Introduction to phylogenetic trees and tree-thinking Copyright 2005, D. A. Baum (Free use for non-commercial educational pruposes) Phylogenetics is the study of the relationships of organisms to each other. A central concept in this field is a phylogenetic tree, a depiction of the inferred evolutionary relationships of species to each other. Phylogenetic trees are very useful for organizing knowledge of biological diversity and for providing insights into events that occurred during evolution. Thus, being able to correctly interpret such trees is an essential tool for a modern biologist. This document is intended to provide you with a brief overview of the important principles and a list of specific skills you need to acquire to be able to extract information from phylogenies. What a tree represents Start by imagining one generation of plants of a particular species, for example, shepherd s purse, growing side by side in a meadow and producing offspring by exchanging pollen. If we focus on five individual plants in the parental generation (G1) and the offspring generation (G2), the pedigree could look like the following. Here we have assumed that each individual has two different parents whereas, in many plants, self-pollination can occur. Parents Generation 1 Offspring Generation 2 Now expand your image to encompass all the plants in this population and several generations. It might look something like the following. Note, each individual has two parents, but gives rise to a variable number of offspring in the next generation.
G 1 G 2 G 3 G 4 G 5 Imagine taking the proceeding and getting rid of the organisms and only keeping the descent relationships, the glue that holds the population together. This would look like the following: Now, expand your field of view to include many more individuals and generations. For example, the image to the right is derived from a similar diagram as the one above but now includes about 250 individuals and 80 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 could see would be a fuzzy line. Past Present Individual populations may be fairly isolated for some period of time. However, on an evolutionary timescale seeds and pollen occasionally move between the discrete populations that
comprise 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 the graphic to the left. As a matter of convention, when we start looking at longer time frames it is normal to invert the arrow of time, placing the past at the bottom and present at the top. This convention probably arose because in fossil beds, older (ancestral) fossils tend to lie in lower strata than fossils of lesser age. Thus the preceding figure should be redrawn. Present During evolution, lineages often split. This occurs when populations or groups of populations become genetically isolated from one another. Because of the fact that species are considered to be evolutionary lineages, lineage-splitting is Past often called speciation. Possible causes include migration of a few individuals to a new, isolated region (e.g., an island) or the splitting of a formerly contiguous range by geological or climatic events (e.g., mountains, rivers, patches of inhospitable environments arise). If populations remain isolated for a long time then they will tend to acquire differences and these differences will tend to make it impossible for individuals from different lineages to mate successfully and create viable offspring. Thus, it is a useful simplification to assume that once speciation happens, the two descendant species never exchange genes again. Lineages can diverge from one another, but they do not converge. To the right is an example of what we might see if we followed the fate of one initial species for long enough that it gave rise to four species. This example includes three lineages (species) that became established but became extinct before the end of the observation period. This is a simple phylogenetic tree. Ignoring the extinct species, we can summarize the tree as follows. The initial speciation event gave rise to two lineages, one of which later split to give rise to descendant species A and B, whereas the other gave rise to C and D. This means that A and B are more closely related to each other than to C and D (and conversely C and D are more closely related to each other than to A/B). The issue of relationships will be discussed further below. In practice, we are not able to watch lineages evolving. Instead of starting from one ancestor and observing evolution occurring in a forward direction, phylogenies are generally approached in the reverse direction. We start from a sample of living species, and ask, what is the shape Ancestral species A B C D Descendant species A B C D
of the phylogenetic tree that connects this set of species? We can pretty much ignore species that because extinct before the present. Suppose we were studying species A, B, C, and D. In that case, all the relevant information we can obtain would be summarize in the simplified diagram shown to the right. Evolutionary relatedness and phylogenies When biologists talk of relatedness they are usually referring to the recency of common ancestry: two living species are closely related if their most recent common ancestor (often abbreviated MRCA) lived close to the present, and more distantly related if their MRCA lived in the more distant past. To help make the logic clear, think about the relationships within families. The MRCA s of you and your first cousins are your grandparents, whereas the MRCA s of you and your second cousins are your great-grandparents. Your grandparents are situated only two generations before you, whereas your great-grandparents are situated three generations back. This provides a solid foundation for the claim that you are more closely related to your first than your second cousins. Phylogenetic trees contain information about the relative recency of common ancestry and, thus, provide a succinct way of determining the degree of relationships among species. For example, in the tree above you should be able to see that the species A shares a more recent common ancestor with species B than with species C. Hence, the tree above shows us definitively that species A is more closely related to species B than to species C. Definitions and conventions Most of the trees that you will encounter are rooted, meaning that one branch, usually unlabelled, is taken to correspond to the common ancestor of all the species included in the tree. Here is a simple rooted tree. bacteria birds marsupials Homo sapiens Terminals/Taxa node root The labels at the top of the tree could be individual species or sets of species that comprise one branch of the tree of life. General terms for the items represented by these labels are terminals or taxa (in more mathematical circles they are called leaves ). The branching points, corresponding to inferred speciation events, are called nodes. The internal branches or internodes connect two nodes whereas external branches or tips connect a terminal and a node.
