Time Tree Lab

TIME TREE LAB ACTIVITY Using the timetree app on my phone or Timetree.org website, I determined the divergence time between the horse and the other species. Based on these results I can construct a tree showing relationships based on genetic analysis Time of divergence 1 – 5 relatedness Horse (Equus caballis) Grey whale (Eschrichtius robustus) 79 mya 3 Asiatic Tapir (Tapirus indicus) 55 mya 2 Black Rhino (Diceros bicornis) 54 mya 1 Elephant (Loxodonta africana) 101 mya 5 Hippopotamus (Hippopotamus amphibious) 79 mya 3 This tree is incomplete. I would need to run the divergence comparison for all the possible relationships. (YOU WILL COMPLETE THE TABLES). By completing the analysis, you will be able to see clusters of more closely related animals and not just offshoots from a single species. Activity: Step 1: Complete the timetree tables for the example above. Create an example phylogeny from your results. Access the timetree app (only on iPhone or iPad) or Timetree.org (The timetree.org is a little better, but the app works fine). You will be using the “Get Divergence for a pair of Taxa.” Enter the first species in the top box and the second species in the second box. Click “Search”, to get access to the species, which should appear in the “Resolve Ambiguity” boxes. Next, click “Show Time” to get the estimated time of divergence. In the chart below, you will see the Estimated Time is 79 mya. That means that the horse (Equus caballis) and the grey whale (Eschrichtius robustus) separated from each other’s common ancestor about 79 million years ago. Steps to complete this lab: 1. Complete Case 1: a. Run “timetree” analysis and fill in tables. b. Create phylogeny from these analyses. 2. Complete Case 2: a. Create a hypothetical phylogeny for the order carnivora. b. Answer questions about your hypothesized phylogeny. c. Run “timetree” analysis and fill in tables. d. Create phylogeny from these analyses. 3. Answer review questions. Submit the tables, phylogenies and questions to the timetree submission board on the Unit 2 labs. EXAMPLE FROM ABOVE – You will use this data for your phylogeny Time of divergence 1 – 5 relatedness Horse (Equus caballis) Grey whale (Eschrichtius robustus) 79 mya 3 Asiatic Tapir (Tapirus indicus) 55 mya 2 Black Rhino (Diceros bicornis) 54 mya 1 Elephant (Loxodonta africana) 101 mya 5 Hippopotamus (Hippopotamus amphibious) 79 mya 3 Species 1 Species2 Time of divergence 1 – 5 relatedness Grey whale (Eschrichtius robustus) Horse (Equus caballis) Asiatic Tapir (Tapirus indicus) Black Rhino (Diceros bicornis) Elephant (Loxodonta africana) Hippopotamus (Hippopotamus amphibious) Species 1 Species2 Time of divergence 1 – 5 relatedness Asiatic Tapir (Tapirus indicus) Horse (Equus caballis) Grey whale (Eschrichtius robustus) Black Rhino (Diceros bicornis) Elephant (Loxodonta africana) Hippopotamus (Hippopotamus amphibious) Species 1 Species2 Time of divergence 1 – 5 relatedness Elephant (Loxodonta africana) Horse (Equus caballis) Asiatic Tapir (Tapirus indicus) Black Rhino (Diceros bicornis) Grey whale (Eschrichtius robustus) Hippopotamus (Hippopotamus amphibious) Species 1 Species2 Time of divergence 1 – 5 relatedness Black Rhino (Diceros bicornis) Horse (Equus caballis) Asiatic Tapir (Tapirus indicus) Elephant (Loxodonta africana) Grey whale (Eschrichtius robustus) Hippopotamus (Hippopotamus amphibious) Species 1 Species2 Time of divergence 1 – 5 relatedness Hippopotamus (Hippopotamus amphibious) Horse (Equus caballis) Asiatic Tapir (Tapirus indicus) Black Rhino (Diceros bicornis) Grey whale (Eschrichtius robustus) Elephant (Loxodonta africana) Once you have completed the Case 1 table set, do some analysis of your results to see if you can see some groupings of species that are more closely related, relative to other species. Create a “phylogeny” based on the timetree data from your tables. Use the phylogeny tool kit PowerPoint slide to find useful pieces to create your phylogeny. To transfer your phylogeny to this sheet, select all your “pieces” and click cut. If all the pieces disappear you have included all of them. Next you will want to paste your piece in the space provided as a JPG (selecting the arrow below the PASTE button and click icon). This will allow the piece to stay in place. Paste your Case 1 phylogeny here: Case 2: Homologies, homoplasies and divergence of member of the order carnivora. The species you will need to work with for Case 2 are: Grizzle bear (Ursus arctos) Lion (Panthera leo) Cal. sea lion (Zalophus californianus) Otter (Enhydra lutris) Wolf (Canus lupus) Red panda (Ailurus fulgens) Step 1. Paste your hypothetical phylogeny here. Step 2: Questions about your phylogeny: 1. What trait or traits did you use to create your groupings? 2. Considering the trait(s) you used to create your classification system, are you assuming each group belongs together because parallel evolution (homologous) or convergent evolution (homoplasy)? 3. Provide an explanation why you have made this assumption. Step 3: Timetree tables Species 1 Species2 Time of divergence 1 – 5 relatedness Grizzle bear (Ursus arctos) Lion (Panthera leo) California sea lion (Zalophus californianus) Sea otter (Enhydra lutris) Wolf (Canus lupus) Red panda (Airlurus fulgens) Species 2 Species2 Time of divergence 1 – 5 relatedness Lion (Panthera leo) Grizzle bear (Ursus arctos) California sea lion (Zalophus californianus) Sea otter (Enhydra lutris) Wolf (Canus lupus) Red panda (Airlurus fulgens) Species 3 Species2 Time of divergence 1 – 5 relatedness California sea lion (Zalophus californianus) Grizzle bear (Ursus arctos) Lion (Panthera leo) Sea otter (Enhydra lutris) Wolf (Canus lupus) Red panda (Airlurus fulgens) Species 4 Species2 Time of divergence 1 – 5 relatedness Sea otter (Enhydra lutris) Grizzle bear (Ursus arctos) Lion (Panthera leo) California sea lion (Zalophus californianus) Wolf (Canus lupus) Red panda (Airlurus fulgens) Species 5 Species2 Time of divergence 1 – 5 relatedness Wolf (Canus lupus) Grizzle bear (Ursus arctos) Lion (Panthera leo) California sea lion (Zalophus californianus) Sea otter (Enhydra lutris) Red panda (Airlurus fulgens) Species 6 Species2 Time of divergence 1 – 5 relatedness Red panda (Airlurus fulgens) Grizzle bear (Ursus arctos) Lion (Panthera leo) California sea lion (Zalophus californianus) Sea otter (Enhydra lutris) Wolf (Canus lupus) Paste your Case 2 phylogeny here: Review questions: 1. How close was your hypothetical phylogeny to your phylogeny based on timetree divergence data? 2. Given the groupings based on the timetree data, what ancestral traits do you see in each group and what evnornmental factors permitted these traits to remain unchanged from the MRCA? What are a few of the derived traits you can think of and what environmental factors may have aided in their development? 3. How you would improve this lab? (this is the first time I’m assigning this lab)