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MBE Advance Access published online on November 21, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl178
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© 2006 The Authors This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Accepted November 15, 2006

Research Article

Variation in Evolutionary Processes at Different Codon Positions

Lee Bofkin 1 and Nick Goldman 1 *

1 EMBL-European Bioinformatics Institute, Hinxton, United Kingdom

* To whom correspondence should be addressed.
Nick Goldman, E-mail: goldman{at}ebi.ac.uk


  Abstract

Evolutionary studies commonly model single nucleotide substitutions and assume that they occur as independent draws from a unique probability distribution across the sequence studied. This assumption is violated for protein coding sequences and we consider modelling approaches where codon positions are treated as separate categories of sites, since within each category the assumption is more reasonable. Such ‘codon-position’ models have been shown to explain the evolution of codon data better than homogenous models in previous studies. This paper examines the ways in which codon-position models outperform homogeneous models and characterises the differences in estimates of model parameters across codon positions. Using the PANDIT database of multiple species DNA sequence alignments, we quantify the differences in the evolutionary processes at the three codon positions in a systematic and comprehensive manner, characterising previously undescribed features of protein evolution. We relate our findings to the functional constraints imposed by the genetic code, protein function and the types of mutation that cause synonymous and non-synonymous codon changes. The results increase our understanding of selective constraints and could be incorporated into phylogenetic analyses or gene-finding techniques in the future. The methods used are extended to an overlapping reading frame data set and we discover that overlapping reading frames do not necessarily cause more stringent evolutionary constraints.

Keywords: adaptive evolution; codon positions; phylogenetic inference; protein coding sequences; sequence evolution.
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