Gene flow weakens genomic clines while selection maintains adaptive loci: two decades of evolution in Drosophila melanogaster natural populations

Using spatiotemporal sampling to understand evolutionary changes over time is highly effective, particularly to gain insights into changes driven by environmental shifts. The latitudinal clines in Drosophila melanogaster in North America provide an excellent system for studying temporal changes. Due to D. melanogasters short generational times, it is possible to observe changes spanning up to 100 generations within a single decade. Using temporal samples across the latitudinal transect could shed light on the processes responsible for the establishment and maintenance of those clines, and help to disentangle demographic and selective forces. To do this, we used pool-seq to obtain genomewide data of 16 new D. melanogaster natural populations collected along the North American east coast from 1997 to 2023. Our data suggest that there has been a homogenization over time. Consistent with this, we observed a reduction in the number of clinal single nucleotide polymorphisms. Polymorphisms that remained clinal had smaller slopes on chromosome 3R, aligned with the reduction in slope of inversions In(3R)Payne and In(3R)Mo. Clinal SNPs tended to be lost more frequently in genomic regions with higher recombination rates, and clinal SNPs identified in 2009/2010 were enriched in functional classes with greater phenotypic impact relative to those from 1997. We also investigated signs of selective sweeps that were shared among locations using a window FST approach, which corroborated previously found signals of selection in the insecticide resistance-linked region of the P450 gene family. Overall, the results indicate that gene flow gradually reduces clinality over time, while the remaining clinal loci are likely shaped by spatially varying selection. Together, these findings highlight how gene flow and selection jointly shape spatial genomic patterns over time in natural populations.