Genomic analysis of European Drosophila melanogaster populations on a dense spatial scale reveals longitudinal population structure and continent-wide selection

80 Genetic variation is the fuel of evolution. However, analyzing dynamics of evolutionary 81 change in natural populations is challenging, genome sequencing of entire populations 82 remains costly and comprehensive sample collection logistically challenging. To tackle this 83 issue and to define relevant spatial and temporal scales of variation for a population 84 genetic model system, the fruit fly Drosophila melanogaster, we have founded the 85 European Drosophila Population Genomics Consortium (DrosEU). Our principal objective 86 is to employ the strengths of this collaborative consortium to extensively sample and 87 sequence natural populations on a continent-wide scale and across distinct timescales. 88 Here we present the first analysis of the first DrosEU pool-sequencing dataset, consisting 89 of 48 population samples collected across the European continent in 2014. The analysis of 90 this comprehensive dataset uncovers novel patterns of variation at multiple levels: 91 genome-wide neutral SNPs, mtDNA haplotypes, inversions and TEs that exhibit previously 92 cryptic longitudinal population structure across the European continent; signatures of 93 selective sweeps shared among the majority of European populations; presumably 94 adaptive clines in inversions; and geographic variation in TEs. Additionally, we document 95 highly variable microbiota among European fruit fly populations and identify several new 96 Drosophila viruses. Our study reveals novel aspects of the population biology of D. 97 melanogaster and illustrates the power of extensive sampling and pooled sequencing of 98 natural populations on a continent-wide scale. 99 100