Genetic diversity and population history of the Japanese black bear (Ursus thibetanus japonicus) based on the genome‐wide analyses

• Published in: Ecological research 2022-09, Vol.37 (5), p.647-657
• Main Authors: Kishida, Takushi, Ohashi, Masataka, Komatsu, Yosuke
• Format: Article
• Language: English
• Subjects: Animal populations; Archipelagoes; Asian black bear; Bears; Deoxyribonucleic acid; Divergence; DNA; Gene flow; Genetic diversity; Genetic variation; Genomes; genomic admixture; Izu Peninsula; male‐biased dispersal; Mitochondria; Mitochondrial DNA; Nucleotide sequence; Philopatry; Pleistocene; Population genetics; population genomics; Populations; Ursus americanus; Ursus thibetanus japonicus
• ISSN: 0912-3814; 1440-1703
• DOI: 10.1111/1440-1703.12335

The Japanese black bear (Ursus thibetanus japonicus) is a subspecies of the Asian black bear endemic to Mainland Japan. It has been reported that the extant Japanese bear population is genetically differentiated into several geographically restricted clusters with an estimated divergence time of 100,000–500,000 years ago. The ancestral population of the Japanese black bear migrated from the continent to the Japanese archipelago in the Pleistocene, and no interaction between continental and Japanese bear populations after their migration has been speculated. However, most of the previous studies are based only on mitochondrial DNA. Here, we sequenced the genome of a Japanese black bear and compared it with that of other Ursus individuals to evaluate the genetic status of this subspecies. We suggest that the Japanese black bear population is genetically almost uniform and has been structured only in recent 30,000 years. This inconsistency between mitochondria and nuclear DNA may be explained by the female philopatry and male‐mediated gene flow of this species. We also suggest ancestral admixture between the Japanese black bear and the Ussuri black bear (Ursus thibetanus ussuricus), implying a complex history of inter‐subspecies interactions of the Japanese black bears. Genomic evidence of ancient admixture between the Asian black bear and the American black bear (Ursus americanus) sheds new light on the population history of the Asian black bears. The genetic diversity of the Japanese black bears is remarkably lower compared to thaother bear populations, and conservation of this subspecies is an urgent issue. In this study, we sequenced the whole genome of a Japanese black bear and compared it with that of other Ursus individuals to reveal the genetic diversity and population history of the Japanese black bear. The Japanese black bear population is suggested to be genetically uniform and has been structured only in recent 30,000 years, indicating the importance of male‐mediated gene flow for maintaining the genetic diversity of this subspecies. We also suggest ancient admixtures between the Japanese black bear and other bear populations, implying complex history of inter‐species/subspecies interactions of this subspecies.