Ancient DNA reveals genetic lineage of Sus scrofa among archaeological sites in Japan

We analyzed 201 Sus bones excavated from one Jomon and nine Yayoi sites in the southwestern Japanese Islands to determine their genetic relatedness using three fragments of the mitochondrial DNA (mtDNA) control region. Three fragments A (194-bp), B (212-bp) and C (166-bp) were independently amplified from 38, 22 and 28 Sus bone specimens, respectively. All three fragments were successfully sequenced from ten specimens to construct 574-bp sequences that were combined with 57 modem Sus scrofa sequences including wild boars and domestic pigs to make a phylogenetic tree. Four of 10 specimens excavated from three sites located in the western part of Japan, were closely related to modern East Asian domestic pigs. The other six specimens from three sites were closely related to modem Japanese wild boars. However, parsimonious networks constructed for each fragment showed the difficulty of clearly distinguishing between Japanese wild boars and East Asian domestic pigs. These results reveal the possibility that even if Sus bones found at Yayoi sites are identified as East Asian domestic pigs, they were brought as exchanges or foods from Continental Asia to Japan through trade, but no evidence showing Sus breeding.