Haplogroup D-M55

Haplogroup D-M55
Possible time of origin	35,000-40,000YBP[1]
Possible place of origin	Japanese archipelago
Ancestor	(Grandparent) D
Defining mutations	M55, M57, M64.1, M179, P37.1, P41.1, P190, 12f2b
Highest frequencies	Japan（Ainu people、Ryukyuan people、Yamato people）

Haplogroup D-M55 also known as Haplogroup D1b is a Y-chromosome haplogroup. It is one of two branches of Haplogroup D1, one of the descendants of Haplogroup D. The other is D1a.

Haplogroup D-M55 is found about 32% ^[2]-39%^[3] in Japanese people and more than 80% in Ainu people.^[4] It occupies the majority in Japan. It is considered that Hapologroup D-M55 was born in Japan 38,000-37,000 years before present.^[5]

More than 40,000 years distinction exists between Haplogroup D-M55 and other subgroups of Haplogroup D.

History

Migration of haplogroup D

Among the subgroups of Hologroup D, the ancestor of D1b went eastward to reach the Japanese archipelago.^[6] Michael F. Hammer of the University of Arizona said: "The ancestors of the Jomon people were in Central Asia about 50,000 years ago. They continued to migrate eastwards and arrived in Japan by the southern Korean and Ryukyuan route and the northern Okhotsk route about 30,000 ago and D1b was born in the Japanese archipelago.^[7]"Mitsuru Sakitani said that Haplogroup D arrived to northern Kyusyu via China and Korean Peninsula about 35,000 years before present, and Haplogroup D1b was born in Japanese archipelago.^[6] The origin of y-DNA Haplogroup is believed to be in Siberia, Central Asia or north of the Tibetan plateau.

Haplogroup D1b prospered as the majority of the Japanese archipelago for about 35,000 years before Yayoi people arrived.

Frequency

High frequency in various places in Japan. Especially high in East Japan and Okinawa.

Aomori：38.5%
Shizuoka：32.8%
Tokushima：25.7%
Kyusyu：26.4%
Okinawa：55.6%

（Hammer et al. 2006^[8]）

Ainu people：87.5%（Tajima et al. 2004^[9]）

Outside Japan, members of D-M55 have been discovered in samples from Micronesia, South Korea, China, and Timor Island. Korea, Micronesia, Timor, and some parts of China all have been incorporated into the Empire of Japan at some point, so some of these cases may be Japanese descendants left behind when the empire was dismantled following World War II.

Micronesia：9.5％（Hammer et al. 2006^[8]）
South Korea: 4.0% (Hammer et al. 2006^[8]), 1.6% (Kim et al. 2011^[10])
Beijing, China (Han): 2.0% (Kim et al. 2011^[10])
Timor Island：0.2%（Meryanne et al. 2014^[11]）

Ancient DNA

A Jomon man excavated from Funadomari remains (about 3,800 - 3,500 YBP) in Rebun Island in Hokkaido belongs to Haplogroup D1b2a(D-CTS220).^[12] This discovery proved the hypothesis that Haplogroup D1b is the Jomon linage.

Phylogenetic tree

By ISOGG phylogenetic tree（ver.12.241）^[13]。

D1b (M55, M57, M64.1/Page44.1, M179/Page31, M359.1/P41.1, P37.1, P190, 12f2.2) - Japan(Mainlands Japanese people、Ainu people、Ryukyuan people)
- D1b1 (M116.1)
  - D1b1a (M125)
    - D1b1a1 (P42)
      - D1b1a1a (P12_1, P12_2, P12_3)
    - D1b1a2 (IMS-JST022457)
      - D1b1a2a (P53.2)
      - D1b1a2b (IMS-JST006841/Page3)
        D1b1a2b1 (CTS3397)
        D1b1a2b1a (Z1500)
        D1b1a2b1a1 (Z1504, CTS8093) - Japan(Aichi prefecture)^[14]
        D1b1a2b1a1a (FGC6373) - Japan(Hiroshima prefecture)^[14]
        D1b1a2b1a1a1 (L137.3) - Japan(Shizuoka prefecture)^[14]
        D1b1a2b1a1a1a (Z40625)
        
