Evidence for a force favouring GC over AT at short intronic sites in Drosophila simulans and D. melanogaster

Abstract

Population genetics studies often make use of a class of nucleotide site free from selective pressures in order to make inferences about population size changes or natural selection at other sites. If such neutral sites can be identified, they offer the opportunity to avoid any confounding effects of selection. Here we investigate evolution at putatively neutrally evolving short intronic sites in natural populations of Drosophila melanogaster and D. simulans, in order to understand the properties of spontaneous mutations and the extent of GC-biased gene conversion in these species. Use of data on the genetics of natural populations is advantageous because it integrates information from large numbers of individuals over long timescales. In agreement with direct evidence from observations of spontaneous mutations in Drosophila, we find a bias in the spectrum of mutations towards AT basepairs. In addition, we find that this bias is stronger in the D. melanogaster lineage than the D. simulans lineage. The evidence for GC-biased gene conversion in Drosophila has been equivocal. Here we provide evidence for a weak force favouring GC in both species, which is stronger in D. simulans. Some homologous short intronic sites have diverged in GC content between the two species, which may have been caused by lineage-specific changes in the extent to which different regions of the genome are subject to a GC (or AT)-favouring force.