Phylogenetic Trees

Systematics is the study of the diversity of living things and their evolutionary (or phylogenetic) relationships. You'll find a detailed discussion of systematics in Chapter 26 of Campbell; you should look over that chapter before doing the systematics lab. I will cover systematics in lecture, but we will also do a lab exercise on this topic. That's why this page is listed under both lab and lecture. You'll learn about various aspects of systematics in Bio 6A, but this page focuses specifically on phylogenetic trees.

Read this page and Chapter 26 (Phylogeny and the Tree of Life) in Campbell before the Systematics lab. Later, on a lab quiz and the midterm, I will ask you some questions about how to make and interpret cladograms.

Systematics Lab Assignment

There will be a lab exercise for you to complete during the Systematics lab. It will be based mostly on the information on this page. Shortly before the lab begins, I will post a new page containing a series of questions; you should work together with your lab partners to answer these during the lab, and turn in your answers before you leave.

Bring a Scantron to lab (the long one with 50 questions per side; it doesn't matter which color).

Go to the Systematics lab assignment (won't be available until shortly before lab).

Objectives

  • By the time you complete this lab, you should be able to interpret cladograms in terms of what they say about phylogeny and evolutionary events.
  • In addition, this lab exercise will give you some practice with reading scientific journal articles.

Remember, you'll be tested on cladograms in both lecture and lab.

Phylogenetic trees show evolutionary history

New species of organisms form when an existing species gets split into two separate groups that don't interbreed. This branching process can be shown in a tree diagram (or dendrogram) called a phylogenetic tree.

Phylogenetic trees show shared ancestry

This diagram says that dogs and cats shared a common ancestor more recently than either shared a common ancestor with goats. Each branching point on the phylogenetic tree is a node. Node A represents a species that split in two to become the ancestor of goats, dogs, and cats. Node B represents a species that split to become the ancestor of dogs and cats, but not goats. The tree diagram shows a phylogeny -- a group of organisms connected by their evolutionary ancestry. Keep in mind that not all phylogenetic trees are correct; they simply show hypotheses about phylogeny. This phylogenetic tree can also be called a cladogram, which means that it follows the specific rules of the cladistic approach to systematics. For the purposes of this class, we don't need to worry about whether a specific tree diagram qualifies as a cladogram. I will often use the terms phylogenetic tree and cladogram interchangeably.

The root is the species that was the ancestor to everything shown in the cladogram.

Phylogenetic trees show evolutionary events

Each node represents a shared ancestor; in general, these ancestors are extinct. In this phylogenetic tree, goats are not the ancestors of cats and dogs; instead, there was some other ancestral species that was the ancestor of goats, cats, and dogs. You don't need to identify the extinct ancestor in order to make a phylogenetic tree; by comparing living species, you can infer that they must have shared an ancestor.

The node doesn't only represent an ancestral species, though. It also represents an evolutionary event in which this ancestral species split into two species, and one species acquired a characteristic that doesn't occur in the other. For example the ancestor of both cats and dogs didn't have retractable claws, but cats do. We could label the cladogram in terms of the presence or absence of these characteristics: branch C has retractable claws and branch D doesn't.

In other words, each branch of a cladogram must be defined by a characteristic that occurs on that branch, but not the adjacent branch. The characteristics used to define the branches are yes/no options: retractable claws on the cat branch, no retractable claws on the dog branch. Of course, there are many differences between cats and dogs, but you only need one evolutionary change to define the cladogram.

A clade is a monophyletic group

Cladograms show groups of organisms that share a common ancestor -- in other words, clades. A clade can also be called a monophyletic group -- in other words, an ancestral species and all of its descendants. A single cladogram can show multiple clades, and one clade can be nested within another.

The question of whether a group of organisms is monophyletic is important in biology. For example, dogs and cats both have carnassial teeth, a feature found only in particular groups of mammals. Did they both inherit this style of dentition from a common ancestor, or did their carnassials evolve separately? In other words, do all the mammals with carnassial teeth form a monophyletic group, with the carnassial teeth first appearing in a shared ancestor? If so, we can say that the carnassial teeth of dogs are homologous to those of cats. If the last common ancestor of cats and dogs didn't have carnassial teeth and the carnassials evolved separately in each group, we'd say that the carnassials of dogs are analogous to those of cats. We'll come back to these teeth later this quarter, in the skeleton lab.

A clade can be rotated around a node

Consider these two variations of our earlier cladogram:

Both these diagrams say exactly the same thing. It doesn't matter whether you put the dog or the cat on top; in either case, the closest ancestor of both dog and cat is at node B and the closest ancestor of both dog and goat is at node A. If you could grab the dog-cat clade and twist it back and forth, you wouldn't be changing the phylogenetic relationships in the diagram.