        D1b1a2b1a1a1b (CTS217)
        
        D1b1a2b1a1a1c (Z38475)
        
        D1b1a2b1a1a2 (FGC6372)
        
        D1b1a2b1a1a3 (CTS10649)
        
        D1b1a2b1a1a4 (Z40609)
        
        D1b1a2b1a1b (Z40614)
        
        D1b1a2b1a1c (Z31543)
        
        D1b1a2b1a1d (FGC30021)
        
        D1b1a2b1a1e (Z31548)
        
        D1b1a2b1a1f (Z31553)
        
        D1b1a2b1a1g (CTS6223)
        
        D1b1a2b1a1h (CTS4093)
        
        D1b1a2b1a1i (Z40687)
        D1b1a2b1a1i1 (Z35641)
        
        D1b1a2b1a1i2 (Z40688)
        
        D1b1a2b1a1j (CTS5058)
        
        D1b1a2b1a1k (FGC34008)
        
        D1b1a2b1a2 (CTS266)
        
        D1b1a2b1a3 (Z40672)
        
        D1b1a2b1b (CTS1372)
        
        D1b1a2b2 (CTS5581)
    - D1b1a3 (CTS10972)
      - D1b1a3a (Z31538)
      - D1b1a3b (CTS232)
  - D1b1b (P120)
  - D1b1c (CTS6609)
    - D1b1c1 (CTS1897/Z1574)
      - D1b1c1a (CTS11032) - Japan(Aichi prefecture)^[14]
        D1b1c1a1 (CTS218/V1105/Z1527)
        D1b1c1a1a (CTS6909)
        D1b1c1a1a1 (CTS6969)
        
        D1b1c1a1a2 (CTS9770)
        
        D1b1c1a1b (CTS3033)
        D1b1c1a1b1 (M2176)
        
        D1b1c1a1b2 (CTS2472)
        
        D1b1c1a1c (M151)
        
        D1b1c1a2 (F8521.3)
      - D1b1c1b (CTS1964)
        D1b1c1b1 (CTS974)
        
        D1b1c1b2 (CTS722)
      - D1b1c1c (Z30644) - Japan(Fukushima prefecture)^[14]
        D1b1c1c1 (CTS4292)
        D1b1c1c1a (Z31517)
        
        D1b1c1c1b (CTS1798)
        
        D1b1c1c2 (Z31512)
      - D1b1c1d (CTS5641) - Japan(Kyoto prefecture)^[14]
      - D1b1c1e (CTS429)
    - D1b1c2 (CTS103)
      - D1b1c2a (Z42462)
- D1b2 (CTS131)
  - D1b2a (CTS220) - Japan(a Jomon man from Rebun Island)^[12]
    - D1b2a1 (CTS10495)
      - D1b2a1a (Z31507)
      - D1b2a1b (CTS624)
    - D1b2a2 (CTS11285) - Japan(Osaka prefecture)^[14]
      - D1b2a2a (PH2316) - Japan(Iwate prefecture)^[14]
        D1b2a2a1 (Z38287)
        D1b2a2a1a (Z38284)
        
        D1b2a2a2 (Z38289) - Japan(Hyogo prefecture)^[14]
      - D1b2a2b (CTS288)
        D1b2a2b1 (CTS1815)
        
        D1b2a2b2 (Z40665)
  - D1b2b (CTS68)

