Editing Ryukyuans (section)

===Genetic studies===
According to the recent genetic studies, the Ryukyuans share more [[alleles]] with the [[Jōmon people|southern Jōmon]] (16,000–3,000 years ago) [[hunter-gatherer]]s than the [[Yayoi people|Yayoi]] people, who had rice farming culture, have smaller genetic contributions from Asian continental populations, which supports the dual-structure model of K. Hanihara (1991), a widely accepted theory 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">{{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 |pmid=27581845 |pmc=5285490 }}</ref><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> Within the Japanese population the Ryukyu make a separate and one of the two genome-wide clusters along the main-island [[Honshu]].<ref name="DOI 10.1038/jhg.2016.110" /><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> The Jōmon ancestry is estimated at approximately 28%,<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> with recent studies estimating it at ~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=2023-07-20 |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 |volume=68 |issue=11 |language=en |pages=759–767 |doi=10.1038/s10038-023-01180-y |pmid=37468573 |pmc=10597838 |issn=1435-232X|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=2024-11-12 |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> Ryukyuans share continental ancestors (i.e., Northeast Asian and East Asian) with the Yamato Japanese. These continental components were not directly introduced from the continent but by immigrants from the main islands of Japan, who already possessed the tripartite ancestor. This migration has been estimated to have occurred around the 11th century AD, which corresponds to the [[Gusuku period|Gusuku Period]],<ref name="Jinam" /> marking the end of the prehistoric period in the area. Until this transition, it is widely accepted that people with Jomon-like genetic characteristics continued to inhabit the region for at least several thousand years. Therefore, the elevated levels of Jomon ancestry in Okinawa can be attributed to this historical event.<ref name=":1" /> An ancient population found in the Ryukyu Islands (specifically [[Miyako Island]]) called the "{{ill|Nagabaka|ja|長墓遺跡}} ({{nihongo2|長墓}}) were found to have more northern coastal East Asian ancestry after 2800 [[Before Present|BP]] or 775 AD, and is linked with population interactions between Ryukyu Islands and [[Sui dynasty|Sui-era China]].<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>

According to archaeological evidence, there is a prehistoric cultural differentiation between the Northern Ryukyu Islands ([[Amami Islands]] and [[Okinawa Islands]]) and the Southern Ryukyu Islands ([[Miyako Islands]] and [[Yaeyama Islands]]). The genome-wide differentiation was pronounced, especially between Okinawa and Miyako. It is considered to have arisen due to genetic drift rather than admixture with people from neighboring regions, with the divergence dated to the [[Holocene]], and without major genetic contribution of the [[Pleistocene]] inhabitants to the present-day Southern Islanders.<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> The Amami Islanders are also slightly more similar to the mainland population than the Okinawa 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 |doi=10.1371/journal.pone.0035000 |pmid=22509376 |pmc=3318002 |page=e35000|bibcode=2012PLoSO...735000N|doi-access=free}}</ref> An autosomal DNA analysis from [[Okinawa Island|Okinawan]] samples concluded that they are most closely related to other Japanese and East Asian contemporary populations, sharing on average 80% admixture with mainland Japanese and 19% admixture with Chinese population, and that have isolate characteristics.<ref name="Gerontology2014"/> The population closest to Ryukyu islanders is the mainland Japanese, followed by the Korean and Chinese populations. However, Taiwan aborigines were genetically distant from the Ryukyu islanders, even though these populations are geographically very close.<ref name=":0" />

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=2021-11-08 |language=ja}}</ref>]]