Haplogroup D-M55

{{Infobox haplogroup

| name = D-M55

| map =

| origin-date = 45,357 (95% CI 52,258 - 39,364) ybp{{cite web | url=https://discover.familytreedna.com/y-dna/D-Z3660/scientific?section=tmrca | title=Welcome to FamilyTreeDNA Discover }}

45,200 (95% CI 48,500 <-> 42,000) ybpYFull Haplogroup YTree v7.02.01 as of March 15, 2019.

| origin-place =possibly Japanese archipelago

| TMRCA = 21,434 (95% CI 24,812 - 18,513) ybp{{cite web | url=https://discover.familytreedna.com/y-dna/D-M64/scientific?section=tmrca | title=Welcome to FamilyTreeDNA Discover }}

21,000 (95% CI 22,800 <-> 19,300) ybp

| ancestor =D-M174

| descendants =

| mutations = M55, M57, M64.1, M179, P37.1, P41.1, P190, 12f2b

| members = Japanese people, Jōmon people, Ainu people、 Ryukyuan people

}}

Haplogroup D-M55 (M64.1/Page44.1) also known as Haplogroup D1a2a is a Y-chromosome haplogroup. It is one of two branches of Haplogroup D1a. The other is D1a1, which is found with high frequency in Tibetans and other Tibeto-Burmese populations and geographical close groups. D is also distributed with low to medium frequency in Central Asia, East Asia, and Mainland Southeast Asia.

Haplogroup D-M55 is found in about 33%YOUICHI SATO, TOSHIKATSU SHINKA, ASHRAF A. EWIS, AIKO YAMAUCHI, TERUAKI IWAMOTO, YUTAKA NAKAHORI [https://www.jstage.jst.go.jp/article/ase/122/3/122_140709/_article Overview of genetic variation in the Y chromosome of modern Japanese males.]{{cite journal|title=Y-chromosomal Binary Haplogroups in the Japanese Population and their Relationship to 16 Y-STR Polymorphisms|first3=N.|last3=Takezaki|first2=K.|last2=Minaguchi|author=Nonaka, I.|journal=Annals of Human Genetics|date=February 2, 2007|pmid=17274803|doi=10.1111/j.1469-1809.2006.00343.x|volume=71|issue=Pt 4|pages=480–95|hdl=10130/491|s2cid=1041367|hdl-access=free}}{{cite journal | vauthors = Sato Y, Shinka T, Ewis AA, Yamauchi A, Iwamoto T, Nakahori Y | year = 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}} of present-day Japanese males. It has been found in fourteen of a sample of sixteen or 87.5% of a sample of Ainu males in one study published in 2004{{cite journal | last1 = Tajima | first1 = Atsushi | display-authors = etal | year = 2004| title = "(March 2, 2004). "Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages | journal = Journal of Human Genetics | volume = 49 | issue = 4| pages = 187–193 | doi = 10.1007/s10038-004-0131-x | pmid = 14997363 | doi-access = free }} and in three of a sample of four or 75% of a sample of Ainu males in another study published in 2005 in which some individuals from the 2004 study may have been retested. It is currently the most common Y-DNA haplogroup in Japan if O1-F265 and O2-M122 (TMRCA approx. 30,000 ~ 35,000 ybp) are considered as separate haplogroups.

In 2017 it was confirmed that the Japanese branch of haplogroup D-M55 is distinct and isolated from other branches of haplogroup D since about 50,000 years ago. The split in D1a may have occurred near the Tibetan Plateau.Mondal, Mayukh & Bergström, Anders & Xue, Yali & Calafell, Francesc & Laayouni, Hafid & Casals, Ferran & Majumder, Partha & Tyler-Smith, Chris & Bertranpetit, Jaume. (2017). Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. Human Genetics. 136. 10.1007/s00439-017-1800-0.

