INTRODUCTION TO SYSTEMATICS

Systematics • Presented by Mayr, Linsley and Usinger in

METHODS AND PRINCIPLES OF
• Science of biological classification SYSTEMATIC ZOOLOGY (1953)
• Embodies the study of organic diversity and • With strongly paleontological view of systematic
provides the comparative framework to study biology but closely associated with evolutionary
the historical aspects of evolution. taxonomy, discussed by G.G. SIMPSON (1961)
• Systematics plays a central role in biology by in PRINCIPLES OF ANIMAL TAXONOMY
providing the means for characterizing the • The most steadfastly defended tenet of
organisms that we study. classical evolutionary taxonomy, was the
• Through the production of classifications that approach advocated by MAYR and SIMPSON --
reflect evolutionary relationships it also allows - that Biological Classifications must portray the
predictions and testable hypotheses. maximum amount of evolutionary information
History Phenetic Point of View
• Plato and Aristotle’s detailed observations of • Extreme empiricists who propounded on the
animals have great scientific value which were quantitative approach of taxonomy in the late
rediscovered in the Middle Ages that had been 1950s like SOKAL, SNEATH, CAIN,
distributed and translated into Latin and Arabic HARRISON, ROHLF, EHRLICH
• 16th century Italian physician Andreas • They moved for taxonomy to be objective and
Caesalpino and 17th century English naturalist operational with the ultimate goal being to
John Ray along with the works of Swedish produce general purpose classifications in
botanist Carolus Linnaeus practiced the which relationships among groups of
beginnings of Systematics. organisms are formed on the BASIS OF
OVERALL SIMILARITY
Three basic fundamental activities of • GILMOUR (1940) stated that a natural
Systematics classification is not one that expresses
1. Recognition of basic units of biological diversity phylogeny, but a classification that groups
in nature taxa to reflect the greatest overall
correspondence of features among the
• SPECIES – often recognized on the basis of
morphological and other characteristics organisms classified.
observable during Linnaeus time. • Pheneticists assess this correspondence by
2. Classification of those species in a hierarchic overall similarity, an approach initially called
scheme as Numerical Taxonomy (the term phenetic was
• Reflects our understanding of their introduced by Mayr in 1965)
phylogenetic relationships – Phylogenetic (Cladistic) Point of View
• Introduction of Darwinian theory of organic
evolution explained some observed • Entomologist HENNIG (1966) believed that “the
relationships among organisms which task of Systematics is the creation of a general
resulted to some evolutionary processes reference system and the investigation of the
3. Placement of information about species and relations that extend from it to all other possible
their classification in a broader context and necessary systems in Biology”
• Uses material data from other disciplines • This Hennig’s idea of classification is intended
that has taxonomic significance to reflect genealogical (relating to the study or
• Morpho-anatomy, ecology, biogeography, tracing of lines of family descent) relationships
developmental biology, physiology, based on SPECIAL SIMILARITY and that
genetics, biochemistry, molecular biology these relationships should be reflected in a
formal hierarchic listing.
Schools of Taxonomy: Development of Taxonomy • SPECIAL SIMILARITY (i.e., shared derived
in the 20th century characters)
• The fundamental challenge of taxonomy is the • Uses terms such as SYNAPOMORPHY,
management and interpretation of vast amounts groupings based solely on shared special
of potentially conflicting information: similarity
• WHICH ORGANISMAL FEATURES ARE How Evolutionary Taxonomy, Phenetics and
IMPORTANT AS EVIDENCE OF GROUPING, Cladistics Differ
WHICH ARE NOT?
• By the 1930’s, nearly all biologists agreed that • These schools of thought differ in answering
an ideal classification should reflect the one fundamental question in systematics:
historical pattern of evolutionary divergence, • WHAT TYPE OF INFORMATION IS COUNTED
generally referred to as PHYLOGENY AS EVIDENCE OF GROUPING?
• Phenetic groups are those with the highest
Phylogeny similarity scores, regardless of whether the
• The representation of the evolutionary history similarities are due to shared changes or
and relationships between groups of organisms. shared lack of change.
• The results are represented in a phylogenetic • Cladists count character-state transformations,
tree that provides a visual output of forming groups of those taxa united by the
relationships based on shared or divergent greatest number of shared transformations.
physical and genetic characteristics. • Evolutionary taxonomists also group taxa based
on character state transformations, except
Evolutionary Taxonomic Point of View
 sometimes they choose to ignore these data in any level (if they are recognizably distinct), it
favor of phenetic similarity. form valid units for systematic analyses.
• Taxa bear CHARACTERS, and it is by these
Two types of approaches to Biological attributes that they are recognized
Classification are recognized… (diagnosed/defined)
• It is the characters that are usually viewed as
the data of systematics or “the material basis of
systematics”
• Diagnosis of species is not always clear cut and
may take on a subjective quality! (BIASES MAY
BE FORMED BY INEXPERIENCED
TAXONOMISTS)

Sensu lato vs. Sensu stricto

Taxonomy, the science of classifying and naming

living organisms, plays a crucial role in
understanding the vast diversity of life on Earth. It
provides a framework for organizing species into
hierarchical groups based on their shared
characteristics and evolutionary relationships.

