MEGA Tetrapods-Danielle Clements - Tagged

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Dec 6, 2023

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MEGA Computer Lab: Tetrapod Evolution NAME:_________________________ This week, we are using MEGA “Molecular Evolutionary Genetics Analysis” to analyze data on our relatives within the tetrapods – four limbed organisms like you and me. These data are DNA sequences from a slowly evolving nuclear protein coding gene ( RAG-1, Hugall et al. 2007 Systematic Biology ). The exercise has two goals: 1. Further your understanding of phylogenetic trees and molecular evolution 2. Increase your knowledge of relationships among mammals, birds, lizards, etc. All MEGA commands are in BOLD CAPS. All questions that you must answer are in bold italics . CLICK on the “Data - MEGA Tetrapods” dataset in BlackBoard and download it, then click on it. That should open the file in MEGA. You can also CLICK on “ DATA ” in MEGA, then choose your data file. PHYLOGENY – CONSTRUCT/TEST NEIGHBOR-JOINING TREE – OK Species on this tree don’t go to the same point because this tree is scaled with amount of sequence divergence - the further to the right, the more species has changed from the common ancestor at the root. I. MAMMALS: 1. Which mammals on the tree are the most closely related to Homo sapiens ? Use SUBTREE (in the 3rd tab down on the left), then FLIP SUBTREE and click on the nodes to rotate/flip so that humans appear at the very top of the page. You should be able to do that in 2 clicks. Did rotating nodes change the relationships at all? Use FLIP SUBTREE again to move humans back to somewhere in the middle. II. REPTILES: Focus on the six reptile species. 2. Are anole lizards more closely related to the snake or to gecko lizards? 3. Are alligators more closely related to anole lizards or to chickens? BIO142

III. AMPHIBIANS: Focus on two amphibian species 4. Here is a stick figure of a salamander (top view) to remind yourself of the general salamander body plan (overall shape). This body plan evolved with the first tetrapods. Extant salamanders have a general shape similar to many other species on the tree. Name 4 species that look similar. 5. Where on the tree did that general tetrapod shape (please confirm you know what a tetrapod is) likely evolve? (Draw a simplified tree using ONLY the groups mammals, fishes, birds, amphibians, and non-avian reptiles.) 6. Then, find four or so branches on the tree where that general ancestral tetrapod shape was lost. Which extant species are they? (Refer back to the tree from MEGA) BIO142

IV. CHRONOGRAM: CLICK ON THE CLOCK ICON (LAST ICON ON TOP RIGHT) – “Select Branch” to specify outgroup as Coelacanth and Lungfish. Select “Ok”, “Skip” and finally “Launch”. This will make a linearized tree. If you can’t see the sequence divergences, click on “Show Node Height Error Bars” (seventh tab from the bottom left). The numbers that appear correspond to the amount of divergence (out of 1) that the species descending from the node differ. These should be converted to %. 7. Approximately what % sequence divergence are alligators and crocodiles? __________ 8. Good fossil data indicate that amniotes last shared a common ancestor roughly 300 MYA. Based on the % sequence divergence between alligators and humans (17%), what is the approximate rate of sequence divergence for the RAG-1 gene? Recall the equation you used for the molecular clock last week: D=μt. Show your work! 9. Based on the rate of sequence divergence calculated above, approximately how long ago did alligators and crocodiles diverge? Show your work! 10.Along which branch would non-avian dinosaurs connect to this tree? Remember that modern birds are descendants from dinosaurs. Add a branch for dinosaurs to the tree below. BIO142

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11. Non-avian dinosaurs went extinct approximately 65 MYA. What % sequence divergence would that correspond to using the μ from above? 12. A. Which of the lineages shown diverged from each other after 65 MYA? Use the calculated divergence and the time scale, and refer to the nodes to find all the lineages that diverged after 65 MYA. B. According to this tree, _________ lineages of mammals & birds existed at the time the non-avian dinosaurs went extinct. BIO142

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