Whole-genome analyses reveal the phylogeny and gene flow of Japanese and Ryukyu wild boars

Background 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 five JWB individuals from Honshu (specifically Tochigi, Aichi, and Kyoto), one from Shikoku (Tokushima), and one from Kyushu (Saga). Additionally, we resequenced two RWB individuals from Okinawa and Ishigaki Islands. Results We analyzed the genomes to clarify the genetic relationships between JWB, RWB, and other lineages of the genus Sus . Phylogenetic trees based on genomic data indicate that the JWB and RWB populations form distinct clades, and these two clades form a monophyletic clade. The JWB/RWB clade diverged from a common ancestor with the Eastern Russian and Northern Chinese wild boars. Principal component analysis confirmed distinct genetic clusters for JWB and RWB. These results suggest that JWB and RWB represent independent boar lineages that evolved following isolation within the Japanese archipelago. However, the f4 statistic indicates gene flow between JWB and Eastern Russian/Northern Chinese boars, suggesting migration across Northern East Asia. Conclusion Overall, our results show that JWB and RWB diverged from East Asian boars through dispersal and isolation within the Japanese archipelago.