GEOL G114 Dinosaurs and Their Relatives

GEOL G114 Spring 2017 Dinosaurs and Their Relatives

Tutorial on phylogenetic trees and synapomorphies

Phylogenetic trees show the relationships of groups of organisms. In paleontology, the evidence for phylogeny comes from analysis of characters of the skeleton (or other fossilizeable parts). This exercise introduces the terminology of trees and characters. It also explains how trees are constructed from characters.

An answer key to the practice questions appears at the end of this guide starting on page 9.

Tree terminology

Phylogenetic trees show the evolutionary connections between taxa. They are made up of branches (the lines), nodes (connection points between lines), and tips (the groups or taxa at the ends of the lines). This tree has seven tips, six nodes (numbered 1 to 6), and twelve branches. The node that is furthest from the tips is also known as the root (Node 1). Another common name for phylogenetic tree is cladogram. Regardless of how the tree is drawn, “down” is the direction along a branch toward the root and “up” is toward the tips.

tip

Ankylosaurus Triceratops Pachycephalosaurus Edmontosaurus Diplodocus Tyrannosaurus Velociraptor

4 6 3 5 2 branch node

Root (lowermost node)

Figure 1. A typical phylogenetic tree

Phylogenetic trees show patterns of ancestry. Each node represents an ancestor of all the tips that lie above it. If you trace the branches of two tips down the tree, the node where the two paths meet is said to represent their last common ancestor. Node 4 is the last common ancestor of Triceratops and Pachycephalosaurus, and Node 2 is the last common ancestor of Triceratops, Pachycephalosaurus, Edmontosaurus, and Ankylosaurus. The term last is used because deeper nodes

Indiana University | Department of Geological Sciences © 2017, P. David Polly are also ancestors. For example, Node 1 is an ancestor of all four tips just mentioned, but it is not the uppermost or last.

Practice questions

1. Which node is the last common ancestor of Diplodocus and Velociraptor? 2. Which node is the last common ancestor of Diplodocus and Triceratops? 3. Which node is the last common ancestor of Edmontosaurus and Tyrannosaurus? 4. Name all the tips descended from Node 3.

Nodes represent groups (clades)

Each node of a tree is equivalent to a group or clade. A clade, also known as a monophyletic group, is often defined as all of the descendants of a common ancestor. Node 2 thus represents a group containing Triceratops, Pachycephalosaurus, Edmontosaurus, and Ankylosaurus, as well as the nodes that lie above it (Nodes 3 & 4). Node 2 is equivalent to the group Ornithischia.

Ankylosaurus Velociraptor Triceratops Pachycephalosaurus Edmontosaurus Diplodocus Tyrannosaurus

4 6 3 5 2

Figure 2. Tree highlighting the clade defined by Node 2, which consists of Triceratops, Pachycephalosaurus, Edmontosaurus, and Ankylosaurus, as well as Nodes 3 and 4.

The clade defined by Node 2 also includes descendants that are not explicitly included on this tree. For example, Stegosaurus would also be part of the clade defined by Node 2 because it is closely related to Ankylosaurus.

Practice question

5. What tips and nodes are included in the clade defined by Node 5?

The information contained in a tree comes from the connections between nodes, not the angle it is drawn or whether the branches are angled, square, or round. The following trees are all the same except for their artistry and the number of tip taxa.

Triceratops 4 3 Pachycephalosaurus

Edmontosaurus Ankylosaurus Triceratops Pachycephalosaurus Edmontosaurus Diplodocus Tyrannosaurus Velociraptor Ankylosaurus Diplodocus Tyrannosaurus Velociraptor Edmontosaurus Pachycephalosaurus Triceratops 4 1 Ankylosaurus 6 6 4 3 5 Diplodocus 5 3 2 2

5 Tyrannosaurus 6 A 1 B Velociraptor 1 C

Velociraptor Ankylosaurus Triceratops Pachycephalosaurus Edmontosaurus Diplodocus Tyrannosaurus Velociraptor Triceratops Edmontosaurus Tyrannosaurus Ankylosaurus Edmontosaurus Tyrannosaurus Pachycephalosaurus Diplodocus Triceratops 4 6 4 6 3 5 2 3 5 3 2 Pruned tree D 1 E 1 1

Figure 3. The same tree drawn in several different styles. Four taxa have been pruned in E to construct a simplified tree that focuses on just Triceratops, Edmontosaurus, and Tyrannosaurus.

