Question: Phylogenies are a fundamental tool for organizing our knowledge of the biological diversity we ob…

Phylogenies are a fundamental tool for organizing our knowledge
of the biological diversity we observe on our planet. But how
exactly do we understand and use these devices?

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A phylogenetic tree, also known as a phylogeny, is a diagram
that depicts the lines of evolutionary descent of different
species, organisms, or genes from a common ancestor. Phylogenies
are useful for organizing knowledge of biological diversity, for
structuring classifications, and for providing insight into events
that occurred during evolution. Furthermore, because these trees
show descent from a common ancestor, and because much of the
strongest evidence for evolution comes in the form of common
ancestry, one must understand phylogenies in order to fully
appreciate the overwhelming evidence supporting the theory of
evolution.

Tree diagrams have been used in evolutionary biology since the time
of Charles Darwin. Therefore, one might assume that, by now, most
scientists would be exceedingly comfortable with “tree
thinking”–reading and interpreting phylogenies. However, it turns
out that the tree model of evolution is somewhat counterintuitive
and easily misunderstood. This may be the reason why biologists
have only in the last few decades come to develop a rigorous
understanding of phylogenetic trees. This understanding allows
present-day researchers to use phylogenies to visualize evolution,
organize their knowledge of biodiversity, and structure and guide
ongoing evolutionary research.

But what exactly is a phylogeny? Moreover, how should one read
and interpret one of these diagrams? In an attempt to answer such
questions, the following sections present a brief introduction to
tree thinking. A more complete view of this subject can be
developed by learning about how traits evolve along trees, how
trees are reconstructed, and how trees are used to study various
aspects of evolution.

What an Evolutionary Tree Represents

Figure 1

Figure Detail

To better understand what a phylogeny represents, start by
imagining one generation of butterflies of a particular species
living the same area and producing offspring. If you focus on four
individual butterflies in both the parental and offspring
generations, the resulting pedigree may appear like the one in
Figure 1B.

Now, expand your image to encompass all the butterflies of this
species in a particular meadow over several generations. A pedigree
for this population might look something like the one in Figure 1C.
Note that each individual in the figure has two parents, but each
gives rise to a variable number of offspring in the next
generation.

Next, imagine taking your pedigree and getting rid of the
organisms, thus keeping only the descent relationships, which are
the glue that holds the population together (Figure 1D inset box).
Then zoom out even farther to include many more individuals (say,
from multiple meadows in the same region) and more generations. For
example, the whole of Figure 1D is derived from a similar diagram
as the inset box, but it now includes more individuals and many
generations. As you can see, if one were to try to represent a
typical population of several thousand individuals that persists
for hundreds or thousands of generations, all one would see would
be a fuzzy line.

Individual populations may be fairly isolated for some period of
time. However, on an evolutionary timescale, migration will occur
among the discrete populations that make up a typical species. This
gene flow between populations has the effect of “braiding” the
population lineages into a single species lineage, which might be
thought of as resembling Figure 1E.

Moreover, during evolution, lineages often split. This occurs
when populations or groups of populations become genetically
isolated from one another. Lineages most commonly split because of
the migration of a few individuals to a new, isolated region (e.g.,
an island). This is sometimes called a founder event.
Alternatively, a formerly contiguous range can be broken up by
geological or climatic events (e.g., the creation of mountains,
rivers, or patches of inhospitable terrain). This phenomenon is
called vicariance. No matter whether populations split due to
founder events or vicariance, if the isolated populations remain
separate, they will start evolving differences from one another
(Figure 1F). After all, a mutation that arises in one population
will have no way to get to the other population. Thus, even a
mutation that would be selectively favored in both populations will
become fixed in only one of the groups.

As a consequence of this genetic isolation, the lineages will
evolve separately, becoming more and more different over time. If
they remain apart for long periods, enough physiological and
behavioral differences may evolve to result in reproductive
isolation, such that it will be impossible for individuals from the
two lineages to reproduce even in the case that they do come back
into contact. Because of this, it is a useful simplification to
assume that once lineages diverge, the two sets of descendants will
remain distinct.

Figure 2: Branching pattern of four
species.

Genetic connections of populations can be depicted by a
phylogenetic tree.

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Figure Detail

Figure 2B shows what we might see if we followed the fate of a
single ancestral lineage (Figure 2A) long enough that it gave rise
to four descendant lineages (species). This example includes three
lineages that were established but became extinct before the end of
the observation period. This diagram is an example of a simple
phylogenetic tree.

