Florida Drosophila melanogaster genomes sampled 13 years apart show increases in warm-associated SNP alleles

We studied genetic change in Drosophila melanogaster using whole-genome SNP data from samples taken 13 years apart in Homestead, FL. This population is at the southern tip of a well-studied US latitudinal cline. On the non-inversion-carrying chromosome arms, 11-16% of SNPs show significant frequency changes. These are enriched for latitudinal clines and genic sites. For clinal SNPs each allele is either the northern- or southern-favored. Seventy-eight to 95 percent with significant frequency increase are southern-favored. Five to seven percent of SNPs also show significant seasonal change and involve increases in the northern-favored allele during the season. On the 2L and 3R chromosome arms there are significant seasonal shifts for common inversions. We identify regions and genes that are candidates for selection. These regions also show correspondence with those associated with soft sweeps in Raleigh, NC. This shift towards southern-favored alleles may be caused by climate shifts or increased African-European admixture.