Mar20_Parsimony - Integrative Biology 200A "PRINCIPLES...

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1 Integrative Biology 200A “PRINCIPLES OF PHYLOGENETICS” Spring 2008 University of California, Berkeley Kipling Will-20 Mar Trees II: Parsimony I. Parsimony, Patterns & Processes Hennig provided fundamental methods for the use of character data to form phylogenies and made the relationship between character evidence and cladograms explicit in a way that had not been done previously. He was not, as far as I know, concerned with parsimony as an optimality criterion, but rather his general paradigm was consistent with parsimony as a guiding principle. Hennig’s Auxiliary Principle – to assume homology if there is no evidence to suggest otherwise — requires that we seek hypotheses maximizing our homologies or conversely, that overturn as few as possible of our initial homologies, given that these initial hypotheses are the result of careful character analysis. The result is to minimize ad hoc hypotheses needed to explain when we fail. Pattern Cladists- put forward that cladistic (in this case = strict parsimony) methods do not need and in fact are better off without an evolution (process) justification. Three things are needed to justify building trees base on synapomorphies, 1. discoverability of characters, 2. hierarchy is the best representation of the natural world and 3. parsimony as an epistemological approach (Brower, A.V.Z. 2000. Evolution Is Not a Necessary Assumption of Cladistics. Cladistics 16, 143–154.) Circularity? Mitter (1981. "Cladistics" in botany. Syst. Zool., 30:373–376.) "there is widespread (but not universal) agreement that . .. systematic methods should be as free as possible from assumptions about how evolution works, because these assumptions are in general not testable without reference to systematic results." In the “estimation school of thought” this problem is addressed through assessment of the impact of model violation and statistical support. Therefore ML and methods of that sort benefit from an evolutionary model based justification.
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Mar20_Parsimony - Integrative Biology 200A "PRINCIPLES...

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