Phylogenetic Tree

AD Scott and DA Baum, University of Wisconsin, Madison, WI, USA

r 2016 Elsevier Inc. All rights reserved.

Glossary Phylogeny The treelike evolutionary history of a group of

Branch The portion of a phylogenetic tree that connects organisms.
two nodes (internal branch) or one node and a tip (external Plesiomorphy An ancestral character state.
branch). Population lineage A group of populations united by
Clade A monophyletic group. Part of a rooted tree that gene flow.
can be separated from the rest of the tree (which includes Relatedness The recency of common ancestry, with more
the root) by cutting a single branch. closely related organisms being those that share more recent
Cladogenesis See lineage splitting. common ancestors.
Cladogram A tree diagram that communicates only the Reticulation Having a netlike population history with
topology (branching pattern). A cladogram provides all the both lineage splitting and fusion.
information relevant to determine the degree of relatedness Root The earliest node in a tree, representing the last
between taxa. common ancestor of all the tips.
Crown node The node that represents the last common Sib taxa Two taxa descended from a common ancestor.
ancestor of a clade of interest. Stem lineage The branch that subtends a clade of interest.
Hybrid speciation When members of two distinct lineages Stem node The node that represents the last common
interbreed and form a new evolutionary lineage distinct ancestor shared by a taxon of interest and any other
from the parental lineages. See also lineage fusion. organisms.
Introgression When individuals from two distinct Synapomorphy A shared derived character state.
lineages produce hybrid offspring that subsequently Taxon (plural ¼ taxa) A formally named group of
interbreed with one of the parental lineages, causing genes organisms. The groups of organisms represented by the tips
from one lineage to be introduced into the other. of a phylogenetic tree.
Lineage fusion When two distinct evolutionary lineages Tip (¼ leaf) The entities (e.g., taxa, genes) whose
merge into a single, hybrid descendant lineage. See also relationships are depicted using a tree diagram.
hybrid speciation. Topology The history of lineage splitting depicted by a
Lineage splitting The division of an ancestral lineage into tree; a rooted tree’s topology being defined by the list of all
two or more descendant lineages. its clades.
Monophyletic Composed of all the descendants of a Trait A heritable feature of a lineage; a character or
particular ancestor. In phylogenetic trees, monopohyletic character state.
groups are clades. Tree thinking The ability to read and interpret
Node A branching point in a phylogenetic tree. phylogenetic trees and use trees to accurately represent the
Outgroup Taxa that are assumed a priori not to be within evolutionary process.
the ingroup and may therefore be used to root a Unrooted tree A tree without a root and, thus, without a
phylogenetic tree. specified time axis.

Introduction This perspective held that organisms could be arranged as the

rungs on a ladder, with rocks and minerals at the bottom
Evolution is a central concept that enriches our understanding moving up through plants and ‘simple’ animals, with humans
of the natural world and has very real societal impacts. For close to the pinnacle. However, we now understand that the
example, evolutionary principles have been harnessed for organisms alive today did not evolve from other living species,
agricultural improvement and to develop protocols for the but from shared ancestors. Furthermore, a ladder is a mis-
appropriate use of antibiotics. Given its broad significance, leading metaphor because it implies that evolution is pro-
individuals at all levels of biological expertise, from the gen- gressive and directed toward a particular endpoint, which it is
eral public to the research biologist, need to be able to think not. Instead, evolution is more accurately described as an ex-
clearly about evolution. Key among the topics that need to be ploration, a freewheeling road trip in an all-terrain vehicle,
mastered is the ability to correctly interpret evolutionary trees perhaps. There is no predetermined destination, no prescribed
and use them as a substrate for visualizing evolutionary route, and no need to stick to predictable roads. Unlike a road
history. trip, however, evolution doesn’t stop. Modern day species are
Describing the relationships among organisms has been a not at destinations, but wherever they happened to be when
challenge since well before the origin of evolutionary theory. we humans decided to map things out. But while we cannot
In antiquity, biological diversity was classified and placed on know their future, we can (in principle) figure out the path
the Great Chain of Being or Ladder of Life, the Scala Naturae. that each species took to its current locale. This broad-scale