History

File:Haplogroup D (Y-DNA) migration.png

File:Y-DNA haplogroup migration in East Asia map.png

Among the subgroups of Haplogroup D, the ancestor of D-M55 went eastward to reach the Japanese archipelago.崎谷満『DNA・考古・言語の学際研究が示す新・日本列島史』（勉誠出版 2009年）(in Japanese) According to Michael F. Hammer of the University of Arizona, haplogroup D originated near the Tibetan Plateau and migrated into Japan were it eventually became D-M55.{{Cite web |url=http://www.eva.mpg.de/genetics/pdf/Japan.pdf |title=Archived copy |access-date=2017-09-29 |archive-date=2009-03-04 |archive-url=https://web.archive.org/web/20090304162550/http://www.eva.mpg.de/genetics/pdf/Japan.pdf |url-status=dead }} Mitsuru Sakitani said that Haplogroup D1 came from Tibet to northern Kyushu via the Altai Mountains and the Korean Peninsula more than 50,000 years ago, and Haplogroup D-M55 (D1a2a) was born in the Japanese archipelago.

Recent studies suggest that D-M55 became dominant during the late Jōmon period, shortly before the arrival of the Yayoi, suggesting a population boom and bust.{{Cite journal|last1=Ohashi|first1=Jun|last2=Tokunaga|first2=Katsushi|last3=Hitomi|first3=Yuki|last4=Sawai|first4=Hiromi|last5=Khor|first5=Seik-Soon|last6=Naka|first6=Izumi|last7=Watanabe|first7=Yusuke|date=2019-06-17|title=Analysis of whole Y-chromosome sequences reveals the Japanese population history in the Jomon period|journal=Scientific Reports|language=en|volume=9|issue=1|pages=8556|doi=10.1038/s41598-019-44473-z|issn=2045-2322|doi-access=free|pmid=31209235|pmc=6572846|bibcode=2019NatSR...9.8556W}}

Frequency

The average frequency in Japanese is about 33%. High frequencies are found in various places in Japan, especially in Hokkaidō, eastern Honshū, southern Kyūshū, and Okinawa.

