Editing Ryukyuans (section)

===Genetic studies===
According to recent genetic studies, the Ryukyuans are a distinct genome-wide cluster within the Japanese people.<ref name="DOI 10.1038/jhg.2016.110">{{cite journal |author1=Hideaki Kanzawa-Kiriyama |author2=Kirill Kryukov |author3=Timothy A Jinam |author4=Kazuyoshi Hosomichi |author5=Aiko Saso |author6=Gen Suwa |author7=Shintaroh Ueda |author8=Minoru Yoneda |author9=Atsushi Tajima |author10=Ken-ichi Shinoda |author11=Ituro Inoue |author12=Naruya Saitou |date=February 2017 |title=A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan |journal=[[Journal of Human Genetics]] |volume=62 |issue=2 |pages=213–221 |doi=10.1038/jhg.2016.110 |pmc=5285490 |pmid=27581845}}</ref><ref>{{cite journal |author1=Yumi Yamaguchi-Kabata |author2=Tatsuhiko Tsunoda |author3=Natsuhiko Kumasaka |author4=Atsushi Takahashi |author5=Naoya Hosono |author6=Michiaki Kubo |author7=Yusuke Nakamura |author8=Naoyuki Kamatani |date=2012 |title=Genetic differences in the two main groups of the Japanese population based on autosomal SNPs and haplotypes |journal=[[Journal of Human Genetics]] |volume=57 |issue=5 |pages=326–334 |doi=10.1038/jhg.2012.26 |pmid=22456480 |doi-access=free}}</ref> They share more alleles with [[Jōmon people|southern Jōmon]] hunter-gatherers than [[Yayoi people|Yayoi]] agriculturalists and have about 28% Jōmon ancestry<ref name="Jinam">{{cite journal |author1=Timothy A Jinam |author2=Hideaki Kanzawa-Kiriyama |author3=Ituro Inoue |author4=Katsushi Tokunaga |author5=Keiichi Omoto |author6=Naruya Saitou |date=October 2015 |title=Unique characteristics of the Ainu population in Northern Japan |url=https://www.researchgate.net/publication/280121130 |journal=[[Journal of Human Genetics]] |volume=60 |issue=10 |pages=565–571 |doi=10.1038/jhg.2015.79 |pmid=26178428 |s2cid=205166287 |access-date=5 February 2017 |doi-access=free}}</ref> although other studies suggest that their Jōmon ancestry is about 36%<ref name=":0">{{Cite journal |last1=Koganebuchi |first1=Kae |last2=Matsunami |first2=Masatoshi |last3=Imamura |first3=Minako |last4=Kawai |first4=Yosuke |last5=Hitomi |first5=Yuki |last6=Tokunaga |first6=Katsushi |last7=Maeda |first7=Shiro |last8=Ishida |first8=Hajime |last9=Kimura |first9=Ryosuke |date=20 July 2023 |title=Demographic history of Ryukyu islanders at the southern part of the Japanese Archipelago inferred from whole-genome resequencing data |journal=Journal of Human Genetics |language=en |volume=68 |issue=11 |pages=759–767 |doi=10.1038/s10038-023-01180-y |issn=1435-232X |pmc=10597838 |pmid=37468573 |doi-access=free}}</ref> and 26.1%.<ref name=":1">{{Cite journal |last=Yamamoto |first=Kenichi |last2=Namba |first2=Shinichi |last3=Sonehara |first3=Kyuto |last4=Suzuki |first4=Ken |last5=Sakaue |first5=Saori |last6=Cooke |first6=Niall P. |last7=Higashiue |first7=Shinichi |last8=Kobayashi |first8=Shuzo |last9=Afuso |first9=Hisāki |last10=Matsūra |first10=Kosho |last11=Mitsumoto |first11=Yojiro |last12=Fujita |first12=Yasuhiko |last13=Tokuda |first13=Torao |last14=Matsuda |first14=Koichi |last15=Gakuhari |first15=Takashi |date=12 November 2024 |title=Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations |url=https://www.nature.com/articles/s41467-024-54052-0 |journal=Nature Communications |language=en |volume=15 |issue=1 |pages=9780 |doi=10.1038/s41467-024-54052-0 |issn=2041-1723 |pmc=11558008}}</ref> This aligns with the dual-structure model proposed by Hanihara (1991), which suggests that the Yamato Japanese are more [[Miscegenation#Genetic admixture|admixed]] with Asian agricultural continental people (from the [[Korean Peninsula]]) than the Ainu and the Ryukyuans, with major admixture occurring in and after the [[Yayoi period]] (3,000–1,700 years ago).