270 Encyclopedia of Evolutionary Biology, Volume 3 doi:10.1016/B978-0-12-800049-6.00203-1

 Phylogenetic Tree 271

history of evolutionary relationships is known as ‘phylogeny.’ As in the trees you are already familiar with, tips or leaves
So, if a ladder is not an appropriate metaphor, how can we are subtended by branches. A branch, which represents the
picture phylogeny? No less a scientist than Charles Darwin persistence of a lineage through time, may subtend one or
provided an answer: many leaves. Branches connect to other branches at nodes,
which represents the last common ancestors of organisms at
The affinities of all the beings of the same class have sometimes been the tips of the descendant lineages. A branch connecting a tip
represented by a great tree. I believe this simile largely speaks the to a node is called an external branch, whereas one connecting
truth … the great Tree of Life … covers the earth with ever-branching two nodes is called an internal branch (Figure 1).
and beautiful ramifications. (Darwin, 1859, pp. 131–32)
Reading a tree from the past toward the present, a node
indicates a point where an ancestral lineage (the branch below
the node) split to give rise to two or more descendant lineages
In the one hundred and fifty years since this passage was (the branches above the node). Branching on an evolutionary
written, tree diagrams have come to be an indispensable tool tree is also called ‘cladogenesis’ or ‘lineage splitting.’ After a
for summarizing what is known about evolutionary history lineage splits into two, evolution happens independently in
and guiding research in several fields, such as epidemiology, these newly formed descendant lineages. The sequence of
community ecology, and genomics. High school and uni- lineage splits in a tree creates its structure or ‘topology.’ Tree
versity students also encounter phylogenetic trees in textbooks topology shows us the branching of lineages through time that
and in lectures as a means to organize knowledge of biological gave rise to the tips.
diversity. And trees are even found in popular media and ‘Clades’ are groupings on a tree that include a node and all
museum displays, where they are designed to bring evo- of the lineages descended from that node. The set of all the tips
lutionary discoveries to a general audience. As trees are so in a clade is defined as being ‘monophyletic,’ referring to the
widespread and provide such a useful tool for representing fact that it includes all the descendants of an ancestral lineage.
evolutionary relationships, it is critical that we know how to In Figure 2, we could say that the tree supports monophyly of
read them and understand what they can and cannot tell us, a taxa C, D, and E or, put another way, C, D, and E together form
skill now commonly known as ‘tree thinking’ (O’Hara, 1992; a clade. Clades can be hierarchically nested within one an-
Baum et al., 2005; Baum and Smith, 2012). other, as shown in Figure 2. A tree’s topology can now be
defined more precisely as the set of clades that the tree
contains.
Tree Terminology

Phylogenetic trees, by analogy to botanical trees, are made of

What a Tree Represents
leaves, nodes, and branches (Figure 1). Let us consider a tree
from the canopy down to the trunk, or from the modern day
Phylogenetic trees are a convenient way to represent millions
to the past.
or billions of years of evolution and the shared history of
The leaves of a tree, also called tips, can be species, popu-
diverse organisms. So what are the branches and nodes really
lations, individuals, or even genes. If the tips represent a for-
showing us?
mally named group, they are called taxa (singular: taxon). A
Evolutionary trees are essentially about ancestors and des-
‘taxon’ is a group of organisms at any hierarchical rank, such as
cendants. You are probably familiar with pedigrees, which
a family, genus, or species. The tips of a phylogenetic tree are
may be used to trace the ancestry of purebred dogs, tulip
most commonly living, but may also represent the ends of
varieties, or royal families. Consider for a moment your own
extinct lineages or fossils.
ancestry. Your line of ancestry includes your two parents, your
four grandparents, and so on. You could map out your own
ancestry in a family tree, and trace back your line of descent,
Tips

A B C D E
A B C D E

Branch
(external)

Nodes

Branch
(internal)

Root
Figure 2 Clades are highlighted in a phylogenetic tree. Note clades
Figure 1 Components of a phylogenetic tree. can be hierarchically nested.
272 Phylogenetic Tree

Figure 3 Image showing the ancestry of one person (Winston Churchill). Visualization tool by Bradford F. Lyon located at https://
learnforeverlearn.com/ancestors/.

