A genetic analysis of the Sakishima islanders reveals no relationship with Taiwan aborigines but shared ancestry with Ainu and main‐island Japanese

Abstract

The Sakishima islands are members of the Ryukyu island chain, stretching from the southwestern tip of the Japanese archipelago to Taiwan in the East China Sea. Archaeological data indicate cultural similarities between inhabitants of prehistoric Sakishima and Neolithic Taiwan. Recent studies based on tooth crown traits show remarkably high inter-island diversity among Ryukyu islanders, suggesting that the Sakishima islanders might have genetic backgrounds distinct from main-island Okinawa people. To investigate the genetic diversity of the Ryukyu islanders, we analyzed mtDNA, Y chromosome, and autosomal short tandem repeat loci in a sample of main-island Okinawa people and Sakishima (Miyako and Ishigaki) islanders whose participated in a previous study of tooth crown morphology. Our phylogenetic analysis of maternal (mtDNA) and paternal (Y chromosome) lineages shows that the Sakishima islanders are more closely related to people from the Japanese archipelago than to Taiwan aborigines. Miyako islanders and the Hokkaido Ainu have the first and second highest frequencies (respectively) of the Y-chromosomal Alu-insertion polymorphism, which is a presumable Jomon marker. Genetic diversity statistics show no evidence of demographic reduction or of extreme isolation in each island's population. Thus, we conclude that 1) Neolithic expansion from Taiwan did not contribute to the gene pool of modern Sakishima islanders, 2) male-lineage of the Ryukyu islanders likely shares a common ancestor with the Hokkaido Ainu who are presumably direct descendants of the Jomon people, and 3) frequent reciprocal gene flow among islands has masked the trace of common ancestry in the Ryukyu island chain.

Ancient mitochondrial DNA sequences of Jomon teeth samples from Sanganji, Tohoku district, Japan

“…We found that two Sanganji individuals belonged to haplogroup M7a2 (Table 5, Table 7). In modern populations, haplogroup M7a1 was observed in modern Japanese populations at a high frequency: Ainu, 15.7% (Tajima et al, 2004); mainland Japanese, 9.5% (Maruyama et al, 2003); Ryukyuan, 26.6% (Horai et al, 1996, Matsukusa et al, 2010. However, haplogroup M7a2 was scarcely observed in the mainland Japanese (0.5%), and this haplogroup was not observed in the Ryukyuan.…”

“…The primers used to amplify HVR-1, HVR-2, and haplogroupdetermining regions are listed in Table 2 and Table 3. Analyzed haplogroups were compared with those of modern Japanese and Jomon people (Horai et al, 1996;Shinoda and Kanai, 1999;Shinoda, 2003;Maruyama et al, 2003;Tajima et al, 2004;Tanaka et al, 2004;Adachi et al, 2008Adachi et al, , 2009aAdachi et al, , b, 2011Matsukusa et al, 2010). To further characterize the sub-haplogroups within N9 and M7a, we used additional primers listed in Table 4.…”

The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations

“…16 Mitochondrial DNA and Y chromosomal DNA examinations became popular for human population studies from the 1980s, and a series of papers were published for human populations of the Japanese Archipelago. [20][21][22][23][24][25][26][27][28] All of these studies showed some genetic similarity between the Ainu and the Ryukyuan populations. However, mitochondrial DNA and Y chromosomes are both non-recombining, and the genetic information that can be extracted is limited.…”

Assignment of Y-chromosomal SNPs found in Japanese population to Y-chromosomal haplogroup tree

“…[11][12][13][14] However, these studies have mainly only used information on major haplogroups, and investigations based on more detailed haplogroup classification remain to be made because of the lack of suitable markers. Our group has already described the most detailed Y-chromosomal haplogroup classification in the Japanese population by expanding the YCC tree of 2003, assigning 5 new JSNP markers.…”