• Those that treat overall similarity as important in • “Sensu lato" and "sensu stricto" are Latin terms
group recognition; and, used in taxonomy and scientific classification to
• Those that group by special similarity alone. indicate broader or narrower concepts of a
• A phenetic classification system relies upon the taxonomic group.
phenotypes or physical appearances of • Sensu Lato:
organisms
• Phylogenetic classification uses evolutionary Sensu lato
relationships of organisms.
• “Sensu lato” means "in the broad sense" or "in
We then clarify TAXONOMY and SYSTEMATICS - the wider sense."
as discussed by G.G. Simpson (1961) • It is used to refer to a taxonomic concept that
includes a broader range of species or
• Taxonomy – the theoretical study of organisms.
classification including its bases, principles, • When a taxon is referred to sensu lato, it
procedures, and rules. implies that it encompasses not only the core or
• Systematics – the scientific study of the kinds typical members of the group but also related
and diversity of organism and of any and all taxa that are closely related but may exhibit
relationships among them. some variations or differences.
• As Simpson’s definition suggest, systematics • In sensu lato classification, the boundaries of
has often been used as the more inclusive the taxonomic group are expanded to
term, with taxonomy and classification accommodate these variations.
subsumed within it. • Ex. let's consider the genus Canis, which
• In contrast, others have argued that the terms includes species like Canis lupus (gray wolf),
are synonymous, that systematics is the term Canis familiaris (domestic dog), Canis latrans
having historical precedence and that taxonomy (coyote), and others. If we refer to Canis sensu
should therefore be supplanted. lato, it would mean that we are considering the
• However, Systematics is the most STRONGLY entire genus Canis, including all its species and
COMPARATIVE of all of the biological sciences possible variations.
and its methods and principles transcend the • Ex. Consider the genus Panthera, which
differences between botany and zoology. includes species like Panthera leo (lion),
- is the most strongly HISTORICAL Panthera tigris (tiger), Panthera pardus
subdiscipline within Biology and as such (leopard), and Panthera onca (jaguar). If we
provides the basis for nearly all inferences refer to Panthera sensu lato, it means that we
concerning historical relationships. are considering the entire genus Panthera,
- is directly comparable to historical including all its species and possible variations.
Geology and finds integration in
Paleontology Sensu Stricto:

