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Haplogroup Y

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Haplogroup Y
Possible time of origin11,800 to 33,300 YBP
Possible place of originNortheast Asia
AncestorN9
DescendantsY1, Y2
Defining mutations8392 10398 14178 14693 16126 16223 16231[1]

In human mitochondrial genetics, Haplogroup Y is a human mitochondrial DNA (mtDNA) haplogroup.

Origin

Haplogroup Y is a descendant of haplogroup N9.[citation needed]

Distribution

Haplogroup Y has been found with high frequency in many indigenous populations who live around the Sea of Okhotsk, including approximately 66% of Nivkhs, approximately 43% of Ulchs,[2] approximately 40% of Nanais, approximately 21% of Negidals, and between 75% to 20% of Ainus.[3][4][5][6][7] It is also fairly common among indigenous peoples of the Kamchatka Peninsula (Koryaks, Itelmens) and among certain Austronesian peoples (especially groups closely related to Native Taiwanese).

The distribution of haplogroup Y in populations of the Malay Archipelago contrasts starkly with the absence or extreme rarity of this clade in populations of continental Southeast Asia in a manner reminiscent of haplogroup E. However, the frequency of haplogroup Y fades more smoothly away from its maximum around the Sea of Okhotsk in Northeast Asia, being found in approximately 2% of Koreans[4] and in South Siberian and Central Asian populations with an average frequency of 1%.[8][9]

The Y2 subclade has been observed in 40% (176/440) of a large pool of samples from Nias people in western Indonesia, ranging from a low of 25% (3/12) among the Zalukhu subpopulation to a high of 52% (11/21) among the Ho subpopulation.[10]

