Apr15_Consensus - Integrative Biology 200A "PRINCIPLES OF...

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Integrative Biology 200A “PRINCIPLES OF PHYLOGENETICS” Spring 2008 University of California, Berkeley Kipling Will- Tax day Phylogenetic trees VII- Tree selection, consensus, compromise I. To choose or not to choose? In most cases an optimality criterion will result in a set of equally best trees. There are basically three views on the way to deal with this. A. All trees of the optimal set are equal. So no single tree should be selected. 1. Alternative trees may be discussed and the strict consensus presented. 2. If a procedure requires a single, fully resolved tree then a random one can be used. 3. Using a secondary optimality criterion is not considered valid and (typically) equal weights were used. B. If secondary optimality criterion(a) can be justified it should be included in the initial search. 1. upon recognition that many equal trees result from the first analysis a new analysis with differential weighting or explicit model is used 2. New data can be brought in and/or initial hypotheses revisited. C. Optimal trees represent a select subset of all possible trees and implementing a secondary optimality criterion(a) that selects from those trees is legitimate. 1. Internal evidence a. subjectively preferred character state transformation b. explicit (numerical) secondary optimality criteria methods that concentrate homoplasy and related tree optimality methods 2. External evidence a. correspondence to existing taxon hypotheses b. best fit to characteristics that are cannot be coded as characters SAW - Successive Approximations Character Weighting (Farris 1969)
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This note was uploaded on 08/01/2008 for the course IB 200 taught by Professor Lindberg,mishler,will during the Spring '08 term at University of California, Berkeley.

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Apr15_Consensus - Integrative Biology 200A "PRINCIPLES OF...

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