The Unit of Systematics • "Sensu stricto" means "in the strict sense" or "in
the narrower sense."
• TAXON (pl. TAXA) – in its broad sense (sensu • It is used to refer to a taxonomic concept that
lato), basic unit of Systematics includes a narrower or more restricted range of
• May also refer to a grouping of organism at any species or organisms.
level in the systematic hierarchy, BUT • When a taxon is referred to sensu stricto, it
PERTAINS MORE ON THE SPECIES rank (in implies that it only includes the core or typical
its stricter sense or sensu stricto, the basic unit members of the group, excluding any related
of Systematics is the SPECIES) taxa that may show variations or differences.
• Systematists deal with recognizable or • Ex. Continuing with the previous example, if we
diagnosable taxa, be they at the minimum level refer to Canis sensu stricto, it would mean that
(usually called Species) or at some more we are considering only the core species of the
inclusive level. Whatever they are called taxa at genus Canis, such as Canis lupus (gray wolf)
and excluding other related species like Canis
 familiaris (domestic dog) or Canis latrans ultrastructure and karyology, paleontology,
(coyote). ecology, geography, biochemistry, physiology,
• Let's take the genus Felis, which includes genetics, and molecular biology.
species like Felis catus (domestic cat), Felis • It provides the scientific basis for defining or
chaus (jungle cat), Felis lybica (African wildcat), delimiting species and infraspecific taxa and for
and others. If we refer to Felis sensu stricto, it establishing that these are distinct from other,
means that we are considering only the core closely related and similar taxa. Such studies
species of the genus Felis, such as Felis catus are important in CONSERVATION BIOLOGY, in
(domestic cat), and excluding other related order to determine if a species is rare or
species like Felis chaus (jungle cat) or Felis endangered and warrants protection.
lybica (African wildcat). • It provides an understanding as well of the
history of evolution and geography that may aid
Summary in conservation and management decisions
where priorities must be set as to which regions
• "sensu lato" refers to a broader concept that to preserve.
includes related taxa and variations, while
• The study of systematics, also known as
"sensu stricto" refers to a narrower concept that
biological classification or phylogenetics, holds
includes only the core members of a taxonomic
immense significance in the field of biology. It
group, excluding related taxa or variations.
involves the classification of organisms into
These terms help clarify the extent of inclusion
taxonomic groups and the exploration of their
when discussing taxonomic groups.
evolutionary relationships. By investigating the
• The differentiation between sensu lato and diversity of life on Earth and deciphering the
sensu stricto can have practical implications in intricate patterns of evolutionary history,
conservation and management efforts. By systematics provides a fundamental framework
precisely defining the boundaries of a for understanding the natural world.
taxonomic group, conservationists can identify
• Understanding Biodiversity: Systematics
specific species or populations that require
allows us to comprehend the immense diversity
targeted conservation strategies.
of life on Earth. By organizing organisms into
Systematic Literature taxonomic groups and documenting their
characteristics, systematics provides a
• Descriptive works – monographs or revisions; comprehensive framework for studying and
largely descriptive; may be in the form of a cataloging the vast array of species. It helps us
handbook, field guide, flora or fauna appreciate the richness of life and enables the
• Catalogs and Checklists – e.g. Index Kewensis; identification and description of new species.
Global Biodiversity Information Facility, 2007 • Reconstructing Evolutionary History:
• Theoretical Literature – e.g. Systematic Biology, Systematics allows us to reconstruct the
Cladistics, Taxon and other scientific systematic evolutionary history of organisms. By analyzing
journals ■ Abstracting and Indexing Sources – similarities and differences in their anatomical
biological abstracts, bibliographies features, genetic information, and other traits,
• Resources on the Internet – Tree of Life web scientists can infer how species are related and
project by Maddison and Schultz, 1996- 2008; trace their evolutionary lineages. This
TreeBASE; National Center for Biotechnology knowledge provides insights into the processes
Information; Integrated Taxonomic Information that have shaped life on our planet.
System, Discover Life with nomenclatural info, • Informing Conservation Efforts: Systematics
images, keys, etc. plays a crucial role in conservation biology. By
• Textbooks – Hennig’s Phylogenetic Systematics understanding the evolutionary relationships
(1966); M. Simpson’s Plant Systematics (2010) among species and their distributions,
researchers can identify areas of high
Systematic Collections biodiversity, prioritize conservation efforts, and
make informed decisions about protecting
• Serve as repositories for specimens like threatened species and ecosystems.
museums and herbaria Systematics helps us recognize the unique
• e.g. Index Herbariorum (1974 - onwards), evolutionary lineages that may require special
global directory of herbaria and their associated conservation attention.
staff, with searchable online index which allows • Informing Agriculture and Medicine:
scientists rapid access to data related to 3,400 Systematics contributes to agricultural and
locations where a total of 350 million botanical medical advancements. By studying the
specimens are permanently housed (singular, evolutionary relationships of crop plants,
herbarium; plural, herbaria) scientists can identify wild relatives that
possess desirable traits for crop improvement,
Why study Systematics? such as disease resistance or drought
tolerance. Similarly, understanding the
• It provides a foundation of information about the
evolutionary relationships of disease-causing
tremendous diversity of life.
organisms can aid in the development of
• Systematic research is the basis for acquiring, targeted treatments and preventive measures.
cataloging and retrieving information about life’s
• Enhancing Biological Research: Systematics
diversity; in essence, DOCUMENTATION provides a foundation for various biological
through COLLECTION and STORAGE of
research fields. Whether studying ecology,
REFERENCE SPECIMENS in an accredited behavior, physiology, or other aspects of
museum/herbarium.
organisms, a solid understanding of their
• It is an integrative and unifying science utilizing evolutionary relationships is crucial for
data from all fields of Biology: morphology, designing meaningful experiments and
anatomy, embryology/development, cell interpreting results accurately. Systematics
 helps contextualize research findings within the framework for organizing and comprehending
broader evolutionary context. the complexity of life, enabling us to make
• Informing Biogeography and Climate informed decisions and address critical
Change Studies: Systematics contributes to challenges facing our planet.
the field of biogeography, which examines the
distribution of species across geographic • BIODIVERSITY HOTSPOT - a biogeographic
regions. By understanding the historical region that is both a significant reservoir of
relationships among species, scientists can biodiversity and is threatened with destruction.
explain patterns of species distribution and • It specifically refers to 25 biologically rich areas
investigate how they have been influenced by around the world.
factors such as geographic barriers, climate • To qualify as a biodiversity hotspot, a region
change, and human activities. must meet two strict criteria:
• It must contain at least 0.5% or 1,500 species
Summary of vascular plants as endemics;
• Studying systematics is vital for understanding • And it has to have lost at least 70% of its
biodiversity, reconstructing evolutionary history, primary vegetation.
informing conservation efforts, advancing • Around the world, 35 areas qualify under this
agriculture and medicine, enhancing biological definition which support nearly 60% of the
research, and exploring patterns of species world's plant, bird, mammal, reptile, and
distribution. It provides a fundamental amphibian species, with a very high number of
endemics