In most cases, researchers draw phylogenetic trees in such a way
as to record only those events that are relevant to a set of living
taxa. Most commonly, these taxa are species. For example, Figure 2C
shows the basic tree we could draw to represent the history of the
four “tip” species, A through D. This tree shows that species A and
B share a more recent common ancestor with each other than with
either species C or species D. Likewise, species C and D share a
more recent common ancestor with each other than with either
species A or species B. This example illustrates the fact that a
phylogeny is, at its most basic level, a history of descent from
common ancestry.

Phylogenetic trees are fractal in the sense that the same
pattern is found whether we consider recently diverged lineages or
deep splits in the tree of life. Indeed, the most basic postulate
of evolutionary theory is that the same general phenomenon of
descent from common ancestry applies to both the most diverse
branches of the tree of life and the most similar. As a result, the
tree structure is extremely helpful in tracking biological
diversity at all levels.

The Lexicon of Phylogenetic Inference

Figure 3: Phylogenetic terminology.

A root is the ancestral population from which all the other
species originate. A node represents a branching point from the
ancestral population. Terminals occur at the topmost part of each
branch, and they are labeled by the taxa of the population
represented by that branch.

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Most phylogenetic trees are rooted, meaning that one branch
(which is usually unlabeled) corresponds to the common ancestor of
all the species included in the tree. Note, however, that a tree
can be drawn in any orientation. Figure 3, for example, shows a
simple rooted treewith the root at the bottom and the tips at the
top.

The labels at the “tips” of a phylogeny can correspond to
individual organisms, to species, or to sets of species, as long as
each tip makes up a separate branch on the tree of life. In fact,
in certain contexts, the tips can even correspond to individual
genes. In any case, some general terms for the items represented by
these tips include “terminals,” “terminal taxa,” or “taxa”; in more
mathematical circles, they may also be called “leaves.” As opposed
to tips, the branching points within a tree, which correspond to
inferred speciation events, are called nodes. Each node represents
the last common ancestor of the two lineages descended from that
node. Internal branches or internodes connect two nodes, whereas
external branches connect a tip and a node.

Figure 4: A monophyletic group,
sometimes called a clade, includes an ancestral taxon and all of
its descendants.

A monophyletic group can be separated from the root with a
single cut, whereas a non-monophyletic group needs two or more
cuts.

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Figure Detail

A clade is a piece of a phylogeny that includes an ancestral
lineage and all the descendants of that ancestor. This group of
organisms has the property of monophyly (from the Greek for “single
clan”), so it may also be referred to as a monophyletic group. A
clade or monophyletic group is easy to identify visually: it is
simply a piece of a larger tree that can be cut away from the root
with a single cut (Figure 4a). Accordingly, if a tree needs to be
cut in two places to extract a given set of taxa, then those taxa
are non-monophyletic (Figure 4b).

Clades are natural chunks of trees because there is a portion of
history (specifically, the internal branch that attaches the clade
to the rest of the tree) that is common to all members of the clade
and to no other tips. As a result, statements of common ancestry
that apply to a clade always apply to all tips within the clade.
For instance, if you are told that mammals share a more recent
common ancestor with lizards than with sharks, and if “mammals”
refers to a clade, then you can deduce that all mammalian species
share a more recent common ancestor with lizards than with
sharks.

This is not true of non-monophyletic groups, as can be
illustrated by reference to the traditional (but misleading)
concept of “reptiles,” which included lizards, snakes, crocodiles,
and turtles, but not birds. Because “reptiles” (in this sense) does
not refer to a monophyletic group, it is difficult to make general
statements about the organisms in this group. Furthermore,
researchers now know that crocodiles share a more recent common
ancestor with birds than with lizards, snakes, or turtles. Thus,
current concepts of “Reptilia” generally include birds as members
of this clade. Indeed, it is because of such problems with
non-monophyletic groups that modern systems of classification
strive to give formal names only to monophyletic groups.

How to Read an Evolutionary Tree

Figure 5: Patterns of evolutionary
descent.

The information provided by patterns of evolutionary descent is
the same regardless of the lengths of branches.

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Unless indicated otherwise, a phylogenetic tree only depicts the
branching history of common ancestry. The pattern of branching
(i.e., the topology) is what matters here. Branch lengths are
irrelevant–they are simply drawn in whatever way makes the tree
look most tidy. Thus, the three trees shown in Figure 5 all contain
the same information.

