The wild boar (Sus scrofa) is widely distributed across Eurasia and has also colonized the Japanese archipelago, where two subspecies are recognized: the Japanese wild boar (JWB, Sus scrofa leucomystax) and the Ryukyu wild boar (RWB, Sus scrofa riukiuanus). Before this study, whole-genome sequence data were available for only a single wild boar from Japan whose geographic origin was unknown. As a result, the genetic relationship between JWB and RWB, as well as their evolutionary relationships with continental wild boar populations, remained unclear.
In this study, we determined whole-genome sequences from five JWB individuals collected from Honshu (Tochigi, Aichi, and Kyoto), Shikoku (Tokushima), and Kyushu (Saga), and from two RWB individuals collected from Okinawa and Ishigaki Islands. We combined these newly generated data with previously published wild boar genomes and examined the phylogenetic relationships among populations.
Our analyses showed that JWB and RWB form a single clade, indicating that they descended from a shared ancestral population. The branching pattern observed among JWB individuals is well matched to their geographic distribution across the Japanese archipelago. In addition, we found that JWB and RWB were genetically most closely related to wild boar populations from eastern Russia and northeastern China. Based on divergence-time estimates reported in previous studies, we infer that the ancestral population of JWB/RWB diverged from the Eastern Russian/Northern Chinese lineage approximately 25,000-10,000 years ago. This estimated time range is broadly consistent with archaeological evidence for the presence and dispersal of wild boars in the Japanese archipelago.
We also detected evidence of introgression between JWB and wild boars from eastern Russia and northeastern China. In contrast, no comparable signal was detected between RWB and these continental populations. This finding suggests that JWB experienced genetic contact with continental wild boars after the divergence of JWB and RWB. However, additional genomic data and analyses will be required to determine when this contact occurred and the direction in which gene flow took place.
Overall, our findings suggest that Japanese and Ryukyu wild boars became genetically distinct from continental East Asian wild boars following their dispersal into and subsequent isolation within the Japanese archipelago.
