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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 ancestor
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:
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:
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 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.
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.
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:
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 it
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:
"Taxonomy and phylogeny," by Robert Bear, David Rintoul, Bruce Snyder, Martha Smith-Caldas, Christopher Herren, and Eva Horne, CC BY 4.0. Download the original article for free at http://cnx.org/contents/db89c8f8-a27c-4685-ad2a-19d11a2a7e2e@24.18.
"Organizing life on Earth," by OpenStax College, Biology, CC BY 4.0. Download the original article for free at http://cnx.org/contents/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.8.
The modified article is licensed under a CC BY-NC-SA 4.0 license.
Works cited
John. W. Kimball, "Taxonomy: Classifying Life," Kimball's Biology Pages, last modified December 16, 2013, http://www.biology-pages.info/T/Taxonomy.html.
Jack R. Holt, "Polytomy," Dictionary of Terms,ast revised January 2, 2009, http://comenius.susqu.edu/biol/202/dictionary%20of%20terms/p/polytomy.htm.
References
Baum, David. "Reading a Phylogenetic Tree: The Meaning of Monophyletic Groups." Nature Education 1, no. 1 (2008): 190. http://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-41956.
"Building the Tree." Understanding Evolution. Accessed July 5, 2016. http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_08.
"Cladistics." Wikipedia. Last modified June 19, 2016. https://en.wikipedia.org/wiki/Cladistics.
"Cladistics and Classification." Rediscovering Biology. Accessed July 5, 2016. https://www.learner.org/courses/biology/textbook/compev/compev_3.html.
Holt, Jack R. "Polytomy." Dictionary of Terms. Last revised January 2, 2009. http://comenius.susqu.edu/biol/202/dictionary%20of%20terms/p/polytomy.htm.
Kimball, John W. "Taxonomy." Kimball’s Biology Pages. Last modified December 16, 2013. http://www.biology-pages.info/T/Taxonomy.html.
OpenStax College, Biology. "Determining Evolutionary Relationships." OpenStax CNX. Last modified March 23, 2016. http://cnx.org/contents/GFy_h8cu@10.8:tOc5w74I@5/Determining-Evolutionary-Relat.
"Part 1 - Reading Phylogenetic Trees." Accessed July 5, 2016. http://medsocnet.ncsa.illinois.edu/MSSW/moodle/AuthTut/vpage_beta.php?tid=218&&pid=1055.
"Phylogenetics: DNA Protocol." Intro Biology: BIOL153. Accessed July 5, 2016. http://bcrc.bio.umass.edu/intro/content/phylogenetics-dna-protocol.
Purves, William K., David Sadava, Gordon H. Orians, and H. Craig Heller. "Reconstructing and Using Phylogenies." In Life: The Science of Biology, 496-509. 7th ed. Sunderland, MA: Sinauer Associates, 2003.
"Reconstructing Trees: A Simple Example." Understanding Evolution. Accessed July 5, 2016. http://evolution.berkeley.edu/evolibrary/article/phylogenetics_07.
Reece, Jane B., Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, and Robert B. Jackson. "Phylogeny and the Tree of Life." In Campbell Biology, 547-558. 10th ed. San Francisco: Pearson, 2011.
Thanukos, Anna and Allen Collins. "Phylogenetic Systematics, a.k.a. Evolutionary Trees." Understanding Evolution. Accessed July 5, 2016. http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01.
