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Abstract BackgroundRapid morphological change is emerging as a consequence of climate change in many systems. It is intuitive to hypothesize that temporal morphological trends are driven by the same selective pressures that have established well-known ecogeographic patterns over spatial environmental gradients (e.g., Bergman’s and Allen’s rules). However, mechanistic understanding of contemporary morphological shifts is lacking. ResultsWe combine morphological data and whole genome sequencing from a four-decade dataset in the migratory bird hermit thrush (Catharus guttatus) to test whether morphological shifts over time are accompanied by genetic change. Using genome-wide association, we identify alleles associated with body size, bill length, and wing length. Shifts in morphology and concordant shifts in morphology-associated alleles over time would support a genetic basis for the observed changes in morphology over recent decades, potentially an adaptive response to climate change. In our data, bill size decreases were paralleled by genetic shifts in bill size-associated alleles. On the other hand, alleles associated with body size showed no shift in frequency over time. ConclusionsTogether, our results show mixed support for evolutionary explanations of morphological response to climate change. Temporal shifts in alleles associated with bill size support the hypothesis that selection is driving temporal morphological trends. The lack of evidence for genetic shifts in body size alleles could be explained by a large role of plasticity or technical limitations associated with the likely polygenic architecture of body size, or both. Disentangling the mechanisms responsible for observed morphological response to changing environments will be vital for predicting future organismal and population responses to climate change.