Ancient mitochondrial DNA reveals the origin of Sus scrofa from Rebun Island, Japan

The Kabukai A site (5 to 8C A.D.) of the Okhotsk cultural area is on Rebun Island, a small island near the coast, north-northwest of Hokkaido, Japan. Specimens of Sus scrofa, called the Sakhalin pig, were discovered in five c ultural layers at the Kabukai A site. Ancient: DNA was extracted from the r emains of 42 Sakhalin pig bones. Thirty-nine nucleotide sequences of the 57 4-bp mitochondrial DNA control region, estimated to have originated from at least 21 individuals, were amplified and analyzed phylogenetically. Nine d istinct haplotypes (A1, A2, A3, B1, B2, C1, C2, D1, and D2) from this site were classified into four haplotype groups (A, B, C, and D) by parsimonious network analysis. Phylogenetic analysis of 9 ancient and 55 modern haploty pes indicated that the population of Sakhalin pigs at the Kabukai A site be longed to two distinct clusters; haplotype groups A and B formed a cluster comprised only of themselves, and haplotype groups C and D belonged to the cluster of one of the two genetic groups of Japanese wild boars uniquely di stributed in the western part of Japan, including one northeast Mongolian w ild boar. Analysis of the haplotype distribution among three archaeological sites and their historical transitions among the five layers reflecting th e cultural periods at the Kabukai A site suggests that the Sakhalin pig pop ulations were introduced from Sakhalin island and the Amur River basin in t he northeastern Eurasian continent together with some cultural influences.