White-tailed Eagles (WTE, Haliaeetus albicilla) and Steller’s Sea Eagles (SSE, Haliaeetus pelagicus) are large raptors inhabiting Hokkaido, Japan, and are listed as vulnerable in the Red List 4th Edition (the Japanese Ministry of the Environment). Despite their conservation status, genetic information remains limited, although it is essential for effective conservation and management. In this study, we conducted genetic analysis with whole-genome data to clarify and compare the genetic characteristics of these two eagle species.

Whole-genome resequencing data were obtained from 11 wild WTE and nine wild SSE sampled in Hokkaido. Among the WTE, five individuals were sampled during summer (resident individuals) and six during winter (potentially resident or migratory individuals). All samples were collected from rescued birds kept in Kushiroshitsugen Wildlife Center or birds that died accidentally or from diseases, and sampling was conducted by veterinarians at the Institute for Raptor Biomedicine Japan. We assessed genetic diversity, population structure, and inbreeding levels.

Population structure analyses revealed that Hokkaido WTE consists of two distinct genetic clusters. All summer-sampled individuals and part of the winter-sampled individuals formed one cluster (n = ８), which showed lower genetic diversity and higher inbreeding coefficients compared to the other cluster detected among winter samples (n = ３). In contrast, all SSE exhibited lower overall genetic diversity and higher inbreeding levels than WTE, and no population structuring was observed. These results suggest that WTE in Hokkaido might be genetically differentiated into resident and migratory populations, with the resident group requiring higher conservation priority, while SSE probably facing stronger genetic constraints than the WTE.

Our findings highlight clear interspecific and intraspecific differences in genetic diversity and inbreeding, providing critical genomic insights for the conservation and management of sea eagles in Hokkaido. This study was conducted using samples provided by the Ministry of the Environment and was supported by the Environment Research and Technology Development Fund of ERCA (JPMEERF20244M01).