# Activity+Bear+Phylogenies+ANSWERS - Bio94 Winter2011...

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Unformatted text preview: Bio 94 Winter 2011 Part II – Answers 1) Begin by counting the differences in sequences between each pair of species. Red Panda GTCGATGAGA Brown Bear GATCTCATAA G and A are conserved on the ends of the sequences, but there are 8 differences between them (highlighted). 2) Enter these values in the matrix provided. These numbers are the genetic distance between the species. Great Panda Red Panda Polar Bear Brown Bear Raccoon Great Panda Red Panda 6 Polar Bear 4 8 Brown Bear 4 8 1 Raccoon 6 2 8 8 Half of the table is blacked out. This is because we know the genetic distance between a Raccoon and Raccoon is 0 (not helpful in building a phylogenetic tree). The others are also not necessary to fill in because we know that the distance from species A to species B is the same as from species B to species A. 3) Once you have completed the matrix, identify the lowest number (= the least genetic distance and therefore most closely related). Group these two species and make a new matrix. Great Panda Red Panda Polar Bear/ Raccoon Brown Bear Great Panda Red Panda Polar Bear/ Brown Bear Raccoon 4) Fill in the matrix as before, but average the genetic distances when comparing a species to the new group (Hint: don’t bother counting the differences in sequences after step 2, rather use the most recently created table). Great Panda Red Panda Polar Bear/ Raccoon Brown Bear Great Panda Red Panda 6 Bio 94 Winter 2011 Polar Bear/ Brown Bear Raccoon 4 8 6 2 8 Notice that the value for Great Panda and Red Panda stayed the same. We are still comparing the sequences of individual species rather than groups. When species are grouped, use the values in the previous table and average them. e.g. The distance between Brown Bear and Raccoon is 8. The distance between Polar Bear and Raccoon is 8. (8+8)/2 = 8; this is the distance between Raccoons and the Brown Bear/Polar Bear clade. 5) Keep choosing the lowest number and grouping until everything is grouped together. Great Panda Red Polar Bear/ Panda/Raccoon Brown Bear Great Panda Red Panda/ 6 Raccoon Polar Bear/ 4 8 Brown Bear Great Panda/ Polar Bear/ Red Panda/Raccoon Brown Bear Red Panda/ 7 Raccoon 6) Time to draw the tree. Look back at your tables and group species in the order that they were grouped in the table. First was PB with BB BB PB Then RP with Ra RP Ra BB PB Bio 94 Winter 2011 Then GP with BB/PB RP Ra GP BB PB Now bring it all together RP Ra GP BB PB Look familiar? Take a look at the tree in Part I; these are different methods for reconstructing the evolutionary relationships between organisms. Part III – Answers Does the use of these traits help you to build a better cladogram? Why or why not? How can you explain the occurrence of traits that do not fit neatly into the phylogenetic relationships you found in Parts I and II of this handout? One trait (# adult teeth) is helpful and supports the phylogeny that we constructed. The other two traits have to have each arisen twice (not a very parsimonious explanation) under this tree structure. It may be that these are homoplasies or the product of convergent evolution. Alternatively, the tree that we constructed in Part I may not be correct. Phylogenetic trees are hypotheses! We can’t rewind the history of life and play it back to see what happened, therefore there will always be some uncertainty. ...
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