HISTORY AND DEVELOPMENT OF TAXONOMY AND SYSTEMATICS

SYSTEMATICS • He termed animals with blood, or much known

now as vertebrates, as Enhaima; while he
• defined as a science that includes and called Anhaima those without blood, or simply
encompasses traditional taxonomy, the the invertebrates.
description, identification, nomenclature, and
classification of organisms. THEOPHRASTUS (370-285 BC)
• Its primary goal is the reconstruction of
phylogeny (evolutionary history) of life • He was a student of Aristotle.
(Simpson,2010) • His book entitled “De Historia Plantarum” was
used for taxonomic purposes until the Middle
TAXONOMY Ages in Europe. It contained approximately 480
plant species.
• The science of taxonomy (“arrangement law”) • He classified plants based on growth form or
produces a formal system for naming and habit: Herbs, Undershrub, Shrub and Trees
grouping different species to communicate this • He was able to provide 3 plant genera:
order. Narcissus, Crocus, and Cornus
• a part of the broader science of Systematics
• studies variation among living populations that DIOSCORIDES (40-90 AD)
used to reveal their evolutionary relationships
(Hickman, et al., 2014) • His book entitled “De Materia Medica” was used
in medicine until the 16th century and copies
PRE-LINNAEAN TAXONOMY were reprinted multiple times.
EMPEROR SHEN NUNG (3000 BC) • The book has five volumes and one of its
• He was a legendary emperor known as the famous copy from the 6th century was kept
“Father of Chinese Medicine”. inVienna.
• He wanted to educate his people in agriculture • His classification of medicinal plants was based
and medicine and is said to have tasted on their medical properties
hundreds of herbs to test their medicinal value.
• His pharmacopeia Divine Husbandman’s PLINIUS (40-90 AD)
Materia Medica included 365 medicines derived
from minerals, plants, and animals. • His book, Naturalis Historia, has 160 volumes.
• He described several plants and provided them
EGYPTIANS (1500 BC) Latin names.
• He was considered as the “Father of Botanical
• Around 1500 BC medicinal plants were Latin” because of his works and died in the city
illustrated on wall paintings in Egypt. of Pompeii
• In one of the oldest and largest papyrus rolls, • e.g. Oncorhynchus kisutch
Ebers Papyrus, recorded plants are classified
as medicine for different diseases. TAXONOMY IN MEDIEVAL TIMES

ARISTOTLE (384-332 BC) • Largely based on the Aristotelian system, with

additions concerning the philosophical and
• First Greek biologist to classify organisms existential order of creatures
according to their structural similarities. • This order included concepts such as the
• The first one to classify all living things and “Great Chain of Being” in the Western
divide them into two major groups: plants & scholastic tradition
animals. • Great Chain of Being: derived from the
collective beliefs and principles of Plato,
 Aristotle (in his book Historia Animalium), • He created rules for species descriptions,
Plotinus, and Proclus terminology, and even instructions on how to
build a proper herbarium cupboard.
EARLY TAXONOMISTS • Terms like corolla, stamen, filament and anther
ANDREA CESALPINO (1583) were created by him, as well as well-known
• Considered as “The FirstTaxonomist” taxon names like Mammalia.
• De Plantis Libri XVI (1583) is considered as the
first textbook of Botany; it contained 1500 plant Systema plantarum
species.
• His plant classification was based on growth • he classified flower / flowering plants according
habit, fruits and seeds. to sexual system
• he established 24 classes (23 classes for
BAUHIN BROTHERS (1623 flowering plants & 1 for the flowerless plants)

