Takaki Yamada, Kyohei Ando

The Shikoku population of the Asian black bear (Ursus thibetanus) is one of the smallest and most endangered bear populations in Japan. Once widely distributed across Shikoku Island, it is now restricted to a limited area in eastern Shikoku, with an estimated census size of around 20 individuals. Long-term conservation of this population requires reliable genetic monitoring of population size, reproduction, and genetic diversity.
In this study, we estimated recent population size and reproductive structure using parentage analysis based on nuclear microsatellite DNA, mitochondrial DNA sequences, and newly developed Y-chromosome microsatellite markers. Genetic analyses were conducted using DNA from nine bears captured since 2018, archived samples collected before 2017, and 33 non-invasively collected hair and fecal samples obtained between 2011 and 2024. Individual identification and parentage assignments were performed using 15 nuclear microsatellite loci, with strict replication to minimize genotyping errors.
Population size was estimated for four consecutive 7-year periods since 1997 using a parentage-based estimator. The most recent estimate for 2018–2024 was 19.3 individuals, indicating relative demographic stability with a slight increasing trend, likely reflecting improved monitoring rather than true population growth. Parentage analysis revealed repeated reproduction by a limited number of breeding individuals and the presence of exceptionally old reproductive adults.
Genetic analyses detected three mitochondrial haplotypes but only a single Y-chromosome haplotype, indicating severe loss of paternal genetic diversity. These results suggest long-term genetic erosion caused by a small effective population size and skewed male reproductive success. Our findings highlight the continued vulnerability of the Shikoku population and emphasize the importance of sustained genetic monitoring using advanced molecular tools for evidence-based conservation management.