Populations of short-lived organisms can respond to spatial and temporal environmental heterogeneity through local adaptation. However, the comparative signals of local adaptation across space and time remains poorly understood. Here, we examined patterns of allele frequency change across a latitudinal cline and between seasons at previously reported expression quantitative trait loci (eQTLs). We divided eQTLs into groups by utilizing differential expression profiles of fly populations collected across latitudinal clines or exposed to different environmental conditions. In general, we find that eQTLs are enriched for clinally varying polymorphisms, and that these eQTLs change in frequency in concordant ways across the cline and in response to starvation and chill-coma. The enrichment of eQTLs among seasonally varying polymorphisms is more subtle, and the direction of allele frequency change at eQTLs appears to be somewhat idiosyncratic. Taken together, we suggest that clinal adaptation at eQTLs is at least partially distinct from seasonal adaptation.

1. For original datasets, we downloaded from supplemental materials or websites.

2. For intermediate data, we wrote R scripts to re-group eQTLs by sex and estimated their directional effect on genes.

3. For results data, we wrote R scripts to do the enrichment and directionality analysis.