• Johann (or Jean) and Gaspard (or Caspar) 10th edition of Systema Naturae
Bauhin
• They recognized genera and species as major • he classified animals according to morphology
taxonomic levels. of their heart and blood.
• Binomial nomenclature was partially developed • He also classified them to
by them. “viviparous/oviparous”, “Voluntary
• Pinax Theatri Botanici, a book by Gaspard lungs/external gills” and “with antennae/with
Bauhin contained 6000 plant species. tentacles”
• His classification of plants was in a manner that • He divide them into 6 classes in total:
draws comparison to the Binomial Mammalia, Aves, Amphibia, Pisces, Insecta,
nomenclature of Linnaeus. and Vermes.

JOHN RAY (1682) MAMMALIA

• He established “species” as the ultimate unit of • Divided based upon the number, situation, and
taxonomy. structure of their teeth
• His work Methodus Plantarum Nova has • “Animals that suckle their young by means of
approximately 18,000 plant species. lactiferous teats. In external and internal
• His complicated classification was based on structure, they resemble man: most of them are
many combined characters. quadrupeds; and with man, their natural enemy,
• Aimed at publishing a complete system of inhabit the surface of the Earth. The largest,
nature, which included works on mammals, though fewest in number, inhabit the ocean.”
reptiles, birds, fishes and insects. • 8 orders and 39 genera
• Pioneered entomological taxonomy work. AVES
JOSEPH PITTON DE TOURNEFORT (1700)
• Classified based upon the characters of the bill
• His published work entitled Institutiones Rei and feet
Herbariae has around 9000 plant species listed • “A beautiful and cheerful portion of created
in 698 genera. nature consisting of animals having a body
• His classification was based on floral covered with feathers and down; protracted and
characteristics excluding the presence of naked jaws (the beak), two wings formed for
sexuality in plants flight, and two feet. They are areal, vocal, swift
and light, and destitute of external ears, lips,
LINNAEAN ERA teeth, scrotum, womb, bladder, epiglottis,
CAROLUS LINNAEUS corpus callosum and its arch, and diaphragm.”
• Established a unified taxonomic system for all • 6 orders and 63 genera for Aves
animals and plants
• a Swedish botanist at the University of Uppsala AMPHIBIA
• had passion in collecting organisms and had a • ”Animals that are distinguished by a body cold
great talent in classifying them and generally naked; stern and expressive
• Systema Naturae: used morphology for countenance; harsh voice; mostly lurid color;
arranging specimens in collection. filthy odor; a few are furnished with a horrid
• Much of his classification is now drastically poison; all have cartilaginous bones, slow
altered but the basic principle is still in use. circulation, exquisite sight and hearing, large
• His Systema Naturae 10th Edition was entitled pulmonary vessels, lobate liver, oblong thick
Systema Naturae per regna tria naturae, stomach, and cystic, hepatic, and pancreatic
secundum classes, ordines, genera, species, ducts: they are deficient in diaphragm, do not
cum characteribus, differentiis, synonymis, transpire (sweat), can live a long time without
locis, which translates to “System of nature food, are tenacious of life, and have the power
through the three kingdoms of nature, of reproducing parts which have been
according to classes, orders, genera and destroyed or lost; some undergo a
species, with characters, differences, metamorphosis; some cast (shed) their skin;
synonyms, places.” some appear to live promiscuously on land or in
• He counted and classified 8530 species of the water, and some are torpid during the
flowering plants in 1753 winter.”
• With the works of Linnaeus, botany and zoology • Classified based on the limb structures and the
transformed into a Scientia, a science way they breathe
surrounded by philosophy, order, and systems. • 3 orders and 16 genera
PISCES • Established the “Family” rank in between the
ranks of “Genus” and “Class”.
• “Always inhabiting the waters; are swift in their
motion and voracious in their appetites. They JEAN BAPTISTE DE LAMARCK
breathe by means of gills, which are generally
united by a bony arch; swim by means of • “Lamarckism” – inheritance of acquired
radiate fins and are mostly covered over with characteristics. It is the notion that an organism
cartilaginous scales. Besides the parts they can pass on to its offspring physical
have in common with other animals, they are characteristics that the parent organism
furnished with a nictitant membrane, and most acquired through use or disuse during its
of them with a swim-bladder, by the contraction lifetime.
