Evolutionary Rates and Patterns in Rodent APRT Sequences

Abstract

<p>The nonrandom rates and patterns of sequence evolution found in the adenine phosphoribosyltransferase gene (APRT) from closely related rodent species provide insight into processes involved in molecular evolution. The rodent APRT phylogeny supports the species phylogeny tree previously found using morphological and molecular data. A five-fold slower rate of evolution observed in Mus spicilegus APRT compared to Mus musculus promotes M. spicilegus as a model species to test potential causes of rate variation between species, which may be related to a difference in degree of commensalism experienced by these two species. Rate differences found between individual exons and introns of the APRT, exemplified by the burst of substitutions observed in M. musculus, APRT exons I and V, suggest that regional differences in selection and mutation biases exist. Rate differences between sequence positions are demonstrated with some APRT third codon positions being more prone to substitution than others, indicating local effects on molecular evolution. The directional pattern of evolutionary changes found in the rodent APRTs suggests influences that can be attributed to selection and mutation biases which are possibly affected by sequence content and context. Observed directional patterns include: a distribution of substitutions along the sequence which is influenced by mutation bias and sequence base composition; substitution spectra which result in a net decrease in G/C content throughout rodent APRT evolution: substitutions at dinucleotides that reduce the presence of those dinucleotides in the sequence: and biased codon usage influenced by selection and CpG deamination. The limited divergerice between the rodent APRTs sequenced for this thesis provides strong evidence for the existence of rate differences and detectable patterns in substitutions that provide an intriguing view of the complex nature of molecular evolution and the processes involved. More divergent sequences might not reveal these patterns.</p>