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 1 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 1 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? Indiana University | Department of Geological Sciences © 2017, P. David Polly 2 Trees can be drawn in many ways 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 2 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 1 1 D E 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? Indiana University | Department of Geological Sciences © 2017, P. David Polly 3 Phylogenetic definitions 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. Indiana University | Department of Geological Sciences © 2017, P. David Polly 4 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. Indiana University | Department of Geological Sciences © 2017, P. David Polly 5 Practice questions 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. Indiana University | Department of Geological Sciences © 2017, P. David Polly 6 Ankylosaurus Triceratops Pachycephalosaur Edmontosaurus Diplodocus Tyrannosaurus Velociraptor A.