Similarly, tree diagrams can depict the same information yet be
oriented in different ways. The three trees in Figure 6, for
example, have the same topology and thus the same evolutionary
implications. In each case, the first divergence event separated
the lineage that gave rise to tip A from the lineage that gave rise
to tips B, C, and D. The latter lineage then split into two
lineages, one of which developed into tip B, and the other which
gave rise to tips C and D. What this means is that C and D share a
more recent common ancestor with each other than either shares with
A or B. Tips C and D are therefore more closely related to each
other than either is to tip A or tip B. The diagram also shows that
tips B, C, and D all share a more recent common ancestor with each
other than they do with tip A. Because tip B is an equal distance
(in terms of branch arrangement) from both C and D, we could say
that B is equally related to C and D. Likewise, B, C, and D are all
equally related to A.

Figure 6: Types of phylogenetic
trees.

These trees depict equivalent relationships, despite having
different appearances.

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It might seem confusing that such different-looking trees can
contain the same information. Here, it might be helpful to remember
that the lines of a tree represent evolutionary lineages — and
evolutionary lineages do not have any true position or shape. It is
therefore equally valid to draw the branch leading to tip A as
being on either the right or the left side of the split, as shown
in Figure 7. Similarly, it doesn’t matter whether branches are
drawn as straight diagonal lines, are kinked to make a rectangular
tree, or are curved to make a circular tree. Think of lineages as
flexible pipe cleaners rather than rigid rods; similarly, picture
nodes as universal joints that can swivel rather than fixed welds.
Using this sort of imagery, it becomes easier to see that the three
trees in Figure 7, for example, are equivalent. The basic rule is
that if you can change one tree into another tree simply by
twisting, rotating, or bending branches, without having to cut and
reattach branches, then the two trees have the same topology and
therefore depict the same evolutionary history.

Figure 6: Types of phylogenetic
trees.

These trees depict equivalent relationships despite being
different in

© 2008  Nature Education All rights
reserved.  

It might seem confusing that such different-looking trees can
contain the same information. Here, it might be helpful to remember
that the lines of a tree represent evolutionary lineages–and
evolutionary lineages do not have any true position or shape. It is
therefore equally valid to draw the branch leading to tip A as
being on either the right or the left side of the split, as shown
in Figure 7. Similarly, it doesn’t matter whether branches are
drawn as straight diagonal lines, are kinked to make a rectangular
tree, or are curved to make a circular tree. Think of lineages as
flexible pipe cleaners rather than rigid rods; similarly, picture
nodes as universal joints that can swivel rather than fixed welds.
Using this sort of imagery, it becomes easier to see that the three
trees in Figure 7, for example, are equivalent. The basic rule is
that if you can change one tree into another tree simply by
twisting, rotating, or bending branches, without having to cut and
reattach branches, then the two trees have the same topology and
therefore depict the same evolutionary history.

Figure 7: Relationships on a phylogenetic tree can be depicted
in multiple ways.

These trees depict equivalent relationships despite the fact
that certain internal branches have been rotated so that the order
of the tip labels is different.

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reserved.  

Finally, it’s important to note that in some instances,
rectangular phylogenetic trees are drawn so that branch lengths are
meaningful. These trees are often called phylograms, and they
generally depict either the amount of evolution occurring in a
particular gene sequence or the estimated duration of branches.
Usually, the context of such trees makes it clear that the branch
lengths have meaning. However, when this is not the case, it is
important to avoid reading in any temporal information that is not
shown. For example, Figure 8 may appear to suggest that the node
marking the last split leading to tips A and B (marked x)
occurred after the node separating tip C from tips D and E (marked
y). However, this should not be read into the tree; in
reality, node x could have occurred either before or after
node y.

The Importance of Phylogenetic Trees

Given the increasing use of phylogenies across the biological
sciences, it is now essential that biology students learn what tree
diagrams do (and do not) communicate. Developing “tree thinking”
skills also has other benefits. Most importantly, trees provide an
efficient structure for organizing knowledge of biodiversity and
allow one to develop an accurate, nonprogressive conception of the
totality of evolutionary history. It is therefore important for all
aspiring biologists to develop the skills and knowledge needed to
understand phylogenetic trees and their place in modern
evolutionary theory.

Figure 8: Trees contain information on the relative timing of
nodes only when the nodes are on the same path from the root (i.e.,
when one node is a descendant of another).

In this tree, nodes x and y are not on the same path, so we
cannot tell whether the ancestral organisms in node x lived before
or after those in node y.

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