Data from: Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

Populations arrayed along broad latitudinal gradients often show patterns
of clinal variation in phenotype and genotype. Such population
differentiation can be generated and maintained by both historical
demographic events and local adaptation. These evolutionary forces are not
mutually exclusive and can in some cases produce nearly identical patterns
of genetic differentiation among populations. Here, we investigate the
evolutionary forces that generated and maintain clinal variation
genome-wide among populations of Drosophila melanogaster sampled in North
America and Australia. We contrast patterns of clinal variation in these
continents with patterns of differentiation among ancestral European and
African populations. Using established and novel methods we derive here,
we show that recently derived North America and Australia populations were
likely founded by both European and African lineages and that this
hybridization event likely contributed to genome-wide patterns of parallel
clinal variation between continents. The pervasive effects of admixture
means that differentiation at only several hundred loci can be attributed
to the operation of spatially varying selection using an FST outlier
approach. Our results provide novel insight into the well-studied system
of clinal differentiation in D. melanogaster and provide a context for
future studies seeking to identify loci contributing to local adaptation
in a wide variety of organisms, including other invasive species as well
as temperate endemics.