Patterns of divergence reveal genomic islands of speciation in young semispecies of Drosophila athabasca. Karen M. Wong Miller¹, Michael B. Eisen^2,3, Doris Bachtrog¹. 1) Department of Integrative Biology, University of California, Berkeley, CA; 2) Department of Molecular and Cell Biology, University of California, Berkeley, CA; 3) Howard Hughes Medical Institute, University of California, Berkeley, CA.

   Previous studies utilizing Drosophila have contributed significantly to our understanding of speciation and particularly postzygotic reproductive isolation. However, the difficulty in teasing apart the factors that are important to the actual process of speciation, rather than those that have secondarily accumulated with time has been widely noted. By examining very recently diverged systems, we are more likely to identify the molecular mechanisms responsible for speciation. We use next-generation sequencing technologies to collect whole-genome resequencing data for 28 individuals of Drosophila athabasca, a North American species complex composed of three semispecies. The semispecies are morphologically identical, have overlapping ranges, and show no evidence of postzygotic isolation, however they exhibit behavioral isolation in the form of semispecies-specific male courtship song. With estimated divergence times ranging from ~5-20 kya, the semispecies of D. athabasca are among the youngest incipient species known within Drosophila. We quantified levels of genome-wide diversity and differentiation within and between semispecies and find ~2 Mb of variable sites within D. athabasca, with only 1% of variable sites being private and fixed within semispecies. Furthermore, we find divergence is not evenly distributed across the genome, with the X-chromosome exhibiting increased levels of divergence compared with autosomes, and genome-wide scans showing evidence for islands of speciation between semispecies. The likely presence of variants driving reproductive isolation in these regions, with relatively low levels of divergence throughout the rest of the genome, establishes D. athabasca as an excellent model to study not only the genetic mechanisms driving prezygotic isolation, but also how genomes diverge during incipient speciation.