1 Flower

A flower consists of four concentric circles, or whorls, connected to a base called the receptacle,
outermost whorl (Sepals), protects flower from physical damage, Second whorl (Petals) attracts
pollinators, Third whorl (Stamens) produces pollen grains in the anther, Innermost whorl (Carpel)

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produces eggs in the ovary, Rising from the ovary, is a slender stalk, the style, with a sticky tip, the
stigma

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3.2.7.2 Fruits
A fruit is a mature ripened ovary containing fertilized seeds, fruits aid in the dispersal of seeds to new
habitats

Fig. 3.23: Different ways of dispersing fruit

Flowers protected the egg and improved the odds of its fertilization

Fruits surrounded the seeds and aided in their dispersal

3.3 Plant Adaptations to Life on Land

Organisms in water do not face many of the challenges that terrestrial creatures do. Water supports the
organism; the moist surface of the creature is a superb surface for gas exchange, etc. Approximately
288,700 species of plants are now in existence and most of them are terrestrial

However, green algae, the likely ancestors of plants, are aquatic and not well adapted to living on land

Three major challenges had to be overcome

1. Mineral absorption

2. Water conservation

3. Reproduction on land

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3.3.1 Mineral Absorption

Plants require relatively large amounts of six inorganic minerals; Nitrogen, potassium, calcium,
phosphorus, magnesium and sulphur. Plants absorb these materials through their roots

The first plants developed symbiotic associations with fungi, and these mycorrhizae enabled plants to
extract minerals from rocky soil

3.3.2 Water Conservation

To avoid drying out, plants have a watertight outer covering, termed the cuticle Stomata (singular,
stoma) are pores in the cuticle that allow gas and vapor exchange

Fig 3.24: stoma and cuticle

Regulate opening and closing of the stoma

3.3.3 Reproduction on Land

Spores developed as a means to protect gametes from drying out on land in a plant life cycle, there is
alternation of generations Diploid with haploid

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Fig. 3.25 Generalized plant life cycle

The diploid generation is called the sporophyte and the haploid generation is called the gametophyte.
As plants evolved, the sporophyte tissue dominated

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Fig. 3.26: Two types of gametophytes

3.4 Role of Oxygen

As we all know that oxygen is very important not only to animal but also plant. Oxygen plays
many important roles but in this course we are going to look at the role it play in the
respiration of plant.

Two most important prerequisites of life are continuous supply of materials for growth of
body and energy for carrying out various life processes. All systems, from cell to ecosystem,
require energy to work. However, the energy in the food has to be made available to the cells
in a usable form. This is the role of respiration. Respiration is the process by which energy in
organic molecules is released by oxidation. This energy is made available to the living cells
in the form of ATP (Adenosine Tri Phosphate). The O2 required for respiration is obtained
from the atmosphere. ATP is the energy currency of the cell.

Respiration: Respiration is the stepwise oxidation of complex organic molecules and release
of energy as ATP for various cellular metabolic activities. Respiration involves exchange of
gases between the organism and the external environment. The plants obtain oxygen from
their environment and return carbon dioxide and water vapour into it.

The biochemical process, which occurs within cells and oxides food to obtain energy, is
known as cellular respiration. The processes by which cells obtain energy from complex food
molecules depend upon whether or not oxygen is present in their environment and utilised.
Respiration is termed aerobic when oxygen is utilised. In aerobic respiration the respiration
are followed by an oxygen requiring process that releases much larger quantity of energy in
the form of ATP. This occurs in the mitochondria of the eukaryotes and in the plasma
membrane of the prokaryotes.

The rate of respiration increases with rise in oxygen concentration. As O2 concentration

increases from Zero, the rate of respiration increases. However, beyond a limit the rate of
increase falls.

In plants, the atmospheric air moves in an out by simple diffusion that takes place through

a) The general body surface of the (stains, roots, fruits and seeds);
b) Lenticels (openings in the bark of the tree trunk)
c) Stomata present in the leaves and young stems.

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From the atmosphere gases enter the intercellular spaces inside the plants. As o2 is utilized,
more of it diffuses into the plant. Since co2 is being continuously formed, its concentration
result in tissue spaces becomes higher than in the surrounding air. As a result, it diffuses out
of the plant, especially when it is being used for photosynthesis.

In plants, o2 released during photosynthesis in day time is made available for respiration.
However, rate of photosynthesis is greater than that of respiration. Thus, plants give out
excess o2 in the daytime.

