2Running title: Gene flow between allopatric Drosophila ABSTRACT The fruit fly Drosophila simulans and its sister species D. mauritiana are a model system for studying the genetic basis of reproductive isolation, primarily because interspecific crosses produce sterile hybrid males and their phylogenetic proximity to D. melanogaster. We present an analysis of whole-genome patterns of polymorphism and divergence that shows, on average, the genomes of the two species differ at slightly more than 1% of nucleotide positions and an estimated 40% of autosomal and 60% of X-linked loci are reciprocally monophyletic. However, the analysis also identifies 21 major genomic regions, comprising ~1% of the genome, in which one species is segregating for haplotypes that are more similar to haplotypes from the other species than expected, given the levels of sequence divergence in that genomic region. This disjoint distribution of interspecific coalescence times is consistent with recent introgression between the cosmopolitan D. simulans and the island endemic D. mauritiana. We find that the putatively introgressed regions are more likely to have significantly higher rates of crossing-over and are enriched for genes with significantly slower rates of protein evolution. We also uncover instances in which genes experiencing lineage-specific positive selection closely interact with genes experiencing introgression. Finally, we find that a large introgressing region on the X chromosome has experienced a strong selective sweep in D. mauritiana and also has high levels of homozygosity in D. simulans. A detailed analysis reveals that the introgressing X chromosome haplotypes are closely associated with the presence of the MDox locus, which is the progenitor of the Winters sex-ratio meiotic drive genes. These results highlight how genetic systems that evolve rapidly in allopatry, including selfish meiotic drive elements, remain robust in natural hybrid genotypes and do not systematically promote reproductive isolation. P < 0.001 as the threshold for determination of significance, which corresponds to a proportion of tests that are truly null to be 0.984 and a false discovery rate of 18.3%. We do not perform MK tests that contrast divergence and polymorphism between D. simulans and D. mauritiana, because our primary motivation for the analysis is to determine whether putatively introgressed regions are more or less subject to natural selection over the long-term than a random sample from the genome. Introgression would have the net effect of reducing the number of substitutions between D. simulans and D. mauritiana, while inflating the count of polymorphic sites in the population that receives the introgressing sequences.

Y chromosomes across diverse species convergently evolve a gene-poor, heterochromatic organization enriched for duplicated genes, LTR retrotransposons, and satellite DNA. Sexual antagonism and a loss of recombination play major roles in the degeneration of young Y chromosomes. However, the processes shaping the evolution of mature, already degenerated Y chromosomes are less well-understood. Because Y chromosomes evolve rapidly, comparisons between closely related species are particularly useful. We generated de novo long read assemblies complemented with cytological validation to reveal Y chromosome organization in three closely related species of the Drosophila simulans complex, which diverged only 250,000 years ago and share >98% sequence identity. We find these Y chromosomes are divergent in their organization and repetitive DNA composition and discover new Y-linked gene families whose evolution is driven by both positive selection and gene conversion. These Y chromosomes are also enriched for large deletions, suggesting that the repair of double-strand breaks on Y chromosomes may be biased toward microhomology-mediated end joining over canonical non-homologous end-joining. We propose that this repair mechanism contributes to the convergent evolution of Y chromosome organization across organisms.

During speciation, sex chromosomes often accumulate interspecific genetic incompatibilities faster than the rest of the genome. The drive theory posits that sex chromosomes are susceptible to recurrent bouts of meiotic drive and suppression, causing the evolutionary build-up of divergent cryptic sex-linked drive systems and, incidentally, genetic incompatibilities. To assess the role of drive during speciation, we combine high-resolution genetic mapping of X-linked hybrid male sterility with population genomics analyses of divergence and recent gene flow between the fruitfly species, Drosophila mauritiana and D. simulans. Our findings reveal a high density of genetic incompatibilities and a corresponding dearth of gene flow on the X chromosome. Surprisingly, we find that a known drive element recently migrated between species and, rather than contributing to interspecific divergence, caused a strong reduction in local sequence divergence, undermining the evolution of hybrid sterility. Gene flow can therefore mediate the effects of selfish genetic elements during speciation.

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