Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 1998Quiz 1You may use any books, notes, or references, but you must work independently of other people, inside oroutside of the course: you are on your honor to do so.To keep the amount of writing under control, please confine the answers to the space provided (but writeclearly and large enough to see!); outlines are fine. You of course may type the answer if you want,following the same space constraint (no smaller than 10 pt. font). Include literature citations (author andyear are enough) where you use them.1.(9 points) Briefly describe each of the following morphometric methods, and their possible uses insystematics:a) Bivariate plot!!!b) Procrustes analysis!!!c) Thin-plate spline!!!2.(6 points) You have just overheard an argument about reconstructing relationships between a phenetist,cladist, and an evolutionary biologist. Briefly compare and contrast each individual's position.!!!!!!3. (5 points) How is it possible that branch lengths on a tree produced using UPGMA may not agree withbranch lengths calculated directly from the distance matrix?!!!!!!4. (5 points) What is the difference between divisive and agglomerative clustering methods? Give oneexample of each.!5.(20 points) What are the general attributes of a "good" taxonomic character? Give: a) A list with a few-sentence explanation of each criterion; b) An indication of particular problems faced by morphological andDNA-sequence data for each criterion.!!!!!!!!!!!!!!6. (5 points) You have constructed a tree using the parsimony criterion and a second tree using the largestclique found in your data by compatibility analysis. Why might your two trees have different topologies?!!!7. (10 points) Briefly define the following terms:DNA hybridization!Step matrix!Manhattan distance!Retention index!transversion!character weighting!epistemology!The alternating sister group rule!Dollo parsimony!Median state rule8. (20 points) Briefly contrast the following pairs of terms (Use diagrams if they help):maximum likelihood vs. maximum parsimony!!!Strict consensus trees vs. majority-rule consensus trees!!!transformational vs. taxic homology!!!Lundberg rooting vs. outgroup rooting!!!decay index vs. bootstrap support!!!9. (10 points) Quantitative, continuous characters are an intially attractive set of potential characters thatseem often to contain phylogenetic signal. Discuss why they are so difficult to use. When can they beincluded in an analysis? How?!!!!!!!10. (10 pts.) In which one of the following cases is the maximum parsimony method most likely to beinconsistent (i.e., not converging on the correct tree as more data are added). Why? What properties of datamake the problem
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