Understanding Phylogenetic Trees A tutorial for Biology of the Vertebrates EEB 2214

1. Understanding Phylogenetic Trees A tutorial for Biology of the Vertebrates EEB 2214 Note: best viewed in PowerPoint as a “slide show,” as slides are animated Credits: Animal icons used in this presentation are from Microsoft Clipart (Microsoft Corporation 2006), unless otherwise indicated. The content is based on information (e.g., definitions of terms, main concepts, phylogenetic relationships, etc.) obtained from Pough et al. 1999 and Kardong 2002. This work was spawned from the ideas of E. Jockusch and M. Rubega, based on their experience with students’ difficulties with some important concepts. Presentation was created by Diego Sustaita.

2. which in turn are clustered with other closely related clusters… <next slide> Vertebrates Tetrapods “Invertebrates” …and clustered yet again with other related clusters <next slide> In their simplest forms, phylogenies are clusters of closely related organisms <next slide> “fish” chelicerates amphibians “reptiles” http://ctamp.homestead.com insects mammals birds

3. http://ctamp.homestead.com Monophyletic lineages comprise a common ancestor and all of its descendants; here there are five such groupings <next slide> One comprises frogs and salamanders, and the ancestor common to both of them (depicted here as a red dot, or “node”; these nodes are actual species – usually extinct – whose names you will come to know) <next slide> Another comprises lizards, crocs, and birds (you’ll come to understand why later), and the ancestor common to all of them. What are the other three? But in actuality they go much further, in that they portray evolutionary relationships(relationships among organisms which reflect their historical origin).Species are arranged into monophyleticgroups(groups of two or more taxa having a common ancestor). For example, consider the group below <next slide>

4. Well, there are several morphological, behavioral, and molecular (e.g., DNA) attributes which are indicative of relationships among species. In phylogenetics jargon, these are referred to as “synapomorphies,” which are shared, derived characters. In other words, they are characters which have evolved along the branch leading to the most recent common ancestor, and serve to distinguish one group from all others. Synapomorphies unite groups together, and form the basis of the branching patterns in phylogenetic trees. For example, consider the clade below <next slide> diapsid skull The members of the lineage containing lizards, crocs, and birds possess “diapsid” skulls (two pairs of temporal openings, as opposed to one pair in mammals, or none, in turtles, which results in increased flexibility of the skull during feeding) <next slide> So what are these monophyletic relationships based on? I mean, what could a bird, a croc, and a lizard possibly have in common, other than that they are all tetrapods? <next slide>

5. A feathers B If you are having trouble deciphering who’s related to who, try thinking about it as “which groups share a common ancestor more recently.” Lizards and crocs both share a common ancestor (B), but crocs share a more immediate one with birds (A). So by extension, birds could be considered “reptiles” too... <next slide> But we don’t typically consider birds “reptiles”, because, more formally, they are feathered “archosaurs.” In fact, you learned that the term “reptiles” does NOT represent a monophyletic grouping, because it doesn’t include birds (remember: a monophyletic group must include an ancestor, and ALL of its descendants; the term “fish” presents a similar problem [why???]). You’ll find that – often counterintuitively – conventional ways of grouping organisms aren’t always very descriptive or accurate <next slide> But wait; I still don’t get how crocs are more closely related to birds than they are to lizards. I thought crocs and lizards were both reptiles, and birds were, well, birds…? <next slide>

6. How about now? A B C Your answer should be the same - turtles share a common ancestor with B (the common ancestor to lizards + A [the common ancestor to birds and crocs]), so they are most closely related to all the groups depicted, through common ancestor “C”<next slide> Question: given what has just been presented, with which of the three groups of organisms depicted below is the turtle most closely related? <next slide>

7. Wait… what just happened?Branches in phylogenies are free to spin around each node, so you can’t infer phylogenetic relationships among groups based on their proximity on a tree, unless they are bracketed together <next slide> (Note: may not animate properly in Macs) <next slide>

8. <next slide> … is identical to this… While we are on the topic of presentation, you should know that there are different ways of presenting the same information. Convince yourself that this… <next slide>

9. like this… <next slide> Or even like this…, so it’s important not to think of whatever’s on the right-hand side (birds, in the top example) as the “pinnacle” of evolution <next slide> Now remember that this could be equally presented… <next slide>