Even though these trees are drawn differently, they all show the same pattern of relationships and common ancestry. For example, Tyrannosaurus and Velociraptor are each other’s closest relatives and Edmontosaurus always shares a closer common ancestor with Triceratops than it does with Tyrannosaurus. Contrast the similarity in these trees with the differences in the trees in the following figure.

Ankylosaurus Ankylosaurus Triceratops Diplodocus Velociraptor Edmontosaurus Tyrannosaurus Triceratops Edmontosaurus Pachycephalosaurus Diplodocus Tyrannosaurus Velociraptor Pachycephalosaurus Tyrannosaurus Triceratops Edmontosaurus

A B C

Figure 4. Three trees that show very different relationships from those in Figure 3. The node labels have been removed because they are no longer equivalent between trees.

Practice Question

6. Which trees in Figure 4 show Edmontosaurus to be more closely related to Triceratops than to Tyrannosaurus?

Phylogenetic definitions are a way of mapping a group’s name onto a particular node of a tree.

Figure 5. Phylogenetic definition of Dinosauria is equivalent to the clade defined by Node 1 on this tree. The red lines trace Triceratops and Tyrannosaurus to their common ancestor, and all descendants of that ancestor therefore belong to Dinosauria (which is all 7 taxa on the tree)

Dinosauria is defined as the clade consisting of the last common ancestor of Triceratops and Tyrannosaurus and all descendants of that ancestor. To put the definition into action, first trace down from the two tips to find the node where they join: Node 1. Dinosauria is therefore the clade consisting of all tips and nodes upward from there (including ones that have not been drawn on this tree, like Stegosaurus).

Practice questions

Note that nodes correspond to dinosaur groups as follows: Node 2 = Ornithisichia; Node 3 = Cerapoda; Node 4 = Marginocephalia; Node 5 = Saurischia; Node 6 = Theropoda.

7. Give a phylogenetic definition for Saurischia. 8. Give a phylogenetic definition for Cerapoda. 9. Trace your phylogenetic definition for Saurischia on the trees in Figure 3. Does it pinpoint the same node? What about the trees in Figure 4?

If new evidence falsifies a phylogenetic tree, the definition does not change but the taxa included in a clade might. For example, if Tyrannosaurus was shown to be closely related to Edmontosaurus (Figure 6), then Ankylosaurus, Diplodocus, and Velociraptor would no longer be dinosaurs.

Figure 6. Hypothetical tree in which Tyrannosaurus is closely related to Edmontosaurus. If this were true, the node specified by the definition of Dinosauria would shift and Ankylosaurus, Diplodocus, and Velociraptor would no longer be included.

Practice questions

10. If the tree in Figure 6 were true, would Ornithischia be a subgroup of Dinosauria? 11. Would Cerapoda be a subgroup of Dinosauria?

Trees at their bare minimum

As diagrams, phylogenetic trees are flexible. They can be drawn in any orientation or with as many or as few taxa as the situation demands. Minimally a tree must have three taxa because any fewer would not convey information about which ones are more closely related.

Here are four trees that have been pruned down to three taxa, but remain consistent with Figure 1. Even though these are drawn with vertical lines instead of diagonal ones, you read them the same. Node numbers are shown to help you see the relationship.

Ankylosaurus Ankylosaurus Ankylosaurus Triceratops Triceratops Pachycephalosaurus Edmontosaurus Diplodocus Diplodocus Triceratops Tyrannosaurus Triceratops

3 2 2 4 1 1 1 2 A B C D

Figure 7. Three-taxon trees derived from the tree in Figure 1.

12. Using the same numbering system as Figure 1, put numbers on the nodes of the following trees:

Diplodocus Diplodocus Velociraptor Edmontosaurus Velociraptor Tyrannosaurus Edmontosaurus Triceratops Triceratops Edmontosaurus Tyrannosaurus Tyrannosaurus

A B C D

13. What clade names correspond to the nodes at the root of each of these four trees? 14. Why do trees A, B and C have the same root nodes even though they have different tip taxa? 15. Six different three-taxon trees can be constructed to show Nodes 1 and 3. What are they?

Characters and trees

Phylogenetic trees are built from observations from fossils. Specifically, trees are constructed from characters. First some definitions:

Synapomorphies are characters that are shared by members of a clade that they inherited from their last common ancestor. Example: mesotarsal ankle joint is a synapomorphy of Dinosauria.