A B C D E It is worth noting that even from a zoomed-out perspective,

there are cases where a phylogeny does not appear strictly
treelike. Branches on the tree of life can sometimes grow
together. Such a rendezvous between formerly distinct lineages
is called ‘reticulation.’ Reticulation can be attributed to a few
different biological processes (Figure 5). ‘Introgression’ hap-
pens when hybrids form between two distinct lineages and,
through subsequent crossing, novel genetic material comes to
be transferred from one species to another. In some cases,
lineages can hybridize to form a new lineage that is distinct
from either parental lineage – a process known as ‘hybrid
Figure 4 Close-up of lineage splitting on a tree. Lines of descent speciation.’ Introgression of very few genes (whether by sexual
look sloppy up close, but are represented as clean lines when reproduction or some other mechanism), called horizontal
considered in evolutionary time. gene transfer, is usually best visualized as a treelike population
history with a few genes having a discordant history. Indeed,
so long as introgression and hybrid speciation are rare or
but as you go farther back time, the number of individuals limited to closely related tips, it is appropriate to represent
tends to balloon, at least initially (Figure 3). If you go far evolutionary relationships using the tree metaphor. However,
enough back in time or include many individuals besides in extreme cases the tree metaphor may break down, meaning
yourself from the current generation it rapidly becomes dif- that evolutionary relationships are best represented as a
ficult to map out all of the lines of descent neatly without network.
crisscrossing. Now imagine expanding the pedigree to include If evolution can be summarized as descent with modifi-
every other member of our species. That would be messy and cation, it makes sense that when we talk about evolution, we
certainly not treelike! The problem is that we are thinking at often do so in terms of those modifications (i.e., traits). ‘Traits’
the wrong timescale. are heritable characteristics of organisms. For example, flowers
Evolution may be changed over time, but just how much are a trait shared by all angiosperms, backbones are a trait
time can be hard to grasp. In a short time frame, such as a shared by all vertebrates, and chitin cell walls are a trait shared
human lifespan, the relationship among most organisms by all fungi. Molecular characteristics, such as having the
within a species is not treelike at all. However from a ‘zoomed- amino acid leucine at a certain position in a protein, should
out’ view, we can consider the members of a species to be part also be considered as traits. It is important to understand how
of the same ‘population lineage.’ That is to say that members traits evolve on trees, since traits serve as the basis of tree
of a species share genes frequently enough that they evolve inference (see other articles within the Phylogenetic Methods
more or less as a single unit. The branches of a phylogenetic section for theory and methods of phylogenetic inference).
tree represent these population lineages, which are composed Traits arise due to evolutionary changes within population
of many individuals over many generations (Figure 4). Every lineages (see other articles within the Population Genetics
so often in evolution, a single population lineage splits into section). Once a new trait arises and becomes fixed in a
two (or more) descendant lineages. This happens when a population lineage all descendant lineages are expected to
species is split into two subsets, whose individuals do not have that trait, though due to subsequent evolution it might
exchange genes. When this occurs, the descendant lineages look quite different. All land vertebrates (‘tetrapods’), for ex-
become free to accumulate differences and, if they don’t come ample, are descended from an ancestor with four limbs,
back together and fuse, will eventually give rise to very dif- though the form of their limbs differs greatly among species.
ferent organisms. A node represents such a lineage splitting Some land vertebrates did evolve a lack of limbs, but this
event – the breaking of genetic connections that allowed the occurred by further modifying the trait out of existence rather
descendant lineages to accumulate differences and eventually than by evolutionarily back-tracking to the precursor con-
give rise to distinct descendant clades. dition of having fins (Figure 6).
 Phylogenetic Tree 273

A B C D E A B C D E A B F C D E

(a) (b) (c)

Figure 5 Processes leading to reticulation. (a) Bidirectional introgression into two parental lineages. (b) Unidirectional introgression. (c) Hybrid
speciation.

