Integrative Biology 200A "PRINCIPLES OF PHYLOGENETICS" Spring 2002Quiz 1You may use any books, notes, or references, but you must work independently of other people.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.1. (10 points) Describe how two-point registration ('Bookstein Coordinates') differs from Procrustessuperimposition. Why are the differences important?2. (10 points) How might you use the NCBI's (National Center for Biotechnology Information) web site todetermine if a DNA sample you sequenced was contaminated?3. (10 points) What are the arguments pro and con for rank-free phylogenetic classification versus the currentLinnaean system?4. (20 points) What are the general attributes of a "good" taxonomic character? Give: (a) a list with a one sentenceexplanation; b) An indication of any particular problems faced by morphological and DNA-sequence data for each. (over)5. (10 points) Why might you be uncomfortable using the paleontological criterion for character polarization?What does this method imply about the adequacy of the fossil record?6. (40 points) Briefly contrast the following pairs of terms (Use diagrams if they help):homoplasy vs. homologyontogeny of vertebrates vs. ontogeny of mossessemaphoront vs. OTUepistemology vs. ontologyRFLP analysis vs. mapped restriction site studiesLundberg rooting vs. outgroup rootingparsimony vs. Unwieghted Pair Goup Method (UPGM) for tree buildingordering vs. polarity of character statescontinuous characters vs. discrete-state charactersdivisive vs. agglomerative
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