Homoplasies are characters that evolved independently in two groups and were not found in their last common ancestor. Example: posteriorly pointing pubis is a homoplasy of Ornithischia and Maniraptora. (Note that a posteriorly pointing pubis is a synapomorphy of each one of those groups, but a homoplasy between them).

Reversals are characters that were originally found in the last common ancestor of a clade, but were subsequently lost in one or more of its members. Example: the loss of the antorbital fenestra in some Thyreophora is a reversal.

The characters

In this section, we will consider the characters in the following table. Characters that are present in each taxon are shown with a “Y” (meaning “yes” the character is present in that taxon). For example, Ankylosaurus has a mesotarsal ankle joint, a pubis that points backwards, and a palpebral bone, but it does not have a gap in the cheek teeth or a crest on the squamosal and parietal bones.

Ankylosaurus Triceratops Pachycephalosaur Edmontosaurus Diplodocus Tyrannosaurus Velociraptor A. Mesotarsal ankle Y Y Y Y Y Y Y B. Pubis points backward Y Y Y Y Y C. Palpebral bone Y Y Y Y D. Gap in cheek teeth Y Y Y E. Squamosal and parietal crest Y Y F. Loss of distal carpal 5 Y Y Y G. Accessory antorbital fenestra Y Y

Table 1. Seven characters for seven dinosaur taxa.

Mapping characters onto a tree

Characters can be “mapped” onto a tree by tracing them down from the tips to the node where they converge in common ancestor. For example, Character F (loss of a carpal bone) is found in Diplodocus, Tyrannosaurus, and Velociraptor. As shown on the next page (Figure 8), that character traces down to Node 5, which is Saurischia. Loss of the carpal bone is therefore a synapomorphy of Saurischia (we have not mentioned the loss of the carpal bone as a synapomorphy of Saurischia in class, but you will find it mentioned in your textbook).

Practice questions

16. Can you map the remaining characters onto the tree in Figure 8 (next page)? 17. What problems arise with mapping Character B?

Diplodocus Tyrannosaurus Velociraptor Ankylosaurus Triceratops Pachycephalosaurus Edmontosaurus A Y Y Y Y Y Y Y B Y Y Y Y Y C Y Y Y Y D Y Y Y E Y Y F Y Y Y G Y Y

4 6 3 5 2 F

Figure 8. Tree showing the characters possessed by each tip taxon. Character F has been “mapped” onto the tree, where it appears at Node 5 (Saurischia).

Advanced: hypothesis testing with trees

This is the advanced section. It goes beyond what you need to know for G114, but it will be interesting for anyone who wants to understand how phylogenetic trees are constructed.

The principle is parsimony: the best explanation for a set of data is the simplest one that explains all the observations. In phylogeny, the simplest reason why two or more taxa share a character is by having inherited it from a common ancestor. The alternative is that they evolved the character independently. Parsimony in phylogenetics therefore prefers the tree in which as few characters as possible evolve independently; in other words, the tree with the least homoplasy is preferred. To find the best tree you try all possible rearrangements to find the one with the least number of character changes.

How do you count character changes? Start by looking at the answer to Question 14, which shows all the characters from Table 1 mapped onto the tree from Figure 1. Literally count the colored bars, each of which represents the addition of a character. There are 8 changes, one for six of the characters and two for Character B. We’ll come back to this tree in a minute.

First let’s look at a simple example of three taxa and one character. Let’s use retroverted pubis: Triceratops = Y, Ankylosaurus = Y, Tyrannosaurus = N. There are four possible trees for these three taxa. Map the character onto each one and count...

Triceratops Tyrannosaurus Tyrannosaurus Ankylosaurus Ankylosaurus Ankylosaurus Ankylosaurus Tyrannosaurus Tyrannosaurus Triceratops Triceratops Triceratops Y Y Y Y Y Y Y Y

A B C D

Figure 9. The four possible trees for Triceratops, Ankylosaurus, and Tyrannosaurus.

Tree A has one character change, Trees B, C, and D all have two. Tree A is therefore the most parsimonious, or the one with the least homoplasy. Notice that homoplasy always increases the number of character changes, so we can also refer to Tree A as the one that minimizes the number of changes.

