Molecular Genetic Analysis of 16 th -18 th Century Remains from Ishikobara Site, Nagano Prefecture, Japan

In order to examine the genetic structure and kinship system of an Edo village, we in- vestigated the ancient DNA recovered from the Ishikobara site in Nagano Prefecture, Japan. D- loop and coding region sequences of mitochondrial DNA (mtDNA) were retrieved from the sam- ples of 12 bones and teeth. Ancient DNA was successfully amplified from 9 samples. Each mtDNA sequence was assigned to a relevant haplogroup using the known mtDNA database. The mtDNA data of burials excavated at the site are presented for genetic comparison with an- other Edo population as well as for defining their respective internal variabilities. Maternally relat- ed individuals were identified and a haplotype comparison of these individuals provided additional background information on the local societies. Taking the mtDNA data for the Ishikobara site and other Japanese populations, a phylogenetic analysis was performed in order to reveal the relationships among these populations. The results show that the genetic structures of the Edo villages resemble each other. Compared to the present- day Japanese population, these villages exhibit higher frequencies of haplogroups D4 and G. The loss of other haplogroups in the Edo populations is probably due to genetic drift or the small size of these populations.