Ainu people: 87.5%（Tajima et al. 2004）
Asahikawa (Hokkaido): 63.7% (estimated from Y-STR haplotypes)
Chiba: 45.5%{{cite journal | vauthors = Naitoh S, Kasahara-Nonaka I, Minaguchi K, Nambiar P | title = Assignment of Y-chromosomal SNPs found in Japanese population to Y-chromosomal haplogroup tree | journal = Journal of Human Genetics | volume = 58 | issue = 4 | pages = 195–201 | date = April 2013 | pmid = 23389242 | doi = 10.1038/jhg.2012.159 | doi-access = free }}
Tokyo: 40.4% (21/57 = 36.8% JPT, 23/52 = 44.2%)
Okinawa: 37.6% (0/7 Hateruma,{{cite journal | doi=10.1007/s100380050151 | title=Genetic variations on the y chromosome in the Japanese population and implications for modern human y chromosome lineage | year=1999 | last1=Shinka | first1=Toshikatsu | last2=Tomita | first2=Keiko | last3=Toda | first3=Tatsushi | last4=Kotliarova | first4=Svetlana E. | last5=Lee | first5=Juwon | last6=Kuroki | first6=Yoko | last7=Jin | first7=Dong Kyu | last8=Tokunaga | first8=Katsushi | last9=Nakamura | first9=Hideki | last10=Nakahori | first10=Y. | journal=Journal of Human Genetics | volume=44 | issue=4 | pages=240–245 | pmid=10429363 | s2cid=9593881 | doi-access=free }} 1/20 = 5.0% Iriomote, 8/29 = 27.6% Katsuren, 10/32 = 31.3% Yomitan, 16/49 = 32.7% Ishigaki,{{cite journal | url=https://www.jstage.jst.go.jp/article/asj/124/2/124_161018/_article/-char/ja/ | doi=10.1537/asj.161018 | title=A study of the geographic distribution of y chromosomal and mitochondrial DNA haplogroups in Japanese population by Super Science High School Consortium (SSH) | year=2016 | last1=Totsuka | first1=Shoji | last2=Sato | first2=Youichi | last3=Tanaka | first3=Masashi | journal=Anthropological Science (Japanese Series) | volume=124 | issue=2 | pages=85–91 }} 13/38 = 34.2% Miyako, 13/36 = 36.1% Haebaru, 7/19 = 36.8% Gushikami, 35/87 = 40.2% Okinawa estimated from Y-STR haplotypes, 38/80 = 47.5% Itoman, 25/45 = 55.6% Okinawa)
Kanto region: 37.6%{{cite journal | last1 = Katoh | first1 = Toru | last2 = Munkhbat | first2 = Batmunkh | last3 = Tounai | first3 = Kenichi | display-authors = etal | year = 2005 | title = Genetic features of Mongolian ethnic groups revealed by Y-chromosomal analysis | journal = Gene | volume = 346 | pages = 63–70 | doi = 10.1016/j.gene.2004.10.023 | pmid = 15716011 }}
Kyushu: 35.0% (8/31 = 25.8% Fukuoka Prefecture, 29/104 = 27.9% Kyushu, 90/300 = 30.0% Nagasaki college students, 39/129 = 30.2% Saga Prefectural Chienkan Senior High School students, 34/102 = 33.3% Fukuoka adult men, 7/21 = 33.3% Nagasaki Prefecture, 13/37 = 35.1% Ōita Prefecture, 95/270 = 35.2% Miyazaki Prefecture,Y Seo, Y Takami, T Nakayama, and K Takahama, "Y chromosome DNA polymorphisms and their haplotypes in a Japanese population." Leg Med (Tokyo) 1999 Sep;1(3):145-9. doi: 10.1016/s1344-6223(99)80027-3. 470/1285 = 36.6% Miyazaki Prefecture,Hirofumi Nohara, Ikuko Maeda, Rinnosuke Hisazumi, Taketo Uchiyama, Hiroko Hirashima, Masahito Nakata, Rika Ohno, Tetsuro Hasegawa, and Kenshi Shimizu (2021), "Geographic distribution of Y-STR haplotypes and Y-haplogroups among Miyazaki Prefecture residents." Japanese Journal of Forensic Science and Technology, Vol. 26, Issue 1, p. 17-27. https://doi.org/10.3408/jafst.778 58/151 = 38.4% Kagoshima Prefecture, 5/11 = 45.5% Saga Prefecture, 22/47 = 46.8% Kumamoto Prefecture)
Nagoya: 34.3% (estimated from Y-STR haplotypes)
Sapporo: 33.9% (100/302 = 33.1% Sapporo college students, 72/206 = 35.0% Sapporo adult men)
Kawasaki: 33.0%
Shizuoka: 32.8%
Kanazawa: 32.6% (97/298 = 32.6%, 76/232 = 32.8%)
Aomori: 31.1% (22/79 = 27.8%, 11/27 = 40.7%)
Shikoku: 30% (18/70 = 25.7% Tokushima,{{cite journal | last1 = Hammer | first1 = Michael F. | last2 = Karafet | first2 = Tatiana M. | last3 = Park | first3 = Hwayong | last4 = Omoto | first4 = Keiichi | last5 = Harihara | first5 = Shinji | last6 = Stoneking | first6 = Mark | last7 = Horai | first7 = Satoshi | year = 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 }} 9/31 = 29.0% Shikoku, 119/388 = 30.7% Tokushima college students）
Micronesia: 1/17 = 5.9%（Hammer et al. 2006）
South Korea: 3/75 = 4.0% (Hammer et al. 2006), 12/317 = 3.8% (estimated from Y-STR haplotypes), 8/506 = 1.6% (Kim et al. 2011{{cite journal | last1 = Kim | first1 = Soon-Hee | last2 = Kim | first2 = Ki-Cheol | last3 = Shin | first3 = Dong-Jik | last4 = Jin | first4 = Han-Jun | last5 = Kwak | first5 = Kyoung-Don | last6 = Han | first6 = Myun-Soo | last7 = Song | first7 = Joon-Myong | last8 = Kim | first8 = Won | last9 = Kim | first9 = Wook | year = 2011| title = High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspective on the peopling of Korea | journal = Investigative Genetics | volume = 2011 | issue = 2| page = 10 | doi = 10.1186/2041-2223-2-10 | pmid = 21463511 | pmc = 3087676 | doi-access = free }})
West Timor: 1/497 = 0.2%（Tumonggor et al. 2014{{cite journal | last1 = Tumonggor | first1 = Meryanne K | last2 = Karafet | first2 = Tatiana M | last3 = Downey | first3 = Sean | display-authors = etal | year = 2014 | title = Isolation, contact and social behavior shaped genetic diversity in West Timor | journal = Journal of Human Genetics | volume = 59 | issue = 9| pages = 494–503 | doi = 10.1038/jhg.2014.62 | doi-access = free | pmid = 25078354 | pmc = 4521296 }}）

