The Essentials of Computational Molecular Evolution

  • Stéphane Aris-BrosouEmail author
  • Nicolas Rodrigue
Part of the Methods in Molecular Biology book series (MIMB, volume 855)


In this chapter, we give a brief yet self-contained introduction to computational molecular evolution. In particular, we present the emergence of the use of likelihood-based methods, review the standard DNA substitution models, and introduce how model choice operates. We also present recent developments in inferring absolute dates and rates on a phylogeny and show how state-of-the-art models take inspiration from diffusion theory to link population genetics, which traditionally focuses at a taxonomic level under that of species, and molecular evolution.

Key words

Likelihood Bayes Model choice Phylogenetics Divergence times 



We would like to thank Michelle Brazeau, Eric Chen, Ilya Hekimi, Benoît Pagé, and, in particular, Wayne Sawtell for their critical reading of a draft of this chapter. This work was partly supported by the Natural Sciences Research Council of Canada (N.R., S.A.B.) and the University of Ottawa (S.A.B.).


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Departments of Biology and Mathematics & Statistics and Center for Advanced Research in Environmental GenomicsUniversity of OttawaOttawaCanada
  2. 2.Department of Biology and Center for Advanced Research in Environmental GenomicsUniversity of OttawaOttawaCanada
  3. 3.Quebec Center for Biodiversity ScienceMcGill UniversityMontrealCanada
  4. 4.Agriculture and Agri-Food Canada, Eastern Cereal and Oilseeds Research Center, Central Experimental FarmOttawaCanada

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