References

↑ Shi, Hong; Zhong, Hua; Peng, Yi; Dong, Yong-li; Qi, Xue-bin; Zhang, Feng; Liu, Lu-Fang; Tan, Si-jie; Ma, Runlin Z; Xiao, Chun-Jie; Wells, R Spencer; Jin, Li; Su, Bing (October 29, 2008). "Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations". BMC Biology. BioMed Central. 6: 45. doi:10.1186/1741-7007-6-45. PMC 2605740. PMID 18959782. Retrieved November 21, 2010.
↑ YOUICHI SATO, TOSHIKATSU SHINKA, ASHRAF A. EWIS, AIKO YAMAUCHI, TERUAKI IWAMOTO, YUTAKA NAKAHORI Overview of genetic variation in the Y chromosome of modern Japanese males.
↑ Nonaka, I.; Minaguchi, K.; Takezaki, N. (February 2, 2007). "Y-chromosomal Binary Haplogroups in the Japanese Population and their Relationship to 16 Y-STR Polymorphisms". Annals of Human Genetics. John Wiley & Sons. 71 (Pt 4): 480–95. doi:10.1111/j.1469-1809.2006.00343.x. PMID 17274803.
↑ Atsushi Tajima et al. (March 2, 2004). "Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages". Journal of Human Genetics 49 (4): 187–193. doi:10.1007/s10038-004-0131-x. OCLC 110247689. PMID 14997363.
↑ Shi, Hong; Zhong, Hua; Peng, Yi; Dong, Yong-li; Qi, Xue-bin; Zhang, Feng; Liu, Lu-Fang; Tan, Si-jie; Ma, Runlin Z; Xiao, Chun-Jie; Wells, R Spencer; Jin, Li; Su, Bing (October 29, 2008). "Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations". BMC Biology (BioMed Central) 6: 45. doi:10.1186/1741-7007-6-45. PMC 2605740. PMID 18959782. Retrieved November 21, 2010.
1 2 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)
↑ http://www.eva.mpg.de/genetics/pdf/Japan.pdf
1 2 3 Hammer, Michael F.; Karafet, Tatiana M.; Park, Hwayong; Omoto, Keiichi; Harihara, Shinji; Stoneking, Mark; Horai, Satoshi (2006). "Dual origins of the Japanese: Common ground for hunter-gatherer and farmer Y chromosomes". Journal of Human Genetics 51 (1): 47–58. doi:10.1007/s10038-005-0322-0. PMID 16328082.
↑ Tajima,A. et al. (2004). "Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages". Journal of Human Genetics 49 (4): 187–193.
1 2 Soon-Hee Kim, Ki-Cheol Kim, Dong-Jik Shin, Han-Jun Jin, Kyoung-Don Kwak, Myun-Soo Han, Joon-Myong Song, Won Kim, and Wook Kim, "High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspective on the peopling of Korea." Investigative Genetics 2011, 2:10. http://www.investigativegenetics.com/content/2/1/10
↑ Meryanne K Tumonggor, Tatiana M Karafet, Sean Downey, et al., "Isolation, contact and social behavior shaped genetic diversity in West Timor." Journal of Human Genetics (2014) 59, 494–503; doi:10.1038/jhg.2014.62
1 2 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 (in Japanese)
↑ Y-DNA Haplogroup D and its Subclades - 2017
1 2 3 4 5 6 7 8 9 JAPAN Y-DNA Project