Antorbital
fenestra

Hair

Amniotic egg

Four limbs
Figure 6 Cladogram of tetrapods showing trait evolution.

Lineage splitting is often mistakenly confused with trait Trait present Trait absent
evolution. A lineage splitting event is not necessarily accom-
panied by trait divergence (and even if it did, it might involve
traits that we don’t even know about). It is after lineage
splitting that descendant lineages accumulate independent
mutations, which over time may lead to novel traits. For this Crown node
(trait present) Stem
reason, as in Figure 6, traits are not usually depicted as lineage
evolving on nodes but on branches. If a certain clade has a
unique trait, then we can infer that the last common ancestor
of this clade, represented by the ‘crown node,’ had the trait. We Trait evolves
can also assume that the last ancestor shared between this
clade and its closest relative (its ‘sib taxon’) represented by the
‘stem node’ did not have the trait. This follows because, if stem
Stem node
node individuals had already evolved the trait, then the sister (trait absent)
clade should have it too. Therefore, the correct mapping of the
unique trait is on the ‘stem lineage’ of the clade, the branch Figure 7 Trait evolution and crown/stem terminology.
linking its stem and crown nodes (Figure 7).
So far we have focused on trait evolution along a tree, might think lizards and crocodiles seem more similar. Re-
which may imply that the products of evolution are always latedness does not equal similarity.
visible. It is important to note that evolutionary kinship is not There is a specialized group of terms used to describe traits,
always apparent just by looking at organisms. For example, the based on their distribution and origin. ‘Synapomorphic’ traits
tree in Figure 6 shows that crocodiles are more closely related are ones that are unique to a particular clade. In Figure 6,
to birds than they are to lizards, even though superficially you snakes, lizards, crocodiles, birds, and mammals share the
274 Phylogenetic Tree

synapomorphy of the amnion, which evolved after the di-

vergence of amphibians; animals-with-amnions corresponds
to a monophyletic group. ‘Plesiomorphic’ traits, in contrast,
are those shared by a group of taxa that were inherited from an
ancestor, where some other lineages lost this trait. For
example, ‘four limbs’ is a plesiomorphic trait of tetrapods
(Figure 6); vertebrates-with-four-limbs does not correspond to
a monophyletic group because some tetrapods, such as snakes,
legless lizards, caecilian, and whales, lack external limbs. If two
independent lineages evolve a similar trait, they are said to
share a homoplasious trait. Homoplasy arises when distinct
lineages acquire similar traits.

Do Trees Show Advancement and Progress?

