Data from: Genome-wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation

Models of speciation-with-gene-flow have shown that the reduction in recombination between alternative chromosome arrangements can facilitate the fixation of locally adaptive genes in the face of gene flow and contribute to speciation. However, it has proven frustratingly difficult to show empirically that inversions have reduced gene flow and arose during or shortly after the onset of species divergence rather than represent ancestral polymorphisms. Here we present an analysis of whole genome data from a pair of cactophilic fruit flies, Drosophila mojavensis and D. arizonae, which are reproductively isolated in the wild and differ by several large inversions on three chromosomes. We found an increase in divergence at rearranged compared to colinear chromosomes. Using the density of divergent sites in short sequence blocks we fit a series of explicit models of species divergence in which gene flow is restricted to an initial period after divergence and may differ between colinear and rearranged parts of the genome. These analyses show that D. mojavensis and D. arizonae have experienced post-divergence gene flow which ceased around 270 KY ago and was significantly reduced in chromosomes with fixed inversions. Moreover, we show that these inversions most likely originated around the time of of species divergence which is compatible with theoretical models of speciation with gene flow.

Dryad_data_2015
The folder contains .txt files of counts of divergent sites between D. arizonae and D. mojavensis in 250 and 500 bp blocks of intergenic sequence. These are the input files (readable with the Mathematica function ReadList[]) for fitting the IIM model using an analytic expression for the likelihood derived by Wilkinson-Herbots (2012). For details see Methods in Lohse et al (2015). Each block is summarized as a nested list {{S_div, S_het}, total length, pos}. The four entries are: S_div: Number of divergent sites S_het: Number of heterozygous sites in both species total length: Total physical length of the block in the Dmoj reference genome including sites that did not pass filtering. pos: Position on the scaffold (mean position of all called sites) Blocks containing heterozygous sites or a physical length > 2x the number of called sites were not used in the analysis.

Lohse, Konrad; Clarke, Magnus; Ritchie, Michael G.; Etges, William J. (2015). Data from: Genome-wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation [Dataset]. Dryad. https://doi.org/10.5061/dryad.5jq6p