Phylogenetic Testing for Deviations from the Mutation-Selection Balance

• Activity Number: 64
• Type: Topic Contributed
• Date/Time: Sunday, August 3, 2014 : 4:00 PM to 5:50 PM
• Sponsor: Biometrics Section
• Author(s): Nicolas Rodrigue*+
• Companies: University of Calgary
• Keywords: Evolution ; Markov process ; Bayesian inference ; MCMC

Abstract

Codon substitution models have traditionally been used to measure selective pressures in protein-coding genes by evaluating the ratio of rates of nonsynonymous to synonymous substitutions. Recently, we have proposed a mutation-selection framework in which site-specific purifying selection at the amino acid level is explicitly modeled (Rodrigue et al., PNAS, 2010). Loosely speaking, under this model, substitutions at a given position occur at the neutral or near-neutral rate when they are either synonymous, or when they correspond to replacements within a sub-set of suitable amino acids---substitutions to ill-suited amino acids have much lower rates. As an alternative to traditional methods, we explore the idea of using our recent model as the null against which to test for deviations from the neutral/nearly-neutral regime. We present applications of this approach on a few data set of protein-coding genes, and discuss how the null model can be extended so as to test for different reasons for measured deviations, such selection on codon usage.