Variations in mitochondrial DNA of dogs isolated from archaeological sitesin Japan and neighbouring islands

Sequences of ancient mitochondrial DNA (mtDNA) from archaeological remains of Japanese dogs were determined from 145 ancient dog samples (mainly bones ) from the Jomon (100C-4C B.C.), Yayoi (4C B.C -3C A.D.), Kofun (3-6C A.D.) , Okhotsk (7-12C A.D.) and the Kamakura (12-14C A.D.) Periods. Highly varia ble sequences of the mitochondrial control region (198 base pairs) were amp lified at least twice from independently prepared DNA extracts, and those f rom ancient samples were compared with 28 haplotypes from 178 modern dogs. The 198-bp ancient mtDNA was amplified from 74 ancient dog samples, and the sequences were classified into 19 haplotypes comprising five modern haplot ypes (M1, M2, M5, M10 and M11) identified in modern dogs and 14 ancient hap lotypes showing unique sequences not observed in modern dogs. Haplotype M5 was widely distributed in archaeological sites in northern Japan and Sakhal in, while haplotype M2 was detected from archaeological sites in southern J apan. Three major clusters (CL1 to CL3) were distinguished within the moder n dog control region using phylogenetic analysis; all ancient dogs belonged to the CL1 cluster. From these results, we could not discern which modern Japanese dog breed closely resembles ancient dogs using phylogenetic analys is, but the CL1 cluster was likely distributed in the Japanese archipelago from the Jomon Period.