Genetic diversity of the endangered Japanese golden eagle at neutral and functional loci

The Japanese golden eagle (Aquila chrysaetos japonica) is an endangered subspecies with declining reproductive success. Previous research on this subspecies reported genetic diversity in northern Japan and in captivity using neutral genetic markers, but the situation in other areas of Japan and diversity at functional genetic loci are understudied. Here, we increased wild samples from western Japan and captive samples from zoos and analyzed genetic diversity of mitochondrial DNA, nuclear microsatellite loci, and the major histocompatibility complex (MHC) DRB exon 2 region. In addition, wild Scottish samples were analyzed and literature from European subspecies and other raptor species was surveyed to compare with the Japanese golden eagle. Overall, levels of mtDNA haplotype and microsatellite diversity observed in western Japan were similar to previously studied northern regions. However, microsatellite allelic diversity was lower compared to other golden eagle subspecies. MHC diversity indices, especially in captive Japanese golden eagles, were also low relative to raptors classified as Least Concern by the IUCN. This pattern could be explained by the loss of rare alleles due to genetic drift—a consequence of a declining population—suggesting the possibility of an early population bottleneck. Moreover, genetic structure analyses suggested that the Japanese population likely consists of one gene pool, so the bottleneck may affect the entire population. From these results, we suggest maintaining gene flow between local populations to prevent inbreeding and further loss of alleles, increasing the number of breeding pairs in captivity, and releasing captive individuals to reinforce the wild population. Genetic diversity of the endangered Japanese golden eagle was investigated at mitochondrial, nuclear, and major histocompatibility complex loci. Moderate levels of diversity were observed compared to European populations and non‐endangered raptor species, but results indicated the possibility of an early population bottleneck. Information from this study can be used to inform future conservation management in both wild and captive Japanese golden eagle populations.