Genomic analysis of European Drosophila populations reveals longitudinal structure and continent-wide selection

Genetic variation is the fuel of evolution. However, analyzing evolutionary dynamicsin natural populationsis challenging, sequencing of entire populationsremains costly and comprehensive sampling logistically difficult. To tackle this issue and to define relevant spatial and temporal scalesof variation, we have founded the European Drosophila Population GenomicsConsortium (DrosEU). Here we present the first analysis of 48 D. melanogaster populationsamples collected across Europe in 2014. Our analysis uncovers novel patterns of variation at multiple levels: genome-wide neutral SNPs, mtDNA haplotypes, inversions, and TEs showing previously cryptic longitudinal populationstructure; signatures of selective sweepsshared among populations; presumably adaptive clines in inversions; and geographic variation in TEs. Additionally, we document highly variable microbiota and identify several new Drosophila viruses. Our study reveals novel aspects of the population biologyof D. melanogasterand illustrates the power of extensive sampling and pooled sequencing of populationson a continent-wide scale.