or dilatation of which, they can raise or sink
themselves in their element at pleasure.” AUGUSTIN PYRAMUS DE CANDOLLE
• classification was based on the position of • In his published work in 1813, entitled “Theory
ventral and pectoral fins. elementaire de la botanique”, he stated that
• 5 orders and 50 genera for fishes. published names should have priority according
INSECTA to the date of publication,starting with Linnaeus
(without mentioning a particular year).
• a class comprising all arthropods, including • First attempt: Rules in BotanicalTaxonomy.
insects, crustaceans, and arachnids • His son, Alphonse de Candolle succeeded him
• classified according to their formation of wings. and wrote a book in 1867 entitled, Lois de la
• 7 orders and 73 genera for Insecta. Nomenclature Botanique where 100 botanists
• “A very numerous and various class consisting adopted the rules from
of small animals, breathing through lateral
OTTO KUNTZE
spiracles, armed on all sides with a bony skin,
or covered with hair; furnished with many feet, • He published a book entitled Revesio generum
and moveable antennae (or horns), which Plantarum in which he applied Candolle’s laws.
project from the head, and are the probable • His work contained changed 1000 generic
instruments of sensation.” names and 30,000 species names of plants
VERMES HUGH EDWIN STRICKLAND
• a taxon used by Linnaeus for all non-arthropod • Strickland Code: First Nomenclatural Laws for
invertebrate animals. Zoology.
• classification was based on the structures of • He elaborated the first nomenclatural laws for
their body zoology; assisted by a committee where
• “Animals of slow motion, soft substance, able to Charles Darwin was a member
increase their bulk and restore parts which have
been destroyed, extremely tenacious of life, and NOTABLE DATES IN THE HISTORY OF
the inhabitants of moist places. Many of them TAXONOMY
are without a distinct head, and most of them *1905
without feet. They are principally distinguished • In Europe, an assembly was held on a
by their tentacles (or feelers). By the Ancients Botanical congress inVienna
they were not improperly called imperfect • During this meeting, it was decided that the
animals, as being destitute of ears, nose, head, starting point for priority of botanical names was
eyes and legs; and are therefore totally distinct set to 1753, the year of Linnaeus’ Species
from Insects.” Plantarum.
• classify 5 orders and 69 genera
*1907
POST-LINNAEAN TAXONOMY
GEORGES-LOUIE LECLERC DE BUFFON • American Botanists create their own code and
• One of the few countries in which Linnaean allowed Tautonyms (a scientific name consisting
systematics did not make success is France; of two terms, in which the generic name and
French taxonomists stuck to the beliefs of specific name are the same).
Tournefort and continued to work on a • This is only allowed in the field of Zoology
development of the natural system.
• De Buffon was one of the French taxonomists *1935
who acquired inherited characters in species,
which opened a pathway for an evolutionary • European and American codes merge into one:
theory. International Code of Botanical Nomenclature
(ICN)
MICHEL ADANSON
*1953
• He launched the idea that in classification, one
should not put greater emphasis on some • International Code of Nomenclature for
characters than on others but use a great range Cultivated Plants (ICNCP)
of characters. *1980
ANTOINE LAURENT DE JUSSIUE • Code for Bacteria (Prokaryotes) was
• He changed the system of plants with his established.
Genera Plantarum in 1789. • Cyanobacteria was excluded because it was
• He divided the plants into acotyledons, still included in the botanical code
monocotyledons, and dicotyledons.
FROM PHENETICS TO PHYLOGENIES • The Rule of Monophyly: include all descendants
ERNST HAECKEL & AUGUST EICHLER from one single ancestor (the rule of
• Two German biologists who started the monophyly)
construction of evolutionary trees.
• Haeckel established the term “phylogeny” – PHYLOCODE
evolution of a genetically related group of Kevin de Queiroz & Jacques Gauthier
organisms via the study of protein or gene • Laid the theoretical foundation to a new
evolution by involving the comparison of nomenclatural code for all organisms, the
homologous sequences PhyloCode.
• PhyloCode: First Draft (2000) – classifying
WILLI HENNIG organisms by species and clades.
• Proposed species and clades should have
• Founded the Cladistic Era: 1966 names, and that all ranks above species are
• Synapomorphy: possession by two or more excluded from nomenclature
organisms of a characteristic inherited
exclusively from their common ancestor.