Despite the abandonment of overt ladder thinking there is still Node x

an unfortunate tendency to read a tree as though it supports a
narrative in which some tips are more advanced or primitive Figure 8 Cladogram showing relationships among primates.
than others. This is often apparent in the words biologists use to
describe a tree. For example, vascular plants are sometimes re- Since tree topology refers to the list of clades that a tree
ferred to as ‘higher plants’ and vertebrates as ‘higher animals.’ includes and since all tips within a clade are more closely
But this is misleading since ‘higher plants/animals’ have had just related to one another than to tips outside the clade, tree
as long to evolve from their common ancestors as ‘lower plants/ topology can be seen as a summary of evolutionary relatedness
animals.’ Likewise, some taxa with visible traits that make them among all its tips. This is why tree topology is such an im-
resemble ancestors, such as lungfish, monotremes, liverworts, portant evolutionary concept.
and bacteria, are called ‘primitive’ even though these lineages are Trees can be depicted and modified in a number of dif-
all alive today and have many invisible differences from the ferent ways without changing their topology or the relatedness
ancestors they resemble. And species-poor lineages closely re- among organisms they represent. Regardless of whether a tree
lated to diverse clades are frequently labeled ‘basal’ or ‘early- is orientated left to right, top to bottom, outward from the
diverging’ even though they diverged from their sib taxon at the middle in a circle, or along a diagonal, the key information
same time that the sib taxon diverged from them. There isn’t remains the same. For example, all the trees in Figure 9 show
room here to discuss all of the potentially misleading labels and the same topology and imply the same set of evolutionary
why they are wrong, but we advocate being mindful of these relationships. You can tell this because in all cases the list of
vestiges of ladder thinking. For more on this topic, see Krell and clades is identical. Thus the orientation and style of a tree does
Cranston (2004), Crisp and Cook (2005), and Rigato and not change the relationships it represents.
Minelli (2013). Along the same lines, the nodes of a tree can be rotated
without modifying the topology (Figure 10). Looking at the
two trees in Figure 10 you might think that they imply
something different about evolutionary history. For example,
Relatedness you might think that the first tree implies that species E is the
most advanced or evolutionarily derived, while the second tree
When we say that taxa are closely related, what do we mean? implies something different. However, it turns out that these
‘Relatedness’ refers to the amount of time since a group of two trees have an identical topology, as you will see if you
organisms shared a common ancestor. For example, we say make a list of all the clades shown on each tree. This may serve
chimpanzees are the closest relatives of humans, because we to drum home the idea that trees do not show evolutionary
share a common ancestor with chimps more recently than we progress even when drawn in a form that implies that some
do with any other organism (Figure 8). Using a tree diagram, it tips have changed less since the root.
is simple to tease apart relatedness among taxa. Are chimps or
humans more closely related to gorillas? Set aside your intu-
itions for a moment and look at Figure 8. Trace your way from Branch Length
one of the tips back through the tree to the node representing
the common ancestor of chimps, humans, and gorillas (node Phylogenetic trees come in different flavors, depending on
x). Whether you start with the human tip or the chimpanzee additional information they might contain. Trees may just
tip, you reach the same ancestral node, which means that, show tree topology, in which case they may be called ‘clado-
given this tree, gorillas are equally closely related to humans grams.’ Sometimes, in trees called chronograms, branches are
and chimpanzees. scaled to represent the opportunity for evolutionary change by
Two tips that are each other’s closest relative are called sib drawing branch lengths proportional to time. If we assume
taxa. In Figure 8, humans and chimpanzees are sib taxa. that evolutionary changes occur at a fairly constant rate
Gorillas are sibs to the human–chimpanzee clade. (sometimes called clocklike evolution), the length of a branch
 Phylogenetic Tree 275

F
A G

B D

C
A
D

E E

F
B
G C G F C D E B A
Figure 9 Trees can have different shapes and still retain the same topology.

A B C D E A B E D C

Figure 10 A tree can be rotated around any node without changing the relationships it depicts.

A
A
B
B
C
C

D D

E E

F F

G G
Figure 11 Cladogram (left) versus phylogram. Cladograms only communicate topology, while phylograms have branch lengths proportional to
the expected amount of trait evolution.

on a chronogram tells us the relative probability that a par- in Figure 11) as being more ‘advanced’ than ones with short
ticular trait evolved on this branch. However, this will not be branches. While they might have changed more from the
true when the rate of evolution is not clocklike. In that case we common ancestor, they have had the same amount of time to
can show instead a ‘phylogram,’ a tree whose branch lengths evolve and may be just as well, or better, adapted to their
are drawn proportional to the expected amount of trait evo- specific ecological niche. Thinking clearly about evolution is
lution. On a phylogram long branches indicate places where best accomplished by completely dropping the concept of
most of the changes occurred. advanced and primitive taxa.
In a chronogram where all tips are living, all tips are
equidistant from the root, since the branches represent the
absolute time since divergence from a common ancestor. In a Unrooted Trees
phylogram, in contrast, different tips may be different dis-
tances from the root, indicating the expectation that some tips So far, the tree diagrams we have shown are rooted trees. If a
may have accumulated more derived traits than others. Even tree is rooted, all of the tips can be traced back through
when shown as a phylogram, however, it would be misleading branches to a common ancestor. The ‘root’ of a tree therefore
to view tips or clades subtended by long branches (e.g., taxon F implies a chronological direction, starting in the past at the
276 Phylogenetic Tree

