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Ch02 Problems and Topics

Ch02 Problems and Topics - Problems and Discussion Topics...

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Problems and Discussion Topics with Sample Answers by Joseph Lachance and Paul Bourdeau to accompany Evolution, Second Edition Chapter 2: The Tree of Life: Classification and Phylogeny 1. Suppose we are sure, because of numerous characters, that species 1, 2, and 3 are more closely related to one another than to species 4 (an outgroup). We sequence a gene and find ten nucleotide sites that differ among the four species. The nucleotide bases at these sites are: (species 1) GCTGATGAGT; (species 2) ATCAATGAGT; (species 3) GTTGCAACGT; (species 4) GTCAATGACA. Estimate the phylogeny of these taxa by plotting the changes on each of the three possible phylogenies for species 1, 2, and 3 and determining which tree requires the fewest evolutionary changes. Answer: The numbers inside boxes in the trees below indicate the nucleotide number that changed state. Changes are plotted to maximize the amount of parsimony. The tree on the left requires 12 changes, the middle tree requires 10 changes, and the tree on the right requires 12 changes. This indicates that the middle tree is the most parsimonious (requires the fewest evolutionary changes). Note that character state reversals occurred in the left and right trees. Species DNA sequence Derived vs. ancestral state Species 1 GCTGATGAGT 0111000011 Species 2 ATCAATGAGT 1000000011 Species 3 GTTGCAACGT 0011111111 Species 4 (outgroup) GTCAATGACA 0000000000 © 2009 Sinauer Associates, Inc. 1
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2. There is evidence that many of the differences in DNA sequence among species are not adaptive. Other differences among species, both in DNA and in morphology, are adaptive (as we will see in Chapters 12 and 20). Do adaptive and nonadaptive variations differ in their utility for phylogenetic inference? Can you think of ways in which knowledge of a character’s adaptive function would influence your judgment of whether or not it provides evidence for relationships among taxa? Answer: Adaptive changes can potentially be quite informative (especially if they are key innovations). However, only derived character states that are shared among taxa (synapo- morphies) allow phylogenies to be successfully inferred. Characters that are present in only one species are uninformative, but characters that are present in multiple species can potentially be informative. Some loci are under intense purifying selection, with few sub- stitutions occurring (reducing their efficacy for phylogenetic inference). By contrast,
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