What a phylogenetic tree is. How to read phylogenetic trees and determine which species are most related.

Key points:

  • A phylogenetic tree is a diagram that represents evolutionary relationships among organisms. Phylogenetic trees are hypotheses, not definitive facts.
  • The pattern of branching in a phylogenetic tree reflects how species or other groups evolved from a series of common ancestors.
  • In trees, two species are more related if they have a more recent common ancestor and less related if they have a less recent common ancestor.
  • Phylogenetic trees can be drawn in various equivalent styles. Rotating a tree about its branch points doesn't change the information it carries.

Introduction

Humans as a group are big on organizing things. Not necessarily things like closets or rooms; I personally score low on the organization front for both of those things. Instead, people often like to group and order the things they see in the world around them. Starting with the Greek philosopher Aristotle, this desire to classify has extended to the many and diverse living things of Earth.
Most modern systems of classification are based on evolutionary relationships among organisms – that is, on the organisms’ phylogeny. Classification systems based on phylogeny organize species or other groups in ways that reflect our understanding of how they evolved from their common ancestors.
In this article, we'll take a look at phylogenetic trees, diagrams that represent evolutionary relationships among organisms. We'll see exactly what we can (and can't!) infer from a phylogenetic tree, as well as what it means for organisms to be more or less related in the context of these trees.

Anatomy of a phylogenetic tree

When we draw a phylogenetic tree, we are representing our best hypothesis about how a set of species (or other groups) evolved from a common ancestorstart superscript, 1, end superscript. As we'll explore further in the article on building trees, this hypothesis is based on information we’ve collected about our set of species – things like their physical features and the DNA sequences of their genes.
Nope! A phylogenetic tree may show relationships at various levels. For instance, we could build different phylogenetic trees that showed relationships among populations, subspecies, species, or large clusters of related species.
These various types of groups can all be referred to as taxa, a blanket term for a population or group of populations that form a unit. So, we can build phylogenetic trees for different kind of taxa.
In this article, we'll mostly refer to trees that represent species, just to keep things simple. But the basic principles we're describing can be applied to trees that "zoom in" to populations or "zoom out" to large groups of related species.
In a phylogenetic tree, the species or groups of interest are found at the tips of lines referred to as the tree's branches. For example, the phylogenetic tree below represents relationships between five species, A, B, C, D, and E, which are positioned at the ends of the branches:
Image modified from Taxonomy and phylogeny: Figure 2 by Robert Bear et al., CC BY 4.0
The pattern in which the branches connect represents our understanding of how the species in the tree evolved from a series of common ancestors. Each branch point (also called an internal node) represents a divergence event, or splitting apart of a single group into two descendant groups.
At each branch point lies the most recent common ancestor of all the groups descended from that branch point. For instance, at the branch point giving rise to species A and B, we would find the most recent common ancestor of those two species. At the branch point right above the root of the tree, we would find the most recent common ancestor of all the species in the tree (A, B, C, D, E).
The diagram below shows how each species in the tree can trace its ancestry back to the most recent common ancestor at the branch point above the root:
Image modified from Taxonomy and phylogeny: Figure 2 by Robert Bear et al., CC BY 4.0
Each horizontal line in our tree represents a series of ancestors, leading up to the species at its end. For instance, the line leading up to species E represents the species' ancestors since it diverged from the other species in the tree. Similarly, the root represents a series of ancestors leading up to the most recent common ancestor of all the species in the tree.

Which species are more related?

In a phylogenetic tree, the relatedness of two species has a very specific meaning. Two species are more related if they have a more recent common ancestor, and less related if they have a less recent common ancestor.
We can use a pretty straightforward method to find the most recent common ancestor of any pair or group of species. In this method, we start at the branch ends carrying the two species of interest and “walk backwards” in the tree until we find the point where the species’ lines converge.
For instance, suppose that we wanted to say whether A and B or and B and C are more closely related. To do so, we would follow the lines of both pairs of species backward in the tree. Since A and B converge at a common ancestor first as we move backwards, and B only converges with C after its junction point with A, we can say that A and B are more related than B and C.
Image modified from Taxonomy and phylogeny: Figure 2 by Robert Bear et al., CC BY 4.0
Importantly, there are some species whose relatedness we can't compare using this method. For instance, we can't say whether A and B are more closely related than C and D. That’s because, by default, the horizontal axis of the tree doesn't represent time in a direct way. So, we can only compare the timing of branching events that occur on the same lineage (same direct line from the root of the tree), and not those that occur on different lineages.

Some tips for reading phylogenetic trees

You may see phylogenetic trees drawn in many different formats. Some are blocky, like the tree at left below. Others use diagonal lines, like the tree at right below. You may also see trees of either kind oriented vertically or flipped on their sides, as shown for the blocky tree.
Image modified from Taxonomy and phylogeny: Figure 2 by Robert Bear et al., CC BY 4.0
The three trees above represent identical relationships among species A, B, C, D, and E. You may want to take a moment to convince yourself that this is really the case – that is, that no branching patterns or recent-ness of common ancestors are different between the two trees. The identical information in these different-looking trees reminds us that it's the branching pattern (and not the lengths of branches) that's meaningful in a typical tree.
Another critical point about these trees is that if you rotate the structures, using one of the branch points as a pivot, you don’t change the relationships. So just like the two trees above, which show the same relationships even though they are formatted differently, all of the trees below show the same relationships among four species:
Image modified from Taxonomy and phylogeny: Figure 3 by Robert Bear et al., CC BY 4.0
If you don’t see right away how that is true (and I didn’t, on first read!), just concentrate on the relationships and the branch points rather than on the ordering of species (W, X, Y, and Z) across the tops of the diagrams. That ordering actually doesn’t give us useful information. Instead, it’s the branch structure of each diagram that tells us what we need to understand the tree.
So far, all the trees we've looked at have had nice, clean branching patterns, with just two lineages (lines of descent) emerging from each branch point. However, you may see trees with a polytomy (poly, many; tomy, cuts), meaning a branch point that has three or more different species coming off of itstart superscript, 2, end superscript. In general, a polytomy shows where we don't have enough information to determine branching order.
Image modified from Taxonomy and phylogeny: Figure 2 by Robert Bear et al., CC BY 4.0
If we later get more information about the species in a tree, we may be able to resolve a polytomy using the new information.

Where do these trees come from?

To generate a phylogenetic tree, scientists often compare and analyze many characteristics of the species or other groups involved. These characteristics can include external morphology (shape/appearance), internal anatomy, behaviors, biochemical pathways, DNA and protein sequences, and even the characteristics of fossils.
To build accurate, meaningful trees, biologists will often use many different characteristics (reducing the chances of any one imperfect piece of data leading to a wrong tree). Still, phylogenetic trees are hypotheses, not definitive answers, and they can only be as good as the data available when they're made. Trees are revised and updated over time as new data becomes available and can be added to the analysis. This is particularly true today, as DNA sequencing increases our ability to compare genes between species.
In the next article on building a tree, we’ll see concrete examples of how different types of data are used to organize species into phylogenetic trees.

Attribution

This article is a modified derivative of the following articles:
The modified article is licensed under a CC BY-NC-SA 4.0 license.

Works cited

  1. John. W. Kimball, "Taxonomy: Classifying Life," Kimball's Biology Pages, last modified December 16, 2013, http://www.biology-pages.info/T/Taxonomy.html.
  2. Jack R. Holt, "Polytomy," Dictionary of Terms,ast revised January 2, 2009, http://comenius.susqu.edu/biol/202/dictionary%20of%20terms/p/polytomy.htm.

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