Whole-genome sequencing reveals that Japanese and Ryukyu wild boars share a common ancestor

The wild boar, a species prevalent across Eurasia, has established a presence in the Japanese archipelago, where two distinct subspecies are identified: the Japanese wild boar and the Ryukyu wild boar. Prior to this investigation, only one Japanese wild boar genome sequence was available, leaving the genetic ties between the Japanese and Ryukyu subspecies and their connections to continental wild boar populations uncertain.

For their research, published in BMC Ecology and Evolution, a Japanese team from the Graduate University for Advanced Studies analyzed whole-genome sequences from five Japanese wild boars from Honshu, Shikoku, and Kyushu, alongside two Ryukyu wild boars from Okinawa and Ishigaki islands. They integrated these newly collected genomes with previously published wild boar genomes and evaluated the phylogenetic associations among populations.

The research revealed that the Japanese and Ryukyu wild boars constitute a single genetic group, implying a common ancestral population. The arrangement of Japanese wild boar genomes mirrored their geographic distribution across Japan. Notably, the Japanese and Ryukyu wild boars shared the closest genetic ties with wild boar populations from eastern Russia and northeastern China.

Based on estimates of divergence times, the shared ancestor of Japanese and Ryukyu wild boars separated from the eastern Russian/northern Chinese lineage roughly 25,000–10,000 years ago, a timeframe corroborated by archaeological evidence of wild boar presence and movement in the Japanese archipelago.

Additional evidence suggested genetic exchange between the Japanese wild boar and wild boars from eastern Russia and northeastern China, while no such signal was observed between the Ryukyu wild boar and these continental populations. This indicates that the Japanese wild boar had genetic contact with continental wild boars after their divergence. However, further genomic data and analyses are needed to determine the exact timing and direction of this gene flow.

In summary, the findings indicate that Japanese and Ryukyu wild boars diverged genetically from continental East Asian wild boars after dispersing into and becoming isolated within the Japanese archipelago. The Japanese wild boar experienced later genetic exchange with continental populations, unlike the Ryukyu wild boar.