Sex-biased dispersal potentially underpins the genetic structural mismatch in genetic structure between different inherited genetic regions. However, accurately evaluating the effect of sex-biased dispersal is challenging due to other sex-biased traits and limitations in usable data. The brown bear (Ursus arctos) exhibits extreme male-biased dispersal. In the Hokkaido population of Japan, three divergent maternally inherited mitochondrial DNA lineages were distributed separately, however the paternally inherited nonrecombining region of the Y chromosome analysis did not confirm this distribution pattern. To investigate how the characteristic genetic structure has been shaped and to evaluate the influence of male-biased dispersal on the process, we conducted a reduced-representation genome sequencing of this population, and used published whole-genome resequencing data. The ratio of genetic differentiation between X-chromosomes and autosomes inferred a significant effect of male-biased dispersal both between and within populations. We observed a slight difference within subpopulations, which could be attributed to restricted gene flow, mainly for female bears because of the lowlands. We estimated a historical trend of the brown bear’s relatively suitable habitat decreasing during the Last Glacial Maximum (ca. 21,000 years ago), which could have caused a historical population decline followed by a recent rapid expansion primarily driven by male bears. These results indicate that the Hokkaido population had contracted despite the appearance of the land bridge between Eurasia and Hokkaido Island and has expanded rapidly while being limited by the lowlands. We emphasize the importance of the contribution of male-biased dispersal contributing to migration into new habitats and rapid population colonization.

Robust estimates of demographic parameters are critical for effective wildlife conservation and management, but are difficult to obtain for elusive species. We estimated the breeding and adult population sizes, as well as the minimum population size, in a high-density brown bear population on the Shiretoko Peninsula, in Hokkaido, Japan, using DNA-based pedigree reconstruction. A total of 1,288 individuals, collected in and around the Shiretoko Peninsula between 1998 and 2020, were genotyped at 21 microsatellite loci. Among them, 499 individuals were identified by intensive genetic sampling conducted in two consecutive years (2019 and 2020) mainly by noninvasive methods (e.g., hair and fecal DNA). Among them, both parents were assigned for 330 bears, and either maternity or paternity was assigned to 47 and 76 individuals, respectively. The subsequent pedigree reconstruction indicated a range of breeding and adult (≥4 years old) population sizes: 128–173 for female breeders and 66–91 male breeders, and 155–200 for female adults and 84–109 male adults. The minimum population size was estimated to be 449 (252 females and 197 males) in 2019. Long-term continuous genetic sampling prior to a short-term intensive survey would enable parentage to be identified in a population with a high probability, thus enabling reliable estimates of breeding population size for elusive species.