Data from: Maintenance of local adaptation despite gene flow in a coastal songbird

Adaptation to local environments is common in widespread species and the
basis of ecological speciation. The song sparrow (Melospiza melodia) is a
widespread, polytypic passerine that occurs in shrubland habitats
throughout North America. We examined the population structure of two
parapatric subspecies that inhabit different environments: the Atlantic
song sparrow (M. m. atlantica), a coastal specialist; and the eastern song
sparrow (M. m. melodia), a shrubland generalist. These populations lacked
clear mitochondrial population structure, yet coastal birds formed a
distinct nuclear genetic cluster. We found weak overall genomic
differentiation between these subspecies, suggesting either recent
divergence, extensive gene flow, or a combination thereof. There was a
steep genetic cline at the transition to coastal habitats, consistent with
isolation by environment (IBE), not isolation by distance (IBD). A
phenotype under divergent selection, bill size, varied with the amount of
coastal ancestry in transitional areas, but larger bill size was
maintained in coastal habitats regardless of ancestry, further supporting
a role for selection in the maintenance of these subspecies. Demographic
modeling suggested a divergence history of limited gene flow followed by
secondary contact, which has emerged as a common theme in adaptive
divergence across taxa.