13practiceset2 - BIO 3102 MOLECULAR EVOLUTION PRACTICE...

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BIO 3102 MOLECULAR EVOLUTION PRACTICE QUESTIONS #2 Winter 2013 QUESTION 1. Suppose that the following sequences represent homologous introns (admittedly very short ones) from gene X in organisms 1, 2, 3 and 4, with the dashes denoting gaps. 1 G T C T T T C G T C A G G - T G G A C G T C C C C A G C C C A G 2 G T C T C G A G C C A G T C T G G G T G T T C T C A G C C C A G 3 G T C T T T G A - C A A G A T G A T G A T C C T T A G C C C A G 4 G T C T C G T A A C A G T C T G G G - G T T C T C A G C C C A G a) Use the UPGMA method to reconstruct a phylogenetic tree from these data. Be sure to show your reasoning. What are limitations of the UPGMA method? b) With these same data, use the maximum parsimony method to infer potential relationships. Be sure to show your reasoning, and explain (with examples) how sites can differ in their informational content. c) What are advantages/disadvantages of using intron sequences in tree reconstruction?
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