Phylogenetic tree of human Y-chromosome DNA haplogroups ^{[χ 1]}^{[χ 2]}

A0-T ^{[χ 3]}

A1 ^{[χ 4]}

A1b

A1b1

F1

F2

F3

GHIJK

I

J

LT ^{[χ 5]}

K2 ^{[χ 6]}

L

T

K2a ^{[χ 7]}

K2b ^{[χ 8]}

K2c

K2d

K2e ^{[χ 9]}

K-M2313 ^{[χ 10]}

K2b1 ^{[χ 11]}

P ^{[χ 12]}

NO

S ^{[χ 13]}

M ^{[χ 14]}

P1

P2

Footnotes

↑ Van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau HD (2014). "Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome". Human Mutation. 35 (2): 187–91. doi:10.1002/humu.22468. PMID 24166809.
↑ International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.)
↑ Haplogroup A0-T is also known as A-L1085 (and previously as A0'1'2'3'4).
↑ Haplogroup A1 is also known as A1'2'3'4.
↑ Haplogroup LT (L298/P326) is also known as Haplogroup K1.
↑ Between 2002 and 2008, Haplogroup T-M184 was known as "Haplogroup K2". That name has since been re-assigned to K-M526, the sibling of Haplogroup LT.
↑ Haplogroup K2a (M2308) and its primary subclade K-M2313 were separated from Haplogroup NO (F549) in 2016. (This followed the publication of: Poznik GD, Xue Y, Mendez FL, et al. (2016). "Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences". Nature Genetics. 48 (6): 593–9. doi:10.1038/ng.3559. PMC 4884158. PMID 27111036. In the past, other haplogroups, including NO (M214) and K2e had also been identified with the name "K2a".
↑ Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.
↑ Haplogroup K2e (K-M147) was previously known as "Haplogroup X" and "K2a" (but is a sibling subclade of the present K2a).
↑ K-M2313*, which as yet has no phylogenetic name, has been documented in two living individuals, who have ethnic ties to India and South East Asia. In addition, K-Y28299, which appears to be a primary branch of K-M2313, has been found in three living individuals from India. See: Poznik op. cit.; YFull YTree v5.08, 2017, "K-M2335", and; PhyloTree, 2017, "Details of the Y-SNP markers included in the minimal Y tree" (Access date of these pages: 9 December 2017)
↑ Haplogroup K2b1 (P397/P399) is also known as Haplogroup MS, but has a broader and more complex internal structure.
↑ Haplogroup P (P295) is also klnown as K2b2.
↑ Haplogroup S, as of 2017, is also known as K2b1a. (Previously the name Haplogroup S was assigned to K2b1a4.)
↑ Haplogroup M, as of 2017, is also known as K2b1b. (Previously the name Haplogroup M was assigned to K2b1d.)

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[shi-1] Shi, Hong; Zhong, Hua; Peng, Yi; Dong, Yong-li; Qi, Xue-bin; Zhang, Feng; Liu, Lu-Fang; Tan, Si-jie; Ma, Runlin Z; Xiao, Chun-Jie; Wells, R Spencer; Jin, Li; Su, Bing (October 29, 2008). "Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations". BMC Biology. BioMed Central. 6: 45. doi:10.1186/1741-7007-6-45. PMC 2605740. PMID 18959782. Retrieved November 21, 2010.

[2] YOUICHI SATO, TOSHIKATSU SHINKA, ASHRAF A. EWIS, AIKO YAMAUCHI, TERUAKI IWAMOTO, YUTAKA NAKAHORI Overview of genetic variation in the Y chromosome of modern Japanese males.

[Nonaka2007-3] Nonaka, I.; Minaguchi, K.; Takezaki, N. (February 2, 2007). "Y-chromosomal Binary Haplogroups in the Japanese Population and their Relationship to 16 Y-STR Polymorphisms". Annals of Human Genetics. John Wiley & Sons. 71 (Pt 4): 480–95. doi:10.1111/j.1469-1809.2006.00343.x. PMID 17274803.

[4] Atsushi Tajima et al. (March 2, 2004). "Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages". Journal of Human Genetics 49 (4): 187–193. doi:10.1007/s10038-004-0131-x. OCLC 110247689. PMID 14997363.

[5] Shi, Hong; Zhong, Hua; Peng, Yi; Dong, Yong-li; Qi, Xue-bin; Zhang, Feng; Liu, Lu-Fang; Tan, Si-jie; Ma, Runlin Z; Xiao, Chun-Jie; Wells, R Spencer; Jin, Li; Su, Bing (October 29, 2008). "Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations". BMC Biology (BioMed Central) 6: 45. doi:10.1186/1741-7007-6-45. PMC 2605740. PMID 18959782. Retrieved November 21, 2010.