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Log in Harsh*ta Wadhwa 6 years agoPosted 6 years ago. Direct link to Harsh*ta Wadhwa's post “Can a phylogenetic tree s...” Can a phylogenetic tree show which organism is more evolved, if they evolved at the same nod? • (16 votes) tyersome 6 years agoPosted 6 years ago. Direct link to tyersome's post “Look at (or make) a tree ...” Look at (or make) a tree showing your family going back at least to your grandparents. First question: What does this tell you about people in your family? Phylogenetic trees are really very similar, but for species rather than individuals within a family. Second question: What do you mean by "more evolved"? Does this help? (19 votes) Ahmed Al-Azawy 6 years agoPosted 6 years ago. Direct link to Ahmed Al-Azawy's post “What phylogenetic trees c...” What phylogenetic trees can and can’t tell us • (5 votes) Bilal 6 years agoPosted 6 years ago. Direct link to Bilal's post “One example that comes to...” One example that comes to mind is that a phylogenetic tree determines where two organisms diverged from their common ancestors but not specifically when. These diagrams are not chronological in a direct way, more so a before and after situation. (Hope I helped, correct me if I am wrong) (15 votes) shivkant.95173 7 years agoPosted 7 years ago. Direct link to shivkant.95173's post “how to represent an extin...” how to represent an extinct specie in a tree diagram • (6 votes) Harsh*ta Wadhwa 6 years agoPosted 6 years ago. Direct link to Harsh*ta Wadhwa's post “Ending a line before pres...” Ending a line before present day shows that a species is extinct (9 votes) Omelette Kai 5 years agoPosted 5 years ago. Direct link to Omelette Kai's post “how did a common whale ev...” how did a common whale evolve from a common ancestor? • (4 votes) tyersome 5 years agoPosted 5 years ago. Direct link to tyersome's post “I'm not sure what you mea...” I'm not sure what you mean by a "common whale". The following has information on whale evolution: If that doesn't help, can you please clarify your question? (6 votes) Benjamin Garretson 6 years agoPosted 6 years ago. Direct link to Benjamin Garretson's post “In the phylogenetic tree ...” In the phylogenetic tree containing A,B,C,D,E, what is the closest relative to E? • (0 votes) 5 years agoPosted 5 years ago. Direct link to India's post “E's closest relative is w...” E's closest relative is whatever species is at the first node (the first 2 branches that extend from the root, or trunk) (2 votes) geniusenock2000 7 years agoPosted 7 years ago. Direct link to geniusenock2000's post “how does phylogenetic cla...” how does phylogenetic classification related to phenetic classification? • (1 vote) Ryan Hoyle 7 years agoPosted 7 years ago. Direct link to Ryan Hoyle's post “Phenetic speciation means...” Phenetic speciation means classification of species by appearance alone. For example if two frogs look similar they are called a species even if they cannot mate. (6 votes) Melody Liu 5 years agoPosted 5 years ago. Direct link to Melody Liu's post “The fact that branches ca...” The fact that branches can be rotated and still remain true indicates that branching order (the order in which species are listed) doesn't matter. If that's the case, I don't understand the purpose of polytomy. This article says it's because we don't know the branching order, but why does that matter? • (2 votes) tyersome 5 years agoPosted 5 years ago. Direct link to tyersome's post “I think you may have misu...” I think you may have misunderstood what branching order means — confusingly it doesn't mean the order of the branches! Rotation doesn't change the branching order — it rearranges the order of the branch tips, which we all agree isn't significant. Branching order is being used to describe the sequence in which species split from each other. Thus, a polytomy is a way of acknowledging that there is not yet enough information to say which of the species split off from the common ancestor first. Take the example PQR polytomy — we know that the ancestral population ("PQR") probably first split into one of the following: And then the second population split again. This is what the article means by branching order. Does that help? (4 votes) MagicalSea 6 years agoPosted 6 years ago. Direct link to MagicalSea's post “How would you draw a phyl...” How would you draw a phylogenetic tree given simple DNA sequences between species? • (0 votes) Satwik Pasani 6 years agoPosted 6 years ago. Direct link to Satwik Pasani's post “It is a difficult task. W...” It is a difficult task. What you are asking is phylogenetic reconstruction from genomic sequence analysis. There are some ways to do this. One obvious way is to consider two species closest if they match at more base pairs. But what is difficult is to decide if one arose from the other or if they are at the same level, arising from a different common ancestor. All of this is very difficult and many algorithms are available, especially since genomic data itself is large, complex (different kinds of genomic data is available - RNA, DNA, Methylated DNA etc) and also based on what we know of the function of the genes (difference in functional gene is a more significant difference than the difference in non-functional genes). If you are interested, look up maximum-parsimony methods of phylogenetic tree reconstructions. (8 votes) Caleb Ye 4 years agoPosted 4 years ago. Direct link to Caleb Ye's post “When constructing a phylo...” When constructing a phylogeny, what is the maximum number of branches that can come directly from the same hypothetical common ancestor? • (3 votes) jameshickey2023 4 years agoPosted 4 years ago. Direct link to jameshickey2023's post “How are we able to the si...” How are we able to the similarities between two organisms in one specific branch. • (2 votes) Ivana - Science trainee 4 years agoPosted 4 years ago. Direct link to Ivana - Science trainee's post “To find similarities? Loo...” To find similarities? Look at the structure and function fo the organisms. Comparative anatomy, morphology. (3 votes)Want to join the conversation?
https://evolution.berkeley.edu/evolibrary/article/evograms_03
Phylogenetic classification does consider appearance and phenotype, but it also goes much further in terms of looking at functionality, and comparison of genomes. Phylogentics explains an organisms evolutionary history. This is a more rigorous system than phenetics.
P + "QR"
Q + "PR"
R + "PQ"
Lookign at the biogeography as well.