The tree in Figure 1 is the most parsimonious for the characters in Table 1. All other rearrangements would have more homoplasy. You can see this by mapping the characters onto that tree and comparing the count with what you would get from the tree in Figure 4 where we moved Tyrannosaurus into the wrong place:

Diplodocus Tyrannosaurus Velociraptor Tyrannosaurus Diplodocus Velociraptor Ankylosaurus Ankylosaurus Triceratops Pachycephalosaurus Edmontosaurus Triceratops Pachycephalosaurus Edmontosaurus A Y Y Y Y Y Y Y A Y Y Y Y Y Y Y B Y Y Y Y Y B Y Y Y Y Y C Y Y Y Y C Y Y Y Y D Y Y Y D Y Y Y E Y Y E Y Y F Y Y Y F Y Y Y G Y Y G Y Y

8 character changes 12 character changes

Figure 10. Characters mapped onto tree from Figure 1 (left) and Figure 6 (right). The first tree has only 8 character changes compared to the 12 in the second tree. Parsimony dictates that the first tree is the best hypothesis for these characters.

You can experiment with other trees if you like. For example, switching Velociraptor with Tyrannosaurus on the right hand tree makes the retroverted pubis into a synapomorphy, but it requires character reversals that make it less parsimonious than the tree on the left.

Phylogenetic analysis is done with computerized algorithms that find the tree the minimizes character changes, often from very large sets of characters and many taxa.

1. Node 5. 2. Node 1. 3. Node 1. 4. Triceratops, Pachycephalosaurus, Edmontosaurus. 5. Diplodocus, Tyrannosaurus, Velociraptor, Node 5, and Node 6. 6. Tree A only. 7. Saurischia is the last common ancestor of Diplodocus and Tyrannosaurus and all descendants of that ancestor. Alternatively you could use Diplodocus and Velociraptor, but you could not use Tyrannosaurus and Velociraptor because that would point to Node 6 (Theropoda) instead of Node 5 (Saurischia). 8. Cerapoda is the last common ancestor of Triceratops and Edmontosaurus and all descendants of that ancestor. Alternatively you could use Pachycephalosaurus and Edmontosaurus, but you could not use Triceratops and Pachycephalosaurus because that would point to Node 4 (Marginocephalia) instead of Node 3 (Cerapoda). 9. Regardless of which taxa you used to define Saurischia, they should pinpoint the same node on the trees in Figure 3, but not in Figure 4. 10. No. Ornithischia would not be a subgroup of Dinosauria because the node of Ornithischia (Node 2) would lie below the node for Dinosauria (Node 3). 11. Yes. Cerapoda would be a subgroup of Dinosauria because its node (Node 4) lies within the Dinosauria node (Node 3). 12.

Diplodocus Diplodocus Velociraptor Edmontosaurus Velociraptor Tyrannosaurus Edmontosaurus Triceratops Triceratops Edmontosaurus Tyrannosaurus Tyrannosaurus

3 3 5 6 1 1 1 5 A B C D 13. A. Dinosauria. B. Dinosauria. C. Dinosauria. D. Saurischia. 14. In all three trees the tip taxa trace down to Node 1. 15. The six trees are...

Triceratops Edmontosaurus Diplodocus Triceratops Edmontosaurus Tyrannosaurus Triceratops Edmontosaurus Velociraptor Pachycephalosaurus Pachycephalosaurus Pachycephalosaurus Velociraptor Edmontosaurus Diplodocus Edmontosaurus Tyrannosaurus Edmontosaurus

3 3 3 3 3 3 1 1 1 1 1 1

Diplodocus Tyrannosaurus Velociraptor Ankylosaurus Triceratops Pachycephalosaurus Edmontosaurus A Y Y Y Y Y Y Y B Y Y Y Y Y C Y Y Y Y D Y Y Y E Y Y F Y Y Y G Y Y

4 B* E 6 3 G D 5 2 F C B*

1 A

17. Character B (posterior pointing pubis) is found in all the Ornithischian taxa plus Velociraptor. It could be mapped in at least two ways: at Nodes 2 and on the branch to Velociraptor itself (which would make it a homoplasy) or at the base of the tree at Node 1 with two reversals on the branches leading to Diplodocus and Tyrannosaurus. Based on this tree alone either choice is equally valid, but based on other taxa not included in this tree it is mapped as a homoplasy because more reversals would be required to map it the other way.