In this chapter, we give a not-so-long and 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 divergence times and rates on a phylogeny, before showing how state-of-the-art models take inspiration from diffusion theory to link population genetics, which traditionally focuses at a taxonomic level below that of the species, and molecular evolution. Although this is not a cookbook chapter, we try and point to popular programs and implementations along the way.

Additional Metadata
Keywords Bayes, Divergence times, Likelihood, Model choice, Phylogenetics
Persistent URL
Series Methods in Molecular Biology
Aris-Brosou, S. (Stéphane), & Rodrigue, N. (2019). A not-so-long introduction to computational molecular evolution. In Methods in Molecular Biology. doi:10.1007/978-1-4939-9074-0_3