E
A C

B D

A B E D C A B C D E E A B D C

Figure 12 Different ways to root the same tree. Each of the three root positions changes the tree topology.

base of the tree and moving toward the present at the tips. Another major role for phylogenetic trees is in ancestral state
However, as discussed in the following entries on tree esti- reconstruction: with a tree and a trait that varies among tips, we
mation, methods for inferring phylogenetic trees often yield can determine the likely characteristics of ancestral nodes in the
unrooted trees. An unrooted tree provides little information tree. Analogous methods can also be applied to geographical
about the direction of trait evolution or the degree of re- distribution allowing us to infer an ancestor’s historical range.
latedness of tips. This is because when a set of tips lie on one As discussed in other sections, trees have many other uses
side of an internal branch we do not know if they will repre- including making inferences about causes of character evo-
sent a clade on the correctly rooted tree. As a way to become lution and studying the movement of species in geographic
more comfortable with phylogenetic trees, it is helpful to learn space (see other articles within the Evolutionary Biogeography
how an unrooted tree can be rooted (Figure 12). section). Indeed, scanning through the many sections of this
The most common rooting method is outgroup rooting. To encyclopedia you will see many phylogenetic trees – as clear
do this, we make sure that at least one tip included in a study an indication as any other that being able to think clearly
(the outgroup) is distantly related to the other taxa in the tree about the process and pattern of evolution rests upon a solid
(the ingroup). This requires some prior knowledge of phyl- foundation of phylogenetic trees and ‘tree thinking.’
ogeny, since using an inappropriate outgroup can greatly
change the rooted tree. As Figure 12 shows, where the root is
placed can change the relationships, meaning it is important to See also: Ancestral Reconstruction: Theory and Practice. Bayesian
root trees appropriately. Other rooting methods include mo- Phylogenetic Methods. Distance-Based Phylogenetic Inference.
lecular clock rooting, which assumes that all tips have had Maximum Likelihood Phylogenetic Inference. Parsimony Methods in
roughly the same opportunity for change since the root node, Phylogenetics. Phylogenetic Invariants. Phylogenetic Networks.
and duplicate gene rooting, which takes advantage of ancient Rooting Trees, Methods for
gene duplication events.

Trees as Substrate References

Understanding the relationships among organisms is just a Baum, D.A., Smith, S.D., 2012. Tree Thinking: An Introduction to Phylogenetic
small portion of what we can learn using trees. Once we build Biology. Greenwood Village, CO: Roberts and Co.
a phylogenetic tree, we can use it as a foundation for other Baum, D.A., Smith, S.D., Donovan, S.S., 2005. The tree-thinking challenge. Science
analyses. 310 (5750), 979–980.
Crisp, M.D., Cook, L.G., 2005. Do early branching lineages signify ancestral traits?
For a start, taxonomic decisions are informed by phylo-
Trends in Ecology & Evolution 20 (3), 122–128.
genetic trees. For example, finding that one species in a genus is Darwin, C.R., 1859. On the Origin of Species by Means of Natural Selection, or the
more closely related to members of a different genus might lead Preservation of Favoured Races in the Struggle for Life. London: Murray.
to it to be reassigned to that genus. Indeed, taxonomy now Krell, F.T., Cranston, P.S., 2004. Which side of the tree is more basal? Systematic
strives to only give formal names to monophyletic groups be- Entomology 29 (3), 279–281.
O’Hara, R.J., 1992. Telling the tree: Narrative representation and the study of
cause all members of a clade are more closely related to each evolutionary history. Biology and Philosophy 7 (2), 135–160.
other than to any organisms outside the clade. A monophyletic Rigato, E., Minelli, A., 2013. The great chain of being is still here. Evolution:
group can thus be seen as occupying a single location on the tree Education and Outreach 6 (1), 18.
of life, something that is not true for non-monophyletic groups.