<ref name="DOI 10.1038/jhg.2016.110" /><ref>{{cite journal |author1=Timothy Jinam |author2=Hideaki Kanzawa-Kiriyama |author3=Naruya Saitou |date=2015 |title=Human genetic diversity in the Japanese Archipelago: dual structure and beyond |journal=Genes & Genetic Systems |volume=90 |issue=3 |pages=147–152 |doi=10.1266/ggs.90.147 |pmid=26510569 |doi-access=free}}</ref><ref>{{cite journal |author=Shigeki Nakagome |display-authors=etal |date=July 2015 |title=Model-Based Verification of Hypotheses on the Origin of Modern Japanese Revisited by Bayesian Inference Based on Genome-Wide SNP Data |journal=[[Molecular Biology and Evolution]] |volume=32 |issue=6 |pages=1533–1534 |doi=10.1093/molbev/msv045 |pmid=25758010 |doi-access=free}}</ref><ref name="Gerontology2014">{{cite journal |author=Nasrine Bendjilali |display-authors=etal |date=December 2014 |title=Who Are the Okinawans? Ancestry, Genome Diversity, and Implications for the Genetic Study of Human Longevity From a Geographically Isolated Population |journal=[[The Journals of Gerontology#Series A|Journal of Gerontology: Biological Sciences]] |volume=69 |issue=12 |pages=1474–1484 |doi=10.1093/gerona/glt203 |pmc=4271021 |pmid=24444611}}</ref><ref name="Timothy2012">{{cite journal |last1=Jinam |first1=Timothy |last2=Nishida |first2=Nao |last3=Hirai |first3=Momoki |last4=Kawamura |first4=Shoji |last5=Oota |first5=Hiroki |last6=Umetsu |first6=Kazuo |last7=Kimura |first7=Ryosuke |last8=Ohashi |first8=Jun |last9=Tajima |first9=Atsushi |date=December 2012 |title=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 |journal=[[Journal of Human Genetics]] |volume=57 |issue=12 |pages=787–795 |doi=10.1038/jhg.2012.114 |pmid=23135232 |doi-access=free}}</ref><ref>{{cite journal |author=Kae Koganebuchi |display-authors=etal |date=2012 |title=Autosomal and Y-chromosomal STR markers reveal a close relationship between Hokkaido Ainu and Ryukyu islanders |journal=Anthropological Science |volume=120 |issue=3 |pages=199–208 |doi=10.1537/ase.120322 |doi-access=free}}</ref><ref>{{cite journal |author=Hirotaka Matsukusa |display-authors=etal |date=June 2010 |title=A genetic analysis of the Sakishima islanders reveals no relationship with Taiwan aborigines but shared ancestry with Ainu and main-island Japanese |journal=[[American Journal of Physical Anthropology]] |volume=142 |issue=2 |pages=211–223 |doi=10.1002/ajpa.21212 |pmid=20091849}}</ref> Jōmon ancestry among Ryukyuans is also believed to come from prehistoric Southeast Asia, especially central and southern Ryukyuans, since Mainland Japanese Jōmon populations showed higher affinities with coastal East Asians such as [[Taiwanese indigenous peoples|Taiwanese]], [[Koreans]] and [[Ulchis]]. Northern Ryukyuan Jōmon were more related to Kyushuan Jōmon.<ref name=":3" /> This Jōmon ancestry lasted until the [[Gusuku Period]], around 11th century AD, where there was significant admixture with mainland Japanese, who had tripartite ancestry consisting of Jōmon, East Asian and Northeast Asian ancestries.<ref name=":1" /><ref name="Jinam" /> A 2025 study, however, found substantial northern coastal East Asian ancestry within the {{ill|Nagabaka|ja|長墓遺跡}} ({{nihongo2|長墓}}) population in [[Miyako Island]], deriving from interactions with [[Sui dynasty|Sui-era China]]. This ancestry was introduced after 2800 BP (or 775 AD).<ref>{{Cite journal |last=Liu |first=Juncen |last2=Liu |first2=Yichen |last3=Zhao |first3=Yongsheng |last4=Zhu |first4=Chao |display-authors=3 |date=2025 |title=East Asian Gene flow bridged by northern coastal populations over past 6000 years |url=https://www.nature.com/articles/s41467-025-56555-w#Sec6 |journal=Nature Communications |volume=16 |issue=1322 |via=Nature}}</ref> Overall, admixture rates with mainland Japanese differed between Northern Ryukyuans (77%) and Southern Ryukyuans (81%) which is unexpected due to the geographic distance between the southern islands and mainland Japan.<ref name=":0" /> Mainland Japanese themselves also have high genetic affinities with Ryukyuans, especially contemporary [[Tōhoku region|Tōhoku]], [[Kantō region|Kantō]], and [[Kyushu|Kyūshū]] populations.<ref name=":31">{{Cite journal |last=Watanabe |first=Yusuke |last2=Ohashi |first2=Jun |date=2021 |title=Comprehensive analysis of Japanese archipelago population history by detecting ancestry-marker polymorphisms without using ancient DNA data |url=https://www.biorxiv.org/content/10.1101/2020.12.07.414037v2.full |journal=bioRxiv |via=bioRxiv}}</ref>

