| Summary: | Most species are constrained by geographic barriers to dispersal and geneflow, and such limitations have demographic and genetic consequences. We tested whether a highly vagile bird of prey, the golden eagle (GOEA; Aquila chrysaetos), exhibits disparate genetic signatures among island (Channel Islands, California, USA), peninsular (Baja California Peninsular region, USA) and mainland (California, USA) regions given the contrasting demography and phylogeography among regions. We utilized a SNP assay to estimate heterozygosity, inbreeding coefficients, and the effective population sizes (Ne) of GOEAs. In addition, we sequenced six GOEA genomes to obtain comprehensive measures of homozygosity (i.e., runs of homozygosity, ROHs) burden as well as estimates of nucleotide diversity. Our samples from the Channel Islands were clearly differentiated from both the peninsular and mainland samples, but there was no genetic differentiation between the peninsular and mainland samples. We found that the island samples exhibited signatures of a founder effect, including lower heterozygosity, reduced N e, and a higher ROH burden than the mainland or peninsular samples. Overall, the genetic markers and the whole-genome sequence data indicate that the Channel Islands samples are genetically distinct from the mainland and peninsular samples, likely as a result of a relatively recent demographic bottleneck followed by bouts of genetic drift and inbreeding. We also found that, unlike smaller and less mobile vertebrates (e.g., rodents, passerines, and lizards), the GOEA gene pool near Baja California is relatively homogenous across distinct phylogeographic domains separated by the San Andreas fault. The genetic isolation exhibited by the island GOEAs almost certainly results from their recent colonization (due to bald eagle extirpation associated with DDT exposure) and subsequent anthropogenic removal (due to predation on an endangered island fox).
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