Line length can express time

Now compare these two versions of the phylogenetic tree:

They're almost the same, except for the position of the dog-cat split. Which one is more accurate? To answer that, we need to define the length of the lines on the tree. In some cases, line length corresponds to time; if so, the tree needs a time scale, like this:

According to this phylogenetic tree, the last common ancestor of goat, dog, and cat was 90 million years ago while the last common ancestor of dog and cat was 65 million years ago. Note that we're talking about time before present, so zero is on the right and the scale goes futher back in time as you move left. Technically, a true cladogram would simply show branching order; if line legth is defined as in this example, it's better to call it a phylogenetic tree.

Line length can express evolutionary change

Biologists would love to be able to make accurate phylogenetic trees showing every species that ever existed, with all the branching events labeled in terms of when they occurred. Unfortunately, we don't know enough to do this. It's not possible to pin down the time for every split, because the ancestral species may have disappeared. There is always some uncertainty about the timing of the splits.

Modern tree diagrams are most often made by comparing the DNA or protein sequences of living species and using statistical methods to compare data from different species. Thus, phylogenetic studies often produce trees in which the scale is not millions of years ago, but the number of genetic differences among species.  The computational and statistical methods used in such studies are an essential part of the field of bioinformatics. These complex methods are well beyond Bio 6A, but you can see examples in the research articles cited at the bottom of this page.

A cladogram for rhinos

This diagram comes from the article Osteopathology in Rhinocerotidae from 50 Million Years to the Present by Kelsey Stilson and co-authors (published in PLOS One; CC BY) This fascinating article points out that the rhinoceros family has contained numerous species, ranging in size from big to truly huge. Studying bones of living rhinos and fossils of extinct species, the authors found that the more massive rhinos became, the more likely they were to have bone deformities or injuries. Large size may have helped rhinos to avoid predation, but it caused problems of its own.

Rhinoceros phylogenetic tree

This phylogenetic tree has some interesting features:

  • Time scale. The scale on the top is in terms of --millions of years ago (often abbreviated mya). At right is the present: 0 mya. The scale goes back to 50 mya; before that, there were no rhinoceroses.
  • Some taxa are extinct.  Only one species, Diceros bicornis, the Black Rhinoceros, reaches the present; all the other branches stop before reaching 0 mya, because those species went extinct. Trigonias osborni went extinct over 30 million years ago. The thick blue bars at the ends of the branches represent the age ranges of the fossils used for the study. There are other species of living rhinos, but they weren't included in the study.
  • Pictures of the organisms so we can have some idea what they are. These pictures were drawn by the paper's first author, Kelsey Stilson.
  • An outgroup (also called a sister group). The species at the top, Hyrachyus eximius, is not a rhino; it was a close relative, but outside the rhinoceros clade.

Along with the research article cited above, there is also an interview with Kelsey Stilson. You might be surprised to learn that she began this research project while she was an undergraduate!

A cladogram for carnivores

In the lab exercise, I will ask you some questions based on the cladograms in the article Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates, published in BMC Biology (reference below).

You're not a carnivore

The word "carnivore" can have two meanings. In common usage, it means an animal that eats meat. In the context of the systematics of mammals, it means a member of the order Carnivora. While you might or might not eat meat, you are not part of the order Carnivora. Campbell has a good brief summary of mammalian orders; we'll come back to that topic in lab when we look at skulls.

This research article is about making a detailed cladogram showing the phylogeny of all species in the order Carnivora, in the class Mammalia. As various researchers have analyzed the genomes of various, they have been able to improve their understanding of the particular evolutionary relationships among these species. In this paper, the researchers have created a "supertree" by analyzing the data used in many other studies and creating a tree showing a large number of species.

The statistical methods used in this study are challenging; luckily for both you and me, we only need to look at how the results are presented in cladograms. You don't need to read the whole article, but I recommend reading the abstract and scanning the rest to see how the article is structured. The cladograms themselves are beautiful: packed with information and easy to read if you know what you're looking at.

Figure 2

Look at figure 2 from the article. Fascinating! Of course, it would be more interesting if you knew all the latin names on the right side of the diagram, and people who already know all those names probably aren't taking Bio 6A. Here's a slightly modified version of the same figure; I have added common names for some of the taxa (species or families). If the name is two words, shown in italics, it's the name of a species. Note that the first word (the genus) is capitalized and the second (the specific epithet) is not. If the name is one word, not italicized, and ends in -idae, it's the name of a family.

The purple bars around the nodes represent the level of uncertainty as to when the split occurred. Technically, these are known as 95% confidence intervals. For example, look at the split between the two species on the bottom, Norway rat and house mouse. According to the cladogram, these two branches probably became separate from one another around 22 million years ago. Prior to that, there was a rodent species that became the ancestor to both the mouse and the rat. Of course, researchers aren't certain exactly when this split occurred. According to the data used for this cladogram, we can be 95% certain that the split occurred between approximately 19 and 25 million years ago. The exact date of the split might not seem important, but when there are numerous branches and a high degree of uncertainty, it's impossible to determine which splits happened first.