Ancient DNA

A Jōmon period man excavated from Funadomari remains (about 3,800 - 3,500 YBP) in Rebun Island in Hokkaido belongs to Haplogroup D1a2a2a(D-CTS220).神澤ほか(2016)「礼文島船泊縄文人の核ゲノム解析」第70回日本人類学大会 [http://anthrop-meeting.sakura.ne.jp/70/pdf/ittupan_proceeding%20.pdf] {{Webarchive|url=https://web.archive.org/web/20210615033929/http://anthrop-meeting.sakura.ne.jp/70/pdf/ittupan_proceeding%20.pdf |date=2021-06-15 }}(in Japanese)

The analysis of a Jōmon sample (Ikawazu) and an ancient sample from the Tibetan Plateau (Chokhopani, Ch) found only partially shared ancestry, suggesting a positive genetic bottleneck regarding the spread of haplogroup D from an ancient population related to the Tibetan Chokhopani sample (and modern Tibeto-Burmese groups).{{Cite journal|last1=Boer|first1=Elisabeth de|last2=Yang|first2=Melinda A.|last3=Kawagoe|first3=Aileen|last4=Barnes|first4=Gina L.|date=2020|title=Japan considered from the hypothesis of farmer/language spread|journal=Evolutionary Human Sciences|language=en|volume=2|pages=e13 |doi=10.1017/ehs.2020.7|pmid=37588377 |pmc=10427481 |issn=2513-843X|doi-access=free}}

Phylogenetic tree

By ISOGG tree（Version: 14.151）.{{Cite web|url=https://docs.google.com/spreadsheets/d/1QBUFZl03X92qNN61lQ8VtIKwbBMeuBzvqXQ47IQPBps/edit#gid=437997455|title = 2019-2020 Haplogroup D Tree}}

DE (YAP)
D (CTS3946)
D1 (M174/Page30, IMS-JST021355, Haplogroup D-M174)
D1a (CTS11577)
D1a1 (F6251/Z27276)
D1a1a (M15) Tibet
D1a1b (P99) Tibet, Mongol, Central Asia
D1a2(Z3660)
D1a2a (M64.1/Page44.1, M55) Japan(Yamato people、Ryukyuan people、Ainu people)
D1a2b (Y34637) Andaman Islands（Onge people, Jarawa people）{{cite journal | vauthors = Thangaraj K, Singh L, Reddy AG, Rao VR, Sehgal SC, Underhill PA, Pierson M, Frame IG, Hagelberg E | title = Genetic affinities of the Andaman Islanders, a vanishing human population | journal = Current Biology | volume = 13 | issue = 2 | pages = 86–93 | date = January 2003 | pmid = 12546781 | doi = 10.1016/S0960-9822(02)01336-2 | s2cid = 12155496 | doi-access = free }}{{Cite web |url=https://www.yfull.com/tree/D/ |title=D YTree |access-date=2019-09-02 |archive-date=2019-08-31 |archive-url=https://web.archive.org/web/20190831121238/https://www.yfull.com/tree/D/ |url-status=dead }}
D1b (L1378) Philippines[http://www.isogg.org/tree/ISOGG_HapgrpD.html Y-DNA Haplogroup D and its Subclades - 2014]
D2 (A5580.2) Nigeria, African American, Saudi Arabia, Syria{{Cite journal|last1=Tyler-Smith|first1=Chris|last2=Xue|first2=Yali|last3=Thomas|first3=Mark G.|last4=Yang|first4=Huanming|last5=Arciero|first5=Elena|last6=Asan|last7=Connell|first7=Bruce A.|last8=Jones|first8=Abigail L.|last9=Haber|first9=Marc|date=2019-06-13|title=A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans out of Africa|journal=Genetics|language=en|pages=1421–1428|doi=10.1534/genetics.119.302368|issn=0016-6731|pmid=31196864|doi-access=free|volume=212|issue=4|pmc=6707464}}{{Cite web|url=https://dna-explained.com/2019/06/21/exciting-new-y-dna-haplogroup-d-discoveries/|title=Exciting New Y DNA Haplogroup D Discoveries!|last=Estes|first=Roberta|date=2019-06-21|website=DNAeXplained - Genetic Genealogy|language=en-US|access-date=2019-07-08}}

References

D-M55