Past Work

Recombination, diversity, and divergence— One central question in evolutionary genetics is whether neutral forces like drift and mutation shape nucleotide diversity more than selection. Interestingly, nucleotide diversity within a species is positively associated with local rates of recombination across a genome, and this relationship is consistent across a wide phylogenetic breadth. Both neutral forces (e.g., recombination being mutagenic) and selective forces (e.g., recombination limiting the neutral diversity eroded by selective sweeps and background selection) can explain this observation, but it is unresolved as to which force plays a more dominant role. Thus, this question is central to understanding and interpreting diversity in the genome.

With collaborators, I found strong evidence that recombination preserves diversity in the face of selection in the model system Drosophila on a genomic scale (McGaugh et al., 2012). Our data indicate that a substantial portion of nucleotide diversity in the genome is not governed purely by neutral forces and is instead strongly influenced by an interplay of recombination and selection. Further, in areas of high recombination, I identified that nucleotide diversity near substitutions, many of which were putatively fixed by selective sweeps, recovers in close physical proximity to the substitution. In areas of low recombination, the footprint caused by selection may be larger than in areas of high recombination (Fig. 1). This is expected by long-standing theory, and our data represent one of the first empirical demonstrations.

Recombination, chromosome rearrangements, maintenance of species boundaries—How speciation occurs and genetic differences between taxa are maintained or intensified in the face of hybridization are fundamental questions in evolutionary biology. Inversions are likely important for maintaining differences between diverging populations during the early stages of speciation or when nascent species come in to secondary contact because inversions reduce recombination and genetic exchange between the inverted and standard chromosomal arrangements.

We resequenced 15 genomes to examine the divergence between two sister species of Drosophila that harbor different chrom

osome inversion arrangements. We found that divergence is significantly greater inside the inversions relative to outside of the inversions (Fig. 2; McGaugh & Noor2012). Outside of the inversions, the DNA divergence between the two species resembles within species diversity, suggesting that nucleotide divergence has been nearly homogenized by gene flow in areas not protected by the inversion. We determined that the inversions arose approximately 2mya, but appear to have fixed between species recently (McGaugh & Noor 2012). This suggests that the inversions in this Drosophila system provide the first empirical example supporting a new theory of speciation whereby inversions can arise in allopatry, be maintained as polymorphisms by mutation-selection balance for long periods of time, and are later driven to fixation when the two species come into secondary contact due to selection pressure against hybrids (“mixed geographic mode” theory of speciation proposed by Feder and colleagues in 2011).