Local adaptation in response to spatially varying selection pressures is widely recognized as a ubiquitous feature for many organisms. In contrast, our understanding of local adaptation to temporally varying selection pressures is limited. To advance our understanding of local adaptation to temporally varying selection pressures, we studied genomic signatures of seasonal adaptation in Drosophila melanogaster. We generated whole-genome estimates of allele frequencies from flies sampled during the spring and fall from 15 localities. We show that seasonal adaptation is a general feature fly populations and that the direction of seasonal adaptation can be predicted by weather conditions in the weeks prior to sampling. We find that seasonal changes in allele frequency are mirrored by spatial variation in allele frequency and that seasonal adaptation affects allele frequencies at ~1.0-2.5% of polymorphisms genomewide. Our work demonstrates that seasonal adaptation is a major evolutionary force affecting D. melanogaster populations living in temperate environments.

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Direct observation of evolution in response to natural environmental change can resolve fundamental questions about adaptation, including its pace, temporal dynamics, and underlying phenotypic and genomic architecture. We tracked the evolution of fitness-associated phenotypes and allele frequencies genome-wide in 10 replicate field populations of Drosophila melanogaster over 10 generations from summer to late fall. Adaptation was evident over each sampling interval (one to four generations), with exceptionally rapid phenotypic adaptation and large allele frequency shifts at many independent loci. The direction and basis of the adaptive response shifted repeatedly over time, consistent with the action of strong and rapidly fluctuating selection. Overall, we found clear phenotypic and genomic evidence of adaptive tracking occurring contemporaneously with environmental change, thus demonstrating the temporally dynamic nature of adaptation.