[Sakitani-6] 1 2 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)

[7] ttp://www.eva.mpg.de/genetics/pdf/Japan.pdf

[Hammer-8] 1 2 3 Hammer, Michael F.; Karafet, Tatiana M.; Park, Hwayong; Omoto, Keiichi; Harihara, Shinji; Stoneking, Mark; Horai, Satoshi (2006). "Dual origins of the Japanese: Common ground for hunter-gatherer and farmer Y chromosomes". Journal of Human Genetics 51 (1): 47–58. doi:10.1007/s10038-005-0322-0. PMID 16328082.

[9] Tajima,A. et al. (2004). "Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages". Journal of Human Genetics 49 (4): 187–193.

[Kim2011-10] 1 2 Soon-Hee Kim, Ki-Cheol Kim, Dong-Jik Shin, Han-Jun Jin, Kyoung-Don Kwak, Myun-Soo Han, Joon-Myong Song, Won Kim, and Wook Kim, "High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspective on the peopling of Korea." Investigative Genetics 2011, 2:10. http://www.investigativegenetics.com/content/2/1/10

[11] Meryanne K Tumonggor, Tatiana M Karafet, Sean Downey, et al., "Isolation, contact and social behavior shaped genetic diversity in West Timor." Journal of Human Genetics (2014) 59, 494–503; doi:10.1038/jhg.2014.62

[Kanzawa-12] 1 2 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 (in Japanese)

[13] Y-DNA Haplogroup D and its Subclades - 2017

[ftdna2-14] 1 2 3 4 5 6 7 8 9 JAPAN Y-DNA Project

[vanOven2014-15] Van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau HD (2014). "Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome". Human Mutation. 35 (2): 187–91. doi:10.1002/humu.22468. PMID 24166809.

[ISOGG2015-16] International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.)

[A0-T-17] Haplogroup A0-T is also known as A-L1085 (and previously as A0'1'2'3'4).

[A1-18] Haplogroup A1 is also known as A1'2'3'4.

[LT-19] Haplogroup LT (L298/P326) is also known as Haplogroup K1.

[K2-20] Between 2002 and 2008, Haplogroup T-M184 was known as "Haplogroup K2". That name has since been re-assigned to K-M526, the sibling of Haplogroup LT.

[K2a-21] Haplogroup K2a (M2308) and its primary subclade K-M2313 were separated from Haplogroup NO (F549) in 2016. (This followed the publication of: Poznik GD, Xue Y, Mendez FL, et al. (2016). "Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences". Nature Genetics. 48 (6): 593–9. doi:10.1038/ng.3559. PMC 4884158. PMID 27111036. In the past, other haplogroups, including NO (M214) and K2e had also been identified with the name "K2a".

[K2b-22] Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.

[K2e-23] Haplogroup K2e (K-M147) was previously known as "Haplogroup X" and "K2a" (but is a sibling subclade of the present K2a).

[K-M2313-24] K-M2313*, which as yet has no phylogenetic name, has been documented in two living individuals, who have ethnic ties to India and South East Asia. In addition, K-Y28299, which appears to be a primary branch of K-M2313, has been found in three living individuals from India. See: Poznik op. cit.; YFull YTree v5.08, 2017, "K-M2335", and; PhyloTree, 2017, "Details of the Y-SNP markers included in the minimal Y tree" (Access date of these pages: 9 December 2017)

[K2b1-25] Haplogroup K2b1 (P397/P399) is also known as Haplogroup MS, but has a broader and more complex internal structure.

[P-26] Haplogroup P (P295) is also klnown as K2b2.

[S-27] Haplogroup S, as of 2017, is also known as K2b1a. (Previously the name Haplogroup S was assigned to K2b1a4.)

[M-28] Haplogroup M, as of 2017, is also known as K2b1b. (Previously the name Haplogroup M was assigned to K2b1d.)

Haplogroup D-M55
Possible time of origin	35,000-40,000YBP^[1]
Possible place of origin	Japanese archipelago
Ancestor	(Grandparent) D
Defining mutations	M55, M57, M64.1, M179, P37.1, P41.1, P190, 12f2b
Highest frequencies	Japan（Ainu people、Ryukyuan people、Yamato people）