Data from: Multiple hybridization events between Drosophila simulans and Drosophila mauritiana are supported by mtDNA introgression

The study of speciation has advanced considerably in the last decades due to the increased application of molecular tools. In particular the quantification of gene flow between recently diverged species could be addressed. D. simulans and D. mauritiana diverged, probably allopatrically, from a common ancestor approximately 250,000 years ago. However, these species share one mitochondrial DNA (mtDNA) haplotype indicative of a recent episode of introgression. To study the extent of gene flow between these species, we took advantage of a large sample of D. mauritiana and employed a range of different markers, i.e. nuclear and mitochondrial sequences, and microsatellites. This allowed us to detect two new mtDNA haplotypes (MAU3 and MAU4). These haplotypes diverged quite recently from haplotypes of the siII group present in cosmopolitan populations of D. simulans. The mean divergence time of the most diverged haplotype (MAU4) is approximately 127,000 years, which is more than 100,000 years before the assumed speciation time. Interestingly we also found some evidence for gene flow at the nuclear level since an excess of putatively neutral loci show significantly reduced differentiation between D. simulans and D. mauritiana. Our results suggest that these species are exchanging genes more frequently than previously thought.