Modelling change in codon substituion, using serially sampled sequence data.

Matthew Goode¹, Allen Rodrigo²
¹m.goode@auckland.ac.nz, University of Auckland; ²a.rodrigo@auckland.ac.nz, University of Auckland

Drummond et al, 2001 describe the use of nucleotide sequences sampled over time to estimate substitution rates over a series of time intervals. Here, we extend this approach to codon substitution models. In particular, we use the codon model of Neilsen and Yang 1998 and allow parameters associated with selection and the proportion of selected sites to vary over time. This approach allows us to detect changes in selection over time in populations where evolution can be measured, e.g., HIV and other rapidly evolving viral populations. Nielsen, R., and Z. Yang. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936 Drummond, A., Forsberg, R., Rodrigo,. A. 2001 The Inference of Stepwise Changes in Substitution Rate Using Serial Sequence Samples. Molecular Biology and Evolution 18:1365-1371.