Whole-genome data uncover the basis of local adaptation with gene flow
in a threatened coastal songbird
Abstract
Understanding the genetic basis of local adaptation and the distribution
of standing genetic variation is imperative for biodiversity
conservation as species decline globally. The Atlantic song sparrow
(Melospiza melodia atlantica) is a specialist subspecies of conservation
concern that is adapted to the coastal habitats of eastern North America
and interbreeds with a widespread, parapatric generalist subspecies, the
eastern song sparrow (M. m. melodia). Because the Atlantic and eastern
song sparrows offer an ideal opportunity to explore the evolutionary
dynamics of local adaptation with gene flow, we examined the genomic
architecture of divergence and the basis of coastal adaptation using
whole-genome sequencing of these subspecies. We identified a polygenic
basis for coastal adaptation, with candidate genes related to
osmoregulation, plumage pigmentation, and bill size. Divergent genes
were dispersed throughout a homogenous genomic background, demonstrating
that strong natural selection is the key force maintaining
differentiation between these subspecies despite gene flow. Notably,
some candidate genes were located near centromeres and telomeres,
suggesting regions of suppressed recombination may play some role in the
maintenance of local adaptation despite gene flow in this system. We
found population structure within the Atlantic song sparrow, with
southern barrier islands making a up a key portion of the range of this
subspecies and each island comprising a distinct gene cluster, which may
inform future conservation management decisions. This system emphasizes
the need for high-resolution genomic data to characterize the basis of
adaptive differentiation and inform effective conservation strategies
for systems with extensive gene flow.