The numbers on the purple bars are there to identify each node; the text of the research article explains exactly what data were used to determine each node. For the purposes of this lab, you can ignore those numbers, unless you want to refer to a specific node.

Using this cladogram, you could determine the time of the last common ancestor of any two taxa. In the systematics lab exercise, I will ask you some questions about the relationships and ancestry of some of the taxa shown in the diagram.

Figure 1

Look at figure 1 from the article. This cladogram shows all the known species in the order Carnivora. There are too many species to fit in a regular cladogram, so the authors have created a circular one. The root is in the middle, and the concentric circles are the time scale. This is a common way of expressing cladograms with large numbers of branches. There's a bounty of information in that diagram, but unfortunately it's a little hard to read. (If you look at the figure and click on "download authors' original image," you can see a large and detailed version of the same image.)

If you've read this whole page, you're ready for the systematics lab assignment, which will be available online shortly before the lab.

Review

Vocabulary

You should be able to apply and explain these terms:

  • Clade
  • Cladogram
  • Homology vs. analogy
  • Monophyletic group
  • Node
  • Phylogeny
  • Taxon/taxa. A taxon is any taxonomic grouping of organisms: a species, genus, family, etc. Taxa is the plural of taxon.

Concepts

  • Draw several cladograms that show the same phylogeny in different ways. How do you know if two cladograms show different phylogenetic relationships?
  • What does branch length represent in a cladogram?
  • Looking at two species shown in a cladogram, how do you know if they belong to the same family? To the same order?
  • Suppose you know that a particular biochemical process occurs in both rats and mice. How confident would you be that the same process also occurs in humans? Now suppose that you know that another process occurs in both mice and dogs. In that case, how confident would you be that this process also occurs in humans? Explain your answer in terms of figure 2 above.

Remember, you'll find all this explained in Chapter 25 of Campbell, along with a good deal more about systematics.

References and further reading

Basic references

Flanagan, Jean, 2013. Learning to Read the Tree of Life. PLOS Blogs. This article approaches cladograms from the point of view of how to teach them; it contains some interesting insights into ways of visualizing phylogeny.

Journey into Phylogenetic Systematics. University of California Museum of Paleontology, UC Berkeley. Gives a good overview of the topics covered in this page. The UCMP site is a good source for many topics in evolutionary biology.

Phylogenetic systematics, a.k.a. evolutionary trees, from Understanding Evolution at UC Berkeley.

The Tree-Thinking Challenge. David A. Baum, Stacey DeWitt Smith, Samuel S. S. Donovan, 2005. Science Magazine. Good article about teaching and learning how to use evolutionary trees. The original is behind a paywall, but a copy is available at Bioquest.org.

Research articles discussed in this page

Kelsey T. Stilson, Samantha S. B. Hopkins, Edward Byrd Davis, 2016. Osteopathology in Rhinocerotidae from 50 Million Years to the Present. PLOS One. You might also be interested in the interview about this article and Kelsey Stilson's website.

Nyakatura, K. and Olaf Bininda-Edmonds, 2012. Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates. BMC Biology 2012, 10:12.

Further reading: research articles based on cladograms

Tim H Heupink, Hein van Grouw and David M Lambert, 2014. The mysterious Spotted Green Pigeon and its relation to the Dodo and its kindred. BMC Evolutionary Biology 2014, 14:136. This recent research article shows how modern phylogenetic studies are done. The authors found a dried specimen of an extinct species of pigeon -- the only known example of its species -- in a museum collection. They used DNA methods to compare a small part of its genome to those of other bird species, living and extinct. They present their results in terms of cladograms showing degree of DNA difference among species. For a news article about this study, see Dodos and spotted green pigeons are descendants of an island hopping bird. ScienceDaily, 15 July 2014.

Davis KE, Page RDM. Reweaving the Tapestry: a Supertree of Birds. PLOS Currents Tree of Life. 2014 Jun 9. If you're interested in the phylogenetic relationships of birds, you'll find them here. There are a lot of species of birds on this planet (10,000 species!); this article gives an overview of the relationships among the orders. PLOS Currents Tree of Life is an online scientific journal dedicated to publishing phylogenetic studies. It's filled with cladograms!

Roquet C, Lavergne S, Thuiller W. One Tree to Link Them All: A Phylogenetic Dataset for the European Tetrapoda. PLOS Currents Tree of Life. 2014 Aug 8. Biology's quest to understand the phylogeny of all living things continues. In this article, the authors present a set of incredibly detailed cladograms attempting to show all the tetrapod vertebrates in Europe. If you like being overwhelmed by detail, you'll love this! Scroll to the bottom and click on figure 3 -- I dare you.

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