Channel Islands song sparrow (Melospiza melodia) landscape genomics and adaptation to climate with gene flow dataset

Disentangling the effects of neutral and adaptive processes in maintaining
phenotypic variation across environmental gradients is challenging in
natural populations. Song sparrows (Melospiza melodia) on the California
Channel Islands occupy a pronounced east-west climate gradient within a
small spatial extent, providing a unique opportunity to examine the
interaction of genetic isolation (gene flow) and the environment
(selection) in driving variation. We used reduced representation genomic
libraries to infer the role of neutral processes (drift and restricted
gene flow) and divergent selection in driving variation in
thermoregulatory traits with an emphasis on the mechanisms that maintain
bill divergence among islands. Analyses of 22,029 neutral SNPs confirm
distinct population structure by island with restricted gene flow and
relatively large effective population sizes, suggesting bill differences
are likely not a product of genetic drift. Instead, we found strong
support for local adaptation using 3,294 SNPs in differentiation-based and
environmental association analyses coupled with genome-wide association
(GWA) tests. Specifically, we identified several putatively adaptive and
candidate loci in or near genes involved in bill development pathways
(e.g., BMP, CaM, Wnt), confirming the highly complex and polygenic
architecture underlying bill morphology. Furthermore, we found divergence
in genes associated with other thermoregulatory traits (i.e., feather
structure, plumage color, and physiology). Collectively, these results
suggest strong divergent selection across an island archipelago results in
genomic changes in a suite of traits associated with thermal adaptation
over small spatial scales. Future research should move beyond the study of
univariate traits to better understand the multivariate adaptive responses
to these complex climate regimes.