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Mapping mutations on phylogenies

Part 4. Bioinformatics

4.4. Comparative Analysis and Phylogeny

Short Specialist Review

  1. Rasmus Nielsen1,2

Published Online: 15 APR 2005

DOI: 10.1002/047001153X.g404309

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Nielsen, R. 2005. Mapping mutations on phylogenies. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.4:46.

Author Information

  1. 1

    Ithaca, Cornell University, NY, USA

  2. 2

    University of Copenhagen, Bioinformatics Centre, Copenhagen, Denmark

Publication History

  1. Published Online: 15 APR 2005

Abstract

This chapter provides a short review of recent methodologies developed for mapping mutations on phylogenies. Mapping of mutations, or character changes in general, using the maximum parsimony principle has been one of the most powerful tools in phylogenetics, and it has been used in a variety of different applications, for example, in the detection of correlated evolution and to identify selection acting on DNA sequences. However, many uses of parsimony mappings have been criticized because they focus on only one of many possible mappings and/or because they do not incorporate statistical uncertainty in the mapping. Recently developed probabilistic methods can incorporate statistical uncertainty in the character mappings. In these methods, focus is on a probability distribution of mutational mappings instead of a single estimate of the mutational mapping.

Keywords:

  • phylogeny;
  • Bayesian analysis;
  • mapping mutations;
  • parsimony