Case Study 1_Part Two worksheet 2

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Jan 9, 2024

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BIOL*2400DE – Evolution Case Study 1: Part Two Building a Timetree Worksheet Before completing this worksheet, watch the video introduction to Timetree, be sure to download the files and watch the video introduction to Timetree video on Courselink. Then work through the steps below. Step 1: Divergence times Open the spreadsheet file ( Timetree_spreadsheet.docx ) and refer to TABLE 1 . To complete the table, you will need to do 10 comparisons between pairs of species and enter the common name for each species listed (which you can get from Timetree if it is given, or else Google the species name). For this, you will be using the “ GET DIVERGENCE TIME FOR A PAIR OF TAXA ” feature. For each comparison, enter the name for Species 1 and Species 2 into the boxes for “Taxon 1” and “Taxon 2”. This will give you the divergence time for those two species – that is, how long it has been since they shared a common ancestor. Enter the “median time” information into the last column of TABLE 1 (this is given in millions of years ago, Mya). You will need this information to answer the case study questions. Step 2: More divergence times Now that you are familiar with the general idea of conducting pairwise comparisons to get divergence times between two lineages, we can do some more focused, overlapping comparisons to begin working out which species are more closely related to (i.e., most recently shared a common ancestor with) which other species. To do this, refer to TABLE 2 in your spreadsheet and complete each of the 19 comparisons indicated and enter the “median time” in the last column.

Make some notes about what you notice in doing these sorts of overlapping comparisons. For example, you will notice that some of the divergence times for difference species comparisons are identical. Why might that be? Table 1 had an overlapping median of 319 MYA. Table 2 had overlapping median of 28.8, 429 and 462 MYA. This could be because of overlapping species or species which could have co- existed at the same time causing an overlapping median. Step 3: Evolutionary timeline for a taxon Timetree has another function entitled “ GET AN EVOLUTIONARY TIMELINE FOR A TAXON ”. This will build a timeline for a specific lineage, showing how long ago various major events occurred. For example, when major groups of which the taxon in question is a member first arose, as well as geological and other information. To see this feature in action, try entering a few different species and explore the information provided in the resulting timelines: • Homo sapiens • Rana pipiens • Lumbricus terrestris • Cepaea nemoralis • Drosophila melanogaster Step 4: Build a timetree

Timetree has another function entitled “ BUILD A TIMETREE ”. This will create a phylogeny for whatever group or list of species is requested (as long as there are data available). You can explore this function simply by entering a taxonomic group into the “Specify and Group of Taxa” box. For example, try entering “primates” and see the resulting output. You can specify whether you want the tree to show you relationships among families, genera, or species. Try each and see the outcome. Step 5: Build a phylogeny This feature also allows you to upload your own list of species to include in a phylogeny. To start, upload the file “ TREE1_Table2ForTimetree.txt ”. This includes the same species from TABLE 2 that you compared in Step 2. Now that you see these species on an evolutionary tree, do the observations you made in Step 2 make more sense? What can you say about how closely related species outside a clade are to species within a clade, for example? Yes my observations make sense because I can further understand why there was an overlap of eras for the species. To explain the relationship between a species within the clade to

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species outside a clade, we can use the concept of common ancestry. A good example would be Homo Sapiens and Pan troglodytes. Step 6: Closest living relatives of whales We’re now ready to use the Timetree tool, which is based on DNA sequence data, to explore the question of to whom modern whales are most closely related. To do this, upload the file “ TREE2_MammalsForTimetree.txt ”. This file contains 40 mammal species from many different taxonomic groups. You can find the common names for each of them in the spreadsheet. Once you have the tree for these mammal species, take some time to explore the relationships that it shows. Are the major groups of mammals (monotremes, marsupials, placentals) monophyletic? Which is the sister taxon to primates? Do you see any examples of paraphyly based on traditional taxonomic names? No the major groups are not monophyletic because monotremes are not monophyletic and marsupials and placentals are closely related. Homo Sapiens are the sister taxon to primates. Some examples of paraphyly are Trichechus manatus, Loxodonta africana, Orycteropus afer and Dasypus novemcinctus. Then, consider where whales fall on this tree. Based on this phylogeny, which mammals are the closest living relatives (but NOT ancestors) of whales? The closest living relatives are Hippopotamus (Hippopotamus amphibius).

Is there anything surprising about the placement of whales on this phylogeny? I did not find anything surprising about the placement because it further affirmed the fact that whales are descended from terrestrial mammals. How do you think whales should be classified if we want taxonomic names to be based on evolutionary relationships? I think whales should be classified as Mammals because if we based It on evolutionary relationships, the finding of evolutionary fossils and the subsequent lineages based on the fossils, all point to the fact that whales were once mammals who lived on land. Step 7: Reflection Answer the following questions about your experience with this case study. 1. What aspects of this case study did you find most challenging or confusing? I found it hard to read the second phylogenetic tree because there were so many species and It took time to go through all of them. 2. Did you learn anything or gain a clearer understanding of any specific concepts while completing this case study?

I gained more understanding of how species who may not even be remotely related in this present era, were once from the same ancestor millions of years ago and shows how long evolution has existed. 3. Was there anything that you found particularly interesting or surprising in this case study? I found that it was very interesting how many species that used to exist millions of years ago, have split into many new species and are still abundant today. Once you have completed this worksheet, upload it to Courselink and then proceed to the Case Study 2 – Part Two quiz.

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