Data for: Surrounding landscape, habitat and hybridization dynamics drive population structure and genetic diversity in the Saltmarsh Sparrow (Ammospiza caudacuta)

Determining factors that shape a species’ population genetic structure is
beneficial for identifying effective conservation practices. We assessed
population structure and genetic diversity for Saltmarsh Sparrow
(Ammospiza caudacuta), an imperiled tidal marsh specialist, using 13
microsatellite markers and 964 individuals sampled from 24 marshes across
the breeding range. We show that Saltmarsh Sparrow populations are
structured regionally by isolation-by-distance, with gene flow occurring
among marshes within ~110-135 km of one another. Isolation-by-resistance
and isolation-by-environment also shape genetic variation; several habitat
and landscape features are associated with genetic diversity and genetic
divergence among populations. Human development in the surrounding
landscape isolates breeding marshes, reducing genetic diversity and
increasing population genetic divergence, while surrounding marshland and
patch habitat quality (proportion high marsh and sea-level-rise trend)
have the opposite effect. The distance of the breeding marsh to the
Atlantic Ocean also influences genetic variation, with marshes farther
inland being more divergent than coastal marshes. In northern marshes,
hybridization with Nelson’s Sparrow (A. nelsoni) strongly influences
Saltmarsh Sparrow genetic variation, by increasing genetic diversity in
the population; this has a concomitant effect of increasing genetic
differentiation of marshes with high levels of introgression. From a
conservation perspective, we found that the majority of population
clusters have low effective population sizes, suggesting a lack of
resiliency. To conserve the representative breadth of genetic and
ecological diversity and to ensure redundancy of populations, it will be
important to protect a diversity of marsh types across the latitudinal
gradient of the species range, including multiple inland, coastal and
urban populations, which we have shown to exhibit signals of genetic
differentiation. It will also require maintaining connectivity at a
regional level, by promoting high marsh habitat at the scale of gene flow
(~130 km), while also ensuring “stepping stone” populations across the
range.