Mapping Mutations on Phylogenies

Author: Nielsen R.¹

Source: Systematic Biology, Volume 51, Number 5, 1 September 2002 , pp. 729-739(11)

Publisher: Taylor and Francis Ltd

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Abstract:

Mapping of mutations on a phylogeny has been a commonly used analytical tool in phylogenetics and molecular evolution. However, the common approaches for mapping mutations based on parsimony have lacked a solid statistical foundation. Here, I present a Bayesian method for mapping mutations on a phylogeny. I illustrate some of the common problems associated with using parsimony and suggest instead that inferences in molecular evolution can be made on the basis of the posterior distribution of the mappings of mutations. A method for simulating a mapping from the posterior distribution of mappings is also presented, and the utility of the method is illustrated on two previously published data sets. Applications include a method for testing for variation in the substitution rate along the sequence and a method for testing whether the d_N/d_S ratio varies among lineages in the phylogeny.

Keywords: DATA AUGMENTATION; DNA SEQUENCE EVOLUTION; MARKOV CHAIN MONTE CARLO; PHYLOGENETICS

Document Type: Research article

Affiliations: 1: Department of Biological Statistics, Cornell University, 439 Warren Hall, Ithaca, New York 14853-7801, USA

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