THE CONCEPT OF SPECIES AND SPECIATION

Species • The unique characteristics of the smaller group

can be passed to the future generations
• the basic unit of classification and a taxonomic
rank of an organism Parapatric Speciation
• in Latin literally translates to “appearance”
• an ancient intellectual construct, borne of • Species is spread out over a large geographic
humanity’s attempt to categorize the vast and area; individuals only mate those species in
complex variety of life into manageable units their own geographic region.
(Simpson, 2010) • Sometimes happen when a part of the
• Different kinds of organisms are distinguished environment or habitat has been polluted
based on differences in their appearance
Sympatric Speciation
• Speciation: Species formation
• Very controversial speciation that some
VARIATION OF SPECIES
scientists do not believe to have existed.
• Biological species (or Isolation species): groups • Occurs when there are no physical barriers
of populations that interbreed and are preventing any individuals from mating, when
reproductively isolated from other groups all members are just in proximity with one
(Simpson, 2010). Example: male Tiger + female another.
Lion= Tigon; male Lion + female Tiger= Liger • New species arise spontaneously probably due
• Recognition species: sexually reproducing to different food source or characteristic
systems that are maintained by genetically
Artificial Speciation
based features promoting reproduction
(Paterson, 1985). Example: Crickets with • Newest type of speciation usually achieved
mating song through laboratory experiments
• Evolutionary species: refer to a single,
continuous lineage of ancestral-descendent SPECIES CONCEPT: BIOLOGICAL
populations (Simpson, 2010).
• Cohesion species: defined as the largest or • A species is a group of populations whose
most inclusive group of individuals maintaining members have the potential to interbreed and
genetic and phenotypic cohesion (Templeton, produce viable offspring but do not produce
1989) offspring with members of other groups.
• For us, humans belong to a single biological
TYPES OF SPECIATION species, defined by our capacity to interbreed
Allopatric Speciation successfully.
• Occurs when a species separates into two • However, there are also certain organisms that
separate groups which are isolated from one are able to produce asexually so this rule does
another. not apply to them.
• Begins when a species splits into two or more
geographically separated populations. TYPES OF FERTILIZATION:
• Can be by Vicariant speciation or by a founder
event. • Internal Fertilization - The process of fusion of
• May have occurrence of hybridization male & female gametes taking place inside the
(production of hybrids) body of the female
• External Fertilization - The process of fusion of
Peripatric Speciation male & female gametes on the outside
environment (e.g., bodies of water).
• Occurs when small groups of individuals o Animal examples:
breakoff from the larger group and form new o Arbacia lixula (Black Sea Urchin)
species. o Salmon salar (Atlantic Salmon)
• Differs from allopatric in the sense that in here, o Cryptobranchus alleganiensis
one group is much smaller than the other (Hellbender Salamander)
TYPES OF INTERNAL FERTILIZATION • The disadvantages of this are being subjective
and often prone to misidentification
1. Oviparous: fertilized eggs are laid outside the
female’s body and develop there, receiving SPECIES CONCEPT: ECOLOGICAL
nourishment from the yolk that is a part of the
egg. • Defines species in terms of their ecological
2. Ovoviparous: fertilized eggs are retained in the niche.
female, but the embryo obtains its nourishment • Can accommodate sexual & asexual species.
from the egg’s yolk and the young are fully • Emphasizes the role of disruptive natural
developed when they are hatched. selection as organisms adapt to different
3. Viviparous: young develop within the female, environment
receiving nourishment from the mother’s blood
through a placenta. The offspring develops in SPECIES CONCEPT: PHYLOGENETIC
the female and is born alive (EVOLUTIONARY)

SPECIES CONCEPT: MORPHOLOGICAL • Based on reconstructing evolutionary history of

population.
• Distinguishes species by body shape and other • Can lead to very precise definitions of taxa.
structural features. • Disadvantage: Species identification are difficult
• This species concept is widely used and when you are in the field.
applicable to sexual & asexual organisms.
• Can be used even without information on the
extent of gene flow.

SYSTEMATICS AND THE PHILOSOPHY OF SCIENCE

Objective Knowledge vs. Truth in Science • Alternatively can be defined as a process in