Oxygen that is absorbed is used to oxidize the nutrient, viz; glucose, amino acids and fatty
acids completely producing co2, water and energy. It occurs within the cells and tissues.
Further oxidation of pyruvic acid requires o2. It then enters mitochondria for aerobic
respiration.

4.0 Conclusion

In this unit you learnt:

1. About evolution of the plants

2. About nonvascular and vascular plant
3. About multicellular development
4. Role of oxygen

5.0 Summary

All seed plants are derived from a single common ancestor. The plant kingdom contains multicellular
phototrophs that usually live on land and all plant cells have a cell wall containing the carbohydrate
cellulose, and often have plastids in their cytoplasm. The plant life cycle has an alternation between
haploid (gametophyte) and diploid (sporophyte) generations. There are more than 300,000 living
species of plants known, as well as an extensive fossil record.

Plants divide into two groups: plants lacking lignin-impregnated conducting cells (the
nonvascular plants) and those containing lignin-impregnated conducting cells (the vascular
plants). Living groups of nonvascular plants include the bryophytes: liverworts, hornworts,
and mosses. Water supports the organism; the moist surface of the creature is a superb
surface for gas exchange, etc.

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6.0 TUTOR-MARKED ASSIGNMENT
1. List four key evolutionary innovations serve to trace the evolution of the plant kingdom
2. List four phyla of non flowering seed plant
3. What are the important of xylem and phloem

7.0 REFERENCES/FURTHER READINGS

Labandeira, C. (2007). "The origin of herbivory on land: Initial patterns of plant tissue
consumption by arthropods". Insect Science 14 (4): 259–275. doi:10.1111/j.1744-
7917.2007.00152.x.
"The oldest fossils reveal evolution of non-vascular plants by the middle to late Ordovician Period
(~450-440 m.y.a.) on the basis of fossil spores" Transition of plants to land

Haines, Tim. 2000. Walking with Dinosaurs: A Natural History, (New York: Dorling Kindersley
Publishing, Inc.) ISBN 0-563-38449-2. Page 65.

Behrensmeyer, Anna K., Damuth, J.D., DiMichele, W.A., Potts, R., Sues, H.D. & Wing, S.L. (eds.).
1992. Terrestrial Ecosystems through Time: the Evolutionary Paleoecology of Terrestrial Plants and
Animals, (Chicago & London: University of Chicago Press), ISBN 0-226-04154-9 (cloth), ISBN 0-
226-04155-7 (paper). Page 349.

Butterfield, N. J. (Jan 2009). "Oxygen, animals and oceanic ventilation: an alternative view".
Geobiology 7 (1): 1–7. doi:10.1111/j.1472-4669.2009.00188.x. ISSN 1472-4677. PMID 19200141.
edit

Steemans, P.; Hérissé, L.; Melvin, J.; Miller, A.; Paris, F.; Verniers, J.; Wellman, H. (Apr 2009).
"Origin and Radiation of the Earliest Vascular Land Plants". Science 324 (5925): 353–353. Bibcode
2009Sci...324..353S. doi:10.1126/science.1169659. ISSN 0036-8075. PMID 19372423. edit

omescu, A. M. F.; Rothwell, G. W. (2006). "Wetlands before tracheophytes: Thalloid terrestrial

communities of the Early Silurian Passage Creek biota (Virginia)". Wetlands Through Time.
doi:10.1130/2006.2399(02). ISBN 9780813723990.
http://www.humboldt.edu/biosci/docs/faculty/TomescuRothwell2006.pdf. Retrieved 2011-02-22. edit

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Tomescu, A. M. F.; Honegger, R.; Rothwell, G. W. (2008). "Earliest fossil record of bacterial–
cyanobacterial mat consortia: the early Silurian Passage Creek biota (440 Ma, Virginia, USA)".
Geobiology 6 (2): 120. doi:10.1111/j.1472-4669.2007.00143.x. PMID 18380874. edit

Scott, C.; Glasspool, J. (Jul 2006). "The diversification of Paleozoic fire systems and fluctuations in
atmospheric oxygen concentration" (Free full text). Proceedings of the National Academy of Sciences
of the United States of America 103 (29): 10861–10865. Bibcode 2006PNAS..10310861S.
doi:10.1073/pnas.0604090103. ISSN 0027-8424. PMC 1544139. PMID 16832054.
http://www.pnas.org/cgi/pmidlookup?view=long&pmid=16832054. edit

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