Abstract
Genomic resources are valuable to examine historical demographic patterns and their effects to better inform management and conservation of threatened species. We evaluated population trends and genome‐wide variation in the near‐threatened Orange‐breasted Falcon ( Falco deiroleucus ) and its more common sister species, the Bat Falcon ( F. rufigularis ), to explore how the two species differ in genomic diversity as influenced by their contrasting long‐term demographic histories. We generated and aligned whole genome resequencing data for 12 Orange‐breasted Falcons and 9 Bat Falcons to an annotated Gyrfalcon ( F. rusticolus ) reference genome that retained approximately 22.4 million biallelic autosomal SNPs (chromosomes 1–22). Our analyses indicated much lower genomic diversity in Orange‐breasted Falcons compared to Bat Falcons. All sampled Orange‐breasted Falcons were significantly more inbred than the sampled Bat Falcons, with values similar to those observed in island‐mainland species comparisons. The distribution of runs of homozygosity showed variation suggesting long‐term low population size and the possibility of bottlenecks in Orange‐breasted Falcons contrasting with consistently larger populations in Bat Falcons. Analysis of genetic load suggests that Orange‐breasted Falcons are less likely to experience inbreeding depression than Bat Falcons due to reduced inbreeding load but are at elevated risk from fixation of deleterious gene variants and perhaps a reduced adaptive potential. These genomic analyses highlight differences in the historical demography of two closely related species that have influenced their current genomic diversity and should result in differing strategies for their continued conservation.