Mitochondrial DNA polymorphisms in late Shell midden period skeletal remains excavated from two archaeological sites in Okinawa

To investigate the genetic structure of individuals from the Shell midden (Kaizuka) period in Okinawa Island, sequence polymorphisms in hypervariable region 1 (HVR1), HVR2, the coding region that defines macrohaplogroup M and N, and 24 single nucleotide polymorphisms in the coding region of mitochondrial DNA were analyzed in 29 tooth samples excavated from an Ufutobaru shell midden site and a Gushikawa Gusuku-Gakeshita site. Suspected false-positive results stemming from contamination with contemporary DNA and other questionable data were not included in this study. Six of the 14 Ufutobaru samples and 9 of the 15 Gusuku-Gakeshita samples were successfully analyzed, and haplogroups were assigned. Genetic variation within a group is inherited from the group’s ancestors; therefore, the genetic markers in the contemporary population are expected to be similar to those of its ancestors. High frequencies of haplogroups M7a and D4 are characteristic of the contemporary Okinawa population, and both haplogroups were found among the ancient samples. This finding provides proof of a genetic continuity between the ancient and contemporary populations of Okinawa, at least since the late Shell midden period. In contrast, the existence of haplogroup B4 in these populations hints at their linkage with Taiwanese aborigines.