Repeatability of genome-wide variation for diapause termination between divergent host-associated populations of Rhagoletis pomonella

Seasonal adaptation can result in unanticipated genomic responses as seasonal selection often acts along multiple ecological axes. Such “multifarious selection” may confound forward genetic screens on seasonally adaptive traits because observed genomic patterns may result from correlated responses to selection on unmeasured traits. This had been the case in the apple maggot fly, Rhagoletis pomonella, where decades of research found that apple-infesting populations, which emerge earlier than ancestral hawthorn-infesting populations, harbor a larger amount of allelic variation associated with late emergence. However, recent work has found that emergence-associated genetic variation is concentrated in genomic regions of high linkage disequilibrium that also contains genetic variation for an additional seasonal trait, diapause intensity. Our data suggests that selection for diapause intensity may be dragging along variation in emergence timing, thereby explaining the previously observed counterintuitive patterns. However, the question remains of how apple-infesting populations “compensate” for this putatively maladaptive variation in emergence timing. Using multiple whole genome pooled resequencing (pool-seq) GWAS for emergence timing and diapause intensity in both the apple-
and hawthorn-infesting populations, we search for potential compensatory mechanisms. Given that seasonal selection varies with latitude, the genomic basis of seasonal adaptation may be
idiosyncratic across space. To test the repeatability of the genomic distribution of emergence-associated variants across space, we also performed pool-seq GWAS for emergence timing in R.
pomonella in multiple sympatric populations. This work will provide insight into the genomic basis of seasonal adaptation as well as clarify our understanding of the developmental regulation of insect dormancy.