Table of frequencies of mtDNA haplogroup Y

Population Frequency Count Source Subtypes
Ainu 0.750 8 Inoue 2016 Y1=6
Nivkh (northern Sakhalin) 0.661 56 Starikovskaya 2005 Y1=37
Nivkh (northern Sakhalin) 0.658 38 Duggan 2013 Y1a=25
Ulchi (Old Bulava, New Bulava, Bogorodskoe, and Nizhniy Gavan villages) 0.431 160 Sukernik 2012 Y1a=69
Hezhen (China) 0.400 10 HGDP ([1][2] Lippold 2014) Y1a=4
Indonesian (Nias) 0.400 440 van Oven 2011 Y2=176
Ulch (Old and New Bulava) 0.379 87 Starikovskaya 2005 Y1=33
Negidal 0.212 33 Starikovskaya 2005 Y1=7
Ainu 0.196 51 Satou 2009
Tajima 2004		 Y1=10
Indonesian (Medan, Sumatra) 0.167 42 Hill 2006 Y2=7
Filipino (Palawan) 0.150 20 Scholes 2011 Y2=3
Even (Berezovka) 0.133 15 Duggan 2013 Y1a=2
Filipino 0.129 62 Hill 2007 Y2=8
Evenk (Taimyr) 0.125 24 Duggan 2013 Y1a=3
Koryak 0.097 155 Starikovskaya 2005 Y=15
Evenk (Buryatia) 0.089 45 Derenko 2007 Y=4
Udegey (Gvasiugi, Imeni Lazo, Khabarovsk Krai) 0.087 46 Starikovskaya 2005 Y1=4
Filipino (Mindanao) 0.071 70 Tabbada 2010 Y2=5
Udegey (Gvasyugi, Khabarovsk Krai) 0.065 31 Duggan 2013 Y1a=2
Filipino 0.063 64 Tabbada 2010 Y2=4
Indonesian (Pekanbaru, Sumatra) 0.058 52 Hill 2006 Y2=3
Bukharan Arab (Uzbekistan/Kyrgyzstan) 0.050 20 Comas 2004 Y=1
Kazakh (Uzbekistan/Kyrgyzstan) 0.050 20 Comas 2004 Y=1
Tajik (Uzbekistan/Kyrgyzstan) 0.050 20 Comas 2004 Y=1
Orok (Sakhalin) 0.049 61 Bermisheva 2005 Y=3
Even (Eveno-Bytantaysky & Momsky) 0.048 105 Fedorova 2013 Y1a=5
Filipino (Luzon) 0.045 177 Tabbada 2010 Y2=8
Itelmen 0.043 47 Starikovskaya 2005 Y=2
Batak (Palawan) 0.032 31 Scholes 2011 Y2=1
Gelao (Daozhen County, Guizhou) 0.032 31 Li 2007 Y1=1
Hani (Xishuangbanna, Yunnan) 0.030 33 Wen 2004 Y=1
Khamnigan (Buryatia) 0.030 99 Derenko 2007 Y=3
Korean 0.029 346 Maruyama 2003 Y=10
Evenk (Krasnoyarsk) 0.027 73 Derenko 2007 Y=2
Yakut (Vilyuy River basin) 0.027 111 Fedorova 2013 Y1a=3
Even (Kamchatka) 0.026 39 Duggan 2013 Y1a=1
Tajik (Tajikistan) 0.023 44 Derenko 2007 Y=1
Yakut (Central) 0.023 88 Duggan 2013 Y1a=2
Daur (Evenk Autonomous Banner) 0.022 45 Kong 2003 Y1=1
Han (Xinjiang) 0.021 47 Yao 2004 Y1=1
Mongolian (Ulaanbaatar) 0.021 47 Jin 2009 Y1=1
Kalmyk (Kalmykia) 0.018 110 Derenko 2007 Y=2
Kazakh (Kazakhstan) 0.018 55 Yao 2004 Y1=1
Japanese (Tōhoku) 0.018 336 Umetsu 2005 Y=6
Uzbek (Xinjiang) 0.017 58 Yao 2004 Y1=1
Indonesian (Sulawesi) 0.017 237 Hill 2007 Y2=4
Korean (South Korea) 0.015 203 Umetsu 2005 Y=3
Taiwan aborigines 0.014 640 Peng 2011 Y=9
Buryat (Buryatia) 0.014 295 Derenko 2007 Y=4
Taiwanese 0.013 152 Maruyama 2003 Y=2
Indonesian (Adonara) 0.013 77 Mona 2009 Y2=1
Indonesian (Bali) 0.012 82 Hill 2007 Y2=1
Yakut (vicinity of Yakutsk) 0.012 164 Fedorova 2013 Y1a=2
Chinese 0.011 263 Maruyama 2003 Y=3
Taiwanese (Taipei, Taiwan) 0.011 91 Umetsu 2005 Y=1
Korean (South Korea) 0.011 185 Jin 2009 Y1=1, Y2=1
Kazakh (Kosh-Agachsky, Altai Republic) 0.010 98 Derenko 2012 Y1=1
Japanese (Miyazaki) 0.010 100 Uchiyama 2007 Y=1
Hmong (Jishou, Hunan) 0.010 103 Wen 2005 Y=1
Korean (South Korea) 0.010 103 Derenko 2007 Y=1
Buryat 0.008 126 Kong 2003 Y1=1
Tatar (Buinsk, Tatarstan) 0.008 126 Malyarchuk 2010 Y1b=1
Japanese (northern Kyūshū) 0.008 256 Umetsu 2005 Y=2
Barghut (Hulunbuir) 0.007 149 Derenko 2012 Y1=1
Okinawa 0.006 326 Umetsu 2005 Y=2
Japanese 0.005 211 Maruyama 2003 Y=1
Japanese (Hokkaidō) 0.005 217 Asari 2007 Y=1
Bashkir (Beloretsky, Sterlibashevsky, Ilishevsky, & Perm Oblast) 0.005 221 Bermisheva 2002 Y=1
Korean (South Korea) 0.004 261 Kim 2008 Y=1
Han (southern California) 0.003 