Population genetic analysis of weak selection in the Drosophila subobscura species complex

Until relatively recently, synonymous codons have been thought to be under very little evolutionary constraint. That has changed, and now codon bias (the preferential use of a subset of synonymous codons for each degenerate amino acid) is being observed in nearly every organism in which it is adequately searched for. Synonymous codons are evolving under weak selection. As such, it is expected that the selective forces driving the distributions of these codons to be more efficient in species with larger effective population sizes than species with smaller population sizes. With this in mind I investigate patterns of weak selection in the Drosophila subobscura species complex. D. subobscura is a widespread, continental species with a Palearctic distribution. In contrast, its sister species D. guanche and D. madeirensis are island endemic species with low population sizes that each share a relatively recent common ancestor with D. subobscura. In Chapter 2, I investigate patterns of molecular divergence between D. subobscura and the two island species. I show that there is considerable selection acting on synonymous codons in D. subobscura, but not as strong in the island species (although it still exists). The main consequence of this is that purifying selection acting against unpreferred codons is active in D. subobscura, but synonymous codons are much less constrained in the island species. This causes the common measurement of the ratio of nonsynonymous to synonymous mutations to appear larger in D. subobscura while both components are actually increased in the island species. In Chapter 3, I focus on D. subobscura and look at patterns of polymorphism within this species. I show that there is a genome wide skew towards low frequency variants, while only the unpreferred to preferred mutation class segregates at higher than expected frequencies. This is indicative of purifying selection acting upon most of the genome, and positive selection pushing preferred codons to higher frequencies.