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.