Whole-genome analyses reveal the phylogenetic history of Japanese and Ryukyu wild boars

The ancestral population of wild boar (Sus scrofa) split into Eastern and Western Eurasian lineages, with the Eastern lineage extending its range into the Japanese archipelago. Within this archipelago, there are two subspecies: the Japanese wild boar (JWB, Sus scrofa leucomystax) and the Ryukyu wild boar (RWB, Sus scrofa riukiuanus), which exhibit differences in morphology and habitat. Until now, the whole genomes of JWB and RWB individuals with known origins had not been sequenced, leaving their genetic relationships with other populations unclear. In this study, we resequenced the whole genomes of Japanese wild boar (JWB) individuals from Honshu (Tochigi, Aichi, and Kyoto), Shikoku (Tokushima) and Kyushu (Saga) islands, with one individual sampled from each location. Additionally, we resequenced two RWB individuals from Okinawa and Ishigaki Islands.

We analyzed the genomes to clarify the genetic relationships between JWB, RWB, and other lineages of the genus Sus. Phylogenetic analyses based on whole genome sequence showed that JWB and RWB each formed distinct clades within a monophyletic JWB/RWB lineage, which was sister to Eastern Russian and Northern Chinese wild boars. Principal component analysis further supported their genetic differentiation. Together, these results indicate that JWB and RWB represent independent boar lineages that are likely to have diverged following isolation within the Japanese archipelago. In addition, gene flow between JWB and Eastern Russian/Northern Chinese boars was detected by the f4 statistics.

Overall, our results show that JWB and RWB diverged from East Asian boars through dispersal and isolation within the Japanese archipelago.