According to archaeological evidence, there is cultural and genetic differentiation between Northern Ryukyuan islands ([[Amami Islands]] and [[Okinawa Islands]]) and Southern Ryukyuan islands ([[Miyako Islands]] and [[Yaeyama Islands]]). The differentiation was especially pronounced between Okinawa and Miyako. It arose due to [[Holocene]]-era divergence between the populations and subsequent genetic drift rather than admixture with neighboring populations.<ref name="TakeshiroSato2014">{{cite journal |author=Takehiro Sato |display-authors=etal |date=November 2014 |title=Genome-Wide SNP Analysis Reveals Population Structure and Demographic History of the Ryukyu Islanders in the Southern Part of the Japanese Archipelago |url=https://researchonline.ljmu.ac.uk/id/eprint/2331/1/Main-Text_Ryukyu-Islanders.pdf |journal=[[Molecular Biology and Evolution]] |volume=31 |issue=11 |pages=2929–2940 |doi=10.1093/molbev/msu230 |pmid=25086001 |access-date=5 February 2017 |doi-access=free}}</ref> There is also evidence of Amami islanders being more related to mainland Japanese than Okinawan islanders.<ref>{{cite journal |author=Takeshi Nishiyama |display-authors=etal |date=2012 |title=Detailed Analysis of Japanese Population Substructure with a Focus on the Southwest Islands of Japan |journal=[[PLOS One]] |volume=7 |issue=4 |page=e35000 |bibcode=2012PLoSO...735000N |doi=10.1371/journal.pone.0035000 |pmc=3318002 |pmid=22509376 |doi-access=free}}</ref> But overall, mainland Japanese are genetically the closest to Ryukyuans, followed by Koreans and Chinese. Taiwanese aborigines are genetically distant from Ryukyuans despite being neighbors.<ref name=":0" /> According to an autosomal DNA analysis of Okinawan samples, they are closely related to contemporary East Asian populations, especially Japanese populations. They exhibit about 80% admixture with mainland Japanese, followed by 19% admixture with Chinese populations. They also have isolate characteristics.<ref name="Gerontology2014" />

The female mtDNA and male Y chromosome markers are used to [[Human evolutionary genetics|study human migrations]]. The research on the skeletal remains from the Neolithic [[History of the Ryukyu Islands#Okinawa midden culture|Shell midden period]] (also known as Kaizuka period) in Okinawa, as well from the Gusuku Period, showed predominance of female haplogroups [[Haplogroup D (mtDNA)|D4]] and [[Haplogroup M (mtDNA)|M7a]] and their genetic continuity in the contemporary female population of Okinawa.<ref name="Shinoda2012">{{cite journal |author1=Ken-ichi Shinoda |author2=Tsuneo Kakuda |author3=Naomi Doi |date=2012 |title=Mitochondrial DNA polymorphisms in late Shell midden period skeletal remains excavated from two archaeological sites in Okinawa |url=https://www.kahaku.go.jp/research/publication/anthropology/download/38/BNMNS_D38_51-61.pdf |journal=Bulletin of the National Museum of Nature and Science, Series D |volume=38 |pages=51–61 |access-date=5 February 2017}}</ref><ref name="Shinoda2013">{{cite journal |author1=Ken-ichi Shinoda |author2=Tsuneo Kakuda |author3=Naomi Doi |date=2013 |title=Ancient DNA Analyses of Human Skeletal Remains from the Gusuku Period in the Ryukyu Islands, Japan |url=https://www.kahaku.go.jp/research/publication/anthropology/download/39/BNMNS_D39_1-8.pdf |journal=Bulletin of the National Museum of Nature and Science, Series D |volume=39 |pages=1–8 |access-date=5 February 2017}}</ref> It is assumed that M7a represents "Jomon genotype" introduced by a Paleolithic ancestor from [[Southeast Asia]] or the [[South Asia|southern region of the Asian continent]], around the Last Glacial Maximum with the Ryukyu Islands as one of the probable origin spots; in contrast, the frequency of the D4 haplogroup is relatively high in [[East Asia]]n populations, including in Japan, indicating immigrant Yayoi people, probably by the end of the late Kaizuka period, while haplogroup [[Haplogroup B (mtDNA)|B4]] presumably ancient [[Taiwanese aboriginals|aboriginal Taiwanese]] ancestry.<ref name="Shinoda2012"/><ref name="Shinoda2013"/> However, as in the contemporary Japanese population M7 showed a decrease, whereas the frequency of the haplogroup [[Haplogroup N (mtDNA)|N9b]] showed an increase from the south to north direction, it indicates that the mobility pattern of females and males was different as the distribution of Y haplogroups do not show a geographical gradient in contrast to mtDNA,<ref name="OverviewSato2014">{{cite journal |author=Youichi Sato|display-authors=etal|date=2014 |title=Overview of genetic variation in the Y chromosome of modern Japanese males |journal=Anthropological Science |volume=122 |issue=3 |pages=131–136 |doi=10.1537/ase.140709 |doi-access=free }}</ref> meaning mainly different maternal origins of the contemporary Ryukyuan and Ainu people.<ref>{{cite journal |author=Masashi Tanaka|display-authors=etal|date=2004 |title=Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan |pmc=524407 |journal=Genome Research |volume=14 |issue=10a |pages=1832–1850 |doi=10.1101/gr.2286304 |pmid=15466285}}</ref>[[File:Y-DNA haplogroup migration map in East Asia.png|thumb|Haplogroup dispersal and migration routes into Japan]]
The research on the contemporary Okinawan male Y chromosome showed, in 2006; 55.6% of haplogroup [[Haplogroup D-M55|D-P-M55]], 22.2% [[Haplogroup O-P31|O-P31]], 15.6% [[Haplogroup O-M122|O-M122]], 4.4% [[Haplogroup C-M8|C-M8]], and 2.2% others.<ref name="Hammer2006">{{cite journal|author1=Michael F. Hammer|author2=Tatiana M. Karafet|author3=Hwayong Park|author4=Keiichi Omoto|author5=Shinji Harihara|author6=Mark Stoneking|author7=Satoshi Horai|date=2006|title=Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes|journal=[[Journal of Human Genetics]]|volume=51|issue=1|pages=47–58|doi=10.1007/s10038-005-0322-0|pmid=16328082|doi-access=free}}</ref> It is considered that the Y haplogroups expanded in a [[demic diffusion]]. The haplogroups D and C are considered of Neolithic and Paleolithic origin, with coalescence time of 19,400 YBP and expansion 12,600 YBP (14,500 YBP and 10,820 YBP respectively), and were isolated for thousands of years once land bridges between Japan and continental Asia disappeared at the end of the last glacial maximum 12,000 YBP. The haplogroup O began its expansion circa 4,000–3,810 years ago, and thus the haplogroups D-M55 and C-M8 belong to the Jomon's male lineage, and haplogroup O belongs to the Yayoi's male lineage. Haplogroup [[Haplogroup M (mtDNA)|M12]] is considered as mitochondrial counterpart of Y chromosome D lineage. This rare haplogroup was detected only in Yamato Japanese, Koreans, and Tibetans, with the highest frequency and diversity in Tibet.<ref name="Hammer2006"/><ref name="OverviewSato2014"/>
[[file:Phylogenetic trees for the three Japanese populations and other Asian populations.png|thumb|[[Phylogenetic tree]] of Mainland Japanese, '''Ryukyuan''' (Ryukyuan), Ainu (Ainu) and other Asian ethnic groups<ref name="Timothy2012"/><ref>{{Cite web |title=記者会見「日本列島３人類集団の遺伝的近縁性」|url=https://www.u-tokyo.ac.jp/focus/ja/press/p01_241101.html |website=東京大学 |accessdate=8 November 2021 |language=ja}}</ref>]]