Unless indicated otherwise a phylogenetic tree drawing depicts branching relationships only. The pattern of relationships is what matters and branch-lengths are irrelevant--they are just drawn in such a way that tree looks tidy. Thus, the following three trees contain the same information. A B C D A B C D A B C Similarly, the same information is depicted if the tree is oriented differently or is drawn with rectangular branches: D D C B A B C D A Sometimes rectangular phylogenetic trees are drawn so that branch lengths do mean something. These are often called phylograms. They generally depict either the amount of evolution occurring in a particular gene sequence, or the estimated duration of branches. How to read a tree When looking at a tree the most important this to look at it the relative branching order, because it is this that contains information about relatedness. In doing so one must take care not to be distracted by the shape of the tree and how close two tips are to each other. Considering the tree to the right and looking at taxa A and B one might think that they are closely related because the tip labels are right next to each other. In fact A and B are as distantly related as any pair of taxa on the tree. Indeed B is more closely related to E than to A. A B C D E The problem with looking at the order of taxa along the tips is that two trees showing the same fundamental relationships can have the taxa in different orders. If you recall the way that a phylogeny grows by ancestral lineages splitting in to descendant lineages, it is arbitrary which descendant lineage one draws to the right or left. Thus one can spin parts
of the tree around any internode without changing the implied relationships. If you can change one tree into another tree by simply twisting or bending branches, without ever having to cut and re-attach branches, then the two trees depict the same relationships; indeed they are really just different views of the same tree. For example, these three trees are one and the same: E D C B A A E D C B A B D E C Trees and similarity In interpreting phylogenetic trees it is important to remember that what is depicted is the inferred pattern of lineage branching. While closely related organisms usually look quite similar, sometimes they may not be, because morphological evolution can occur at different rates on different branches of a phylogeny. As a result, two taxa can be quite similar but distantly related or, conversely, quite different but closely related. This is well illustrated by the following phylogeny, which correctly depicts the currently accepted relationships among these familiar organisms (evidence for this tree comes from both molecular and morphological data). mammal lizard crocodile bird According to this tree, crocodiles are more closely related to birds than to lizards. How can that be? It is, after all, an indisputable fact that a crocodile has more morphological similarities to a lizard than to a bird. However, the similarities of crocodiles and lizards, such as the sprawling gait, elongated tail, and scales, are features that trace back to the MRCA of lizards, crocodiles, and birds (and mammals too, actually). While the lizard and crocodile lineage have both retained this ancestral body form, birds (and, to a lesser extent, mammals) underwent dramatic evolutionary divergence. Birds evolved such divergent features as feathers, flight, a wishbone, a keeled sternum, warm-bloodedness, loss of a tail, loss of teeth, and a four-chambered heart. Nonetheless, the number of unique features of birds does not change the fact that a crocodile is more closely related to a bird than to a lizard. Relatedness is about descent not similarity.
Clades and monophyly A clade is a chunk 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 ) and, thus, may also be called a monophyletic group. A clade/monophyletic group is easy to identify visually: it is simply a piece of a larger tree that can be cut-off with a single cut. If one needs to cut the tree in two places to extract a set of taxa then that group is non-monophyletic. Nowadays, systems of classification strive to only give formal names to monophyletic groups. mammal lizard crocodile bird Collapsing and pruning Monophyletic group = clade mammal lizard crocodile bird Phylogenetic trees only depict relationships among the terminals that are included. Nonetheless, the tree like form has the desirable property that pruning taxa off a tree does not change the implied relationships of the remaining taxa. Thus, give the tree on the left, the two trees on the right would both correctly represent the phylogeny for the remaining species. Non-monophyletic group A B C D E F G A B C G A D F G Similarly, if one collapses a monophyletic groups to a single taxon, its relationship to the remainder of the tree is unchanged. A B C D E F G A B C H Clade H
Inferring character evolution using phylogenetic trees One of the main reasons that phylogenetic trees are useful is that they provide a simple way to infer when particular characteristics of living organism evolved. For example, given the following tree, when did seeds evolve? seeds seeds seeds seeds Any number of scenarios are possible, for example, seeds could have evolved four times in the four species to the right or seeds could have been present in the common ancestor of all seven taxa, but have been lost in the three leftmost terminals. However, the simplest or, to use the technical term, most-parsimonious explanation is that there was a single origin of seeds seeds seeds seeds seeds Seeds evolve The parsimony criterion states that the most plausible mapping of a character onto a tree is that which invokes the fewest changes. This does not guarantee that this is what actually happened, but simply means that in the absence of contrary evidence, this is the best bet for the true evolutionary history.