Drosophila Raw sequence reads

To determine the role of chromosomal inversions in the speciation process. We compared the genomic divergence between two D. mojavensis and one D. arizonae populations and found an increase in pairwise divergence at rearranged compared to colinear chromosomes. We used the density of divergent sites in short blocks of intergenic sequence, to fit a series of models of isolation with gene flow to populations of D. mojavensis and D. arizonae in allopatry and sympatry. These analyses suggest that i) D. mojavensis and D. arizonae have experienced post-divergence gene flow which however ceased around 270 KY ago ii) gene flow was significantly reduced in chromosomes harbouring fixed inversion differences and iii) that at least some of these inversions originated around the onset of species divergence. Taken together, these results support those recent models of speciation with gene flow which suggest that inversions arising during or after the onset of species divergence can play a crucial role in the build-up of reproductive isolation.