Genomic differentiation and local adaptation on a microgeographic scale in a resident songbird

Elucidating forces capable of driving species diversification in the face
of gene flow remains a key goal in evolutionary biology. Song sparrows,
Melospiza melodia, occur as 25 subspecies in diverse habitats across North
America, are among the continent’s most widespread vertebrate species, and
are exemplary of many highly variable species for which the conservation
of locally adapted populations may be critical to their range-wide
persistence. We focus here on six morphologically distinct subspecies
resident in the San Francisco Bay region, including three salt-marsh
endemics and three residents in upland and riparian habitats adjacent to
the Bay. We used reduced-representation sequencing to generate 2,773 SNPs
to explore genetic differentiation, spatial population structure, and
demographic history. Clustering separated individuals from each of the six
subspecies, indicating subtle differentiation at microgeographic scales.
Evidence of limited gene flow and low nucleotide diversity across all six
subspecies further supports a hypothesis of isolation among locally
adapted populations. We suggest that natural selection for genotypes
adapted to salt marsh environments and changes in demography over the past
century have acted in concert to drive the patterns of diversification
reported here. Our results offer evidence of microgeographic
specialization in a highly polytypic bird species long discussed as a
model of sympatric speciation and rapid adaptation, and they support the
hypothesis that conserving locally adapted populations may be critical to
the range-wide persistence of similarly highly variable species.