Biology Series Seminar: Dr Nicolas Rodrigue

• In-person event
• 4440Q, Carleton Technology and Training Centre, Carleton University
• 1125 Colonel By Drive, Ottawa, ON, K1S 5B6

• Contact
• Andrew Simons, andrew.simons@carleton.ca

“Measuring departures from a mutation-selection balance in protein-coding evolution”

Dr. Nicolas Rodrigue
Assistant Professor
Department of Biology
Institute of Biochemistry
Carleton University

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.  We have previously 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, whereas 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 nearly-neutral regime.  We have conducted simulation analyses showing that the approach can successfully detect even mild deviations, which are unapparent to the traditional site-models.  Applications on a few real data sets of protein-coding genes are demonstrated, and we discuss how the null model can be extended so as to test for different reasons for measured deviations, such selection on codon usage.

Bioinformatics- Molecular Evolution- Phylogenetic Models