Parallel selection on copy-number variants across continents and species in Drosophila. Daniel R. Schrider^1,2, Matthew W. Hahn^1,2, David J. Begun³. 1) Department of Biology. Indiana Univesity, Bloomington, IN; 2) School of Informatics and Computing. Indiana Univesity, Bloomington, IN; 3) Department of Evolution and Ecology. University of California. Davis, CA.

   Regions of the genome that vary in copy-number within a species, referred to as copy-number variants (CNVs), have been shown to have important functional and evolutionary consequences in a variety of organisms. However, the importance of copy-number variation to adaptation in Drosophila is largely unknown. In order to address this question, we examine pooled sequence data from opposite ends of two latitudinal clines in D. melanogaster and D. simulans. Because extensive gene flow occurs across each of these clines, regions exhibiting strong differentiation in allele frequency across a cline are candidates for local adaptation. This strategy has been used to identify single nucleotide polymorphisms and transposable element insertions that may be experiencing spatially varying selection. We extend this approach to the problem of identifying CNVs differing in allele frequency between two pooled samples. We examine pooled D. melanogaster whole genome sequences from the ends of the latitudinal cline along the East Coast of the United States, and also from the ends of the cline along eastern Australia. We find hundreds of highly differentiated CNVs in each of these clines that represent strong candidates for spatially varying selection. Furthermore, we find that many of these CNVs are differentiated in both continents and in the same direction with respect to distance from the equator. Because this overlap is not expected if these CNVs are not under selection, we have especially high confidence that these CNVs are involved in local adaptation. Finally, we perform the same analysis on D. simulans pooled sequence data from these two clines, finding similarly high numbers of differentiated CNVs, again with many exhibiting the same pattern of differentiation across continents. Several genes were found to reside within differentiated CNVs in both species. Together, these results show that copy-number changes are a major contributor to local adaptation in Drosophila.