which scientific inference leads from the
• The path from basic observation to specific to the general.
“KNOWLEDGE” concerning the natural world is • This approach was attributed to 16th century
neither direct nor obvious. philosopher, Francis Bacon.
• Many scientists are content to gather and • When statements of experience or judgements
interpret evidence within an established of perception are treated as scientific, it was
theoretical framework as “FACTS” without labeled by Karl Popper (1968) as POSITIVIST.
questioning underlying assumptions. • In Inductivist or Positivist perspective,
• PHILOSOPHY as a field of inquiry may help us observations are treated as FACTS.
to gain understanding of issues on: • In the phenetic school of thought, positivism is
- how we judge truthfulness of knowledge we referred as EXTREME EMPIRICISM
acquire
- what ideas represent mere conjecture, w/c
represent knowledge • Deductive approach holds that all observation
- whether or not we can trust our observations should be interpreted as theoretical.
of the real world • It may also be stated that all observations are
theory based.
THEORY OR HYPOTHESIS
• In science, hypothetico-deductive view holds
• Ideas in science are often referred to as that growth of knowledge from the formulation
THEORIES or HYPOTHESES that are critically of theories that imply certain predictions
evaluated. (deductions) can be judged by observations.
• Theory is often used in reference to more • Observations represent TESTS of the theory.
general concepts than hypothesis. • Observations that conform to the deductions
• Term such as TRUTH is being used by news are said to CORROBORATE the theory.
media referring to scientific statements, and • Observations that do not conform to the
even by scientists and philosophers in their deductions are said to FALSIFY the theory.
writings. • The greater and more severe the number of
• But science produces what might be referred as tests passed, the greater the degree of
“OBJECTIVE KNOWLEDGE” corroboration.
• The question of whether such knowledge is, or • And a single nonconforming observation may
can ever be, ABSOLUTELY TRUTHFUL be persuasive as reason to reject the theory
depends on one’s BELIEF that would seem to
FALSIFICATIONIST METHOD
involve an ACT OF FAITH, an approach to the
acquisition of knowledge that science does not • The deductive method of testing theories, also
admit. called as FALSIFICATIONIST approach to
• All scientific statements from hereon will be science, can be tested with the following
treated HYPOTHETICAL (Popper, 1968):
• 1. Logical consistency whereby conclusions are
On Acquiring Scientific Knowledge
compared among themselves;
• INDUCTIVE approach to science that holds • 2. Investigation of the logical form of the theory
scientific knowledge accumulated from to determine whether in fact it is an empirical or
repeated observation of the facts. scientific theory;
• 3. Comparison with other theories to determine to fit the topology), 2. congruence, degree with
whether a given theory would represent a which distributions of individual characters
scientific advance; agree with one another.
• 4. EMPIRICAL TESTING of conclusions • Parsimony as a methodological tool is simply to
(deductions) from the theory (i.e., support interpret evidences (or simplicity of
predictions of a theory and if observations explanation).
match predictions, it corroborates the theory). • As applied to systematics, it is to minimize the
• But Popper further pointed THAT THERE IS NO number of ad hoc explanations of data.
TRUTH IN SCIENCE, and that one should not • It is to maximize the power of the hypothesis to
equate degree of corroboration with explain data
truthfulness… “The advance of science is not
due to the fact that more and more perceptual CHARACTER ANALYSIS
experiences accumulate in the course of time.
Nor is it due to the fact that we are making ever • Detailed examination of methods to establish
better use of our senses.” hierarchic-phylogenetic relationships among
taxa begins with selection of taxa and
Methodological rules applying deductive characters.
approach by Popper (1968) • It lays the groundwork for all subsequent steps
in phylogenetic analysis.
1. “Science is in principle without end. Once you • Central to phylogenetic analysis is
decide on the absolute truth, you retire from the CHARACTER ANALYSIS.
game.” • It is the process of observing, coding and
rechecking character information
2. A corroborated hypothesis should not be dropped
without reason, that is, without a stronger 1. Critical observation of characters or
competing hypothesis. characterization (must perform correct, objective
taxon description/diagnosis!);
3. Parsimony should be applied in the testing of
hypotheses. That is, AD HOC ASSUMPTIONS 2. Appropriate coding of characters which requires
(special pleading) designed to dispose of character weighing and determination of character
observations that would otherwise provide evidence transformation. (Example: (0) as ancestral and (1)
against a theory, should be avoided. as derived; what if there are three character states,
which will be (0), (1) and (2)?);
• PARSIMONY, among the rules, has assumed
the greatest importance in modern systematic 3. Rechecking character information through
practice experimentation or field/lab observation, and
extensive literature review.
PARSIMONY and AD HOC HYPOTHESES
• (Example: Simple determination which are
• Parsimony as an approach to evaluating homologous characters and not among animals
observations is often attributed to 14th century with limbs; among plants with petaloid stamens)
philosopher William of Occam.
• Widely appreciated approach in science, in
which the number of assumptions required to
explain observations should be minimized.
• Extra assumptions beyond the minimum
necessary are often referred as “ad hoc”.
• EXAMPLE of one direct application of
parsimony criterion: In analyzing strength of a
character or character data, it is judged by two
factors --- 1. consistency, using the frequently
used consistency index (a ratio of observed
changes relative to the minimum possible
number of changes required for the character(s)