10. In this phylogeny, for instance, the branch containing birds & crocs can be collapsed into the term “archosaurs” – the group containing birds, crocodiles, and dinosaurs <next slide> You could go further and summarize the whole right-hand branch as “amniotes” (in reference to organisms that produce amniotic eggs) <next slide> http://ctamp.homestead.com Archosaurs Amniotes Also note that phylogenies vary in their degree of detail, and may be collapsed or expanded at any given point, provided that there is enough information about relationships among organisms <next slide>

11. http://ctamp.homestead.com Plethodontidae Now take one family, and consider the diversity of genera (this should look familiar too…) <next slide> By the same token, each group depicted below can be expanded into its own phylogeny <next slide> Mueller et al. 2004

12. ? Now you try. Which of the following terms would you collapse the right-hand side of the following phylogeny into: Archosaurs, Tetrapods, Reptiles, Saurapsids, or Dinosaurs? <next slide> Even if you don’t know what some of these are, you should be able to immediately rule out 3 choices: “Archosaurs” is too restrictive, as we learned a few slides back that it refers to the clade containing birds, crocs, and dinosaurs - (which would be even more restrictive). “Tetrapods” is too broad, as it includes mammals as well. Reptiles, as we just learned, is not monophyletic, so although it includes the common ancestor, it fails to include all of its descendants (which were not depicted, such as birds). The only one left is “saurapsids,” which in fact refers to the clade containing all of these animals (including birds).

13. A In this scenario, A and B diverged from their common ancestor much more recently than did C and D <next slide> B C D 100 million years ago present By now you’ve been introduced to the major concepts, but we left out a few important details. The lengths of the branches were depicted somewhat arbitrarily here, but sometimes they do mean something. Occasionally we’ll encounter a tree in which branch lengths are drawn proportional to time<next slide>

14. A B C E D D C C E D E C E D This trichotomy represents three possible resolutions, because no pair of taxa is depicted as a sister group to the third taxon. With more information, one of the three possibilities may become better supported. Note that phylogenies are essentially working hypotheses, which are continuously updated with new findings <next slide> Also, the goal of a phylogeny is to break everything down into dichotomous, monophyletic sister groups, but this doesn’t always happen. If there is a lack of information about relationships among species – either because there has been minimal divergence among a set of species, or the group simply has not been studied (or both) – polytomies (= a node with more than two immediate descending branches) often emerge (right-hand clade containing species C-D-E, below). <next slide>

15. OK. Now its your turn. Here is an array of organisms to be assembled into a phylogeny. So, where do you start? Well, you could probably get most of the way just by gestalt. But eventually, you will need to now some key pieces of info – remember those synapomorphies from Biology 108???? <next slide>

16. 1 2 3 4 5 6 7 8 9 Match the letter of each group with the number of the its corresponding position on the cladogram: a b c d e f g h i Once you think you have it, go onto the next slide…

17. And grouping snakes and lizards together – you’ll recall from lecture that lizards, snakes, and tuataras form the “lepidosaur”group <next slide> A few trickier points are the distinction between marsupial (kangaroo) and placental (bear & squirrel) mammals <next slide> The oyster (a mollusc) and sea star (an echinoderm) were a cheap trick from Biology 108 – they are both invertebrates, but molluscs are protostomes, and enchinoderms and chordates are deuterostomes You should have come up with something like this: <next slide> 4 = d 6 = h 7 = g 8 = c 9 = i 5 = e 1 = f 2 = b 3 = a How else might have you correctly arranged these species? <next slide>

18. 1 2 3 4 5 6 7 8 9 http://ctamp.homestead.com One more time just to make sure it sank in: a b c d e f g h i Once you think you have it, go onto the next slide…

19. http://ctamp.homestead.com This is what you should have (right out of your lecture notes…) Mammalia (Artiodactyla) (Cetacea) Petromyzo-ntoides Chondrich-thyes Lepido-sauria Aves Myxinoidea Amphibians (Urodela) 8 = g 5 = a 7 = i 1 = e 2 = f 3 = h 6 = d 9 = c 4 = b Epilogue: We’ve shown you the appropriate phylogenetic groupings of the taxa portrayed throughout the tutorial, however we haven’t really described the synapomorphies that form the bases of the groupings. You should review your notes and make sure you have a handle on the major synapomorphies which characterize the major groups we are covering, as a starting point to determining their relationships.