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Parsimony, Phylogeny, and Genomics$
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Victor A. Albert

Print publication date: 2006

Print ISBN-13: 9780199297306

Published to Oxford Scholarship Online: September 2007

DOI: 10.1093/acprof:oso/9780199297306.001.0001

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Parsimony and its presuppositions

Parsimony and its presuppositions

(p.43) Chapter 3 Parsimony and its presuppositions
Parsimony, Phylogeny, and Genomics

Elliott Sober

Oxford University Press

The use of a principle of parsimony in phylogenetic inference is both widespread and controversial. It is controversial because biologists, who view phylogenetic inference as first and foremost a statistical problem, have pressed the question of what one must assume about the evolutionary process if one is entitled to use parsimony in this way. They suspect, not just that parsimony makes assumptions about the evolutionary process, but that it makes highly specific assumptions that are often implausible. That it must make some assumptions seems clear to them because they are confident that the method of maximum parsimony must resemble the main statistical procedure used to make phylogenetic inferences: the method of maximum likelihood. Likelihoodists suspect that parsimony nonetheless involves an implicit model. The question for them is to discover what that model is. This chapter discusses parsimony's ostensive presuppositions by examining the relationship that exists between maximum likelihood and maximum parsimony among simple examples in which parsimony and likelihood disagree.

Keywords:   likelihoodist, law of likelihood, frequentist, Bayesian, presuppositions, evolutionary model, probability

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