Genome-Wide SNP Analysis Reveals Population Structure and Demographic History of the Ryukyu Islanders in the Southern Part of the Japanese Archipelago

2014/08/01 by Takehiro Sato, Shigeki Nakagome, Chiaki Watanabe +11 · 6 citations
Biochemistry, Genetics and Molecular Biology · #Forensic and Genetic Research #Genetic diversity and population structure #Genetic Associations and Epidemiology #Archipelago #Biology #Population #Land bridge #Genetic structure #Geography #Evolutionary biology #Ecology #Demography #Biological dispersal #Genetic variation

paper · doi:10.1093/molbev/msu230

openalex publication_date 2014/08/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/13

Abstract

The Ryukyu Islands are located to the southwest of the Japanese archipelago. Archaeological evidence has revealed the existence of prehistoric cultural differentiation between the northern Ryukyu islands of Amami and Okinawa, and the southern Ryukyu islands of Miyako and Yaeyama. To examine a genetic subdivision in the Ryukyu Islands, we conducted genome-wide single nucleotide polymorphism typing of inhabitants from the Okinawa Islands, the Miyako Islands, and the Yaeyama Islands. Principal component and cluster analyses revealed genetic differentiation among the island groups, especially between Okinawa and Miyako. No genetic affinity was observed between aboriginal Taiwanese and any of the Ryukyu populations. The genetic differentiation observed between the inhabitants of the Okinawa Islands and the Miyako Islands is likely to have arisen due to genetic drift rather than admixture with people from neighboring regions. Based on the observed genetic differences, the divergence time between the inhabitants of Okinawa and Miyako islands was dated to the Holocene. These findings suggest that the Pleistocene inhabitants, whose bones have been found on the southern Ryukyu Islands, did not make a major genetic contribution, if any, to the present-day inhabitants of the southern Ryukyu Islands.

Citations

• Kernel Approximate Bayesian Computation for Population Genetic Inferences
• Autosomal and Y-chromosomal STR markers reveal a close relationship between Hokkaido Ainu and Ryukyu islanders
• A genetic analysis of the Sakishima islanders reveals no relationship with Taiwan aborigines but shared ancestry with Ainu and main‐island Japanese
• A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals
• Metric dental diversity of Ryukyu Islanders: a comparative study among Ryukyu and other Asian populations
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• Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data
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• MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
• Genetic Structure of Human Populations
• PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
• Bayes Factors

Cited by

• Unique characteristics of the Ainu population in Northern Japan
• Human genetic diversity in the Japanese Archipelago: dual structure and beyond
• The allele frequency of ALDH2*Glu504Lys and ADH1B*Arg47His for the Ryukyu islanders and their history of expansion among East Asians
• A comparative study of craniofacial measurements between Ryukyuan and mainland Japanese females using lateral cephalometric images
• Population genomics of East Asian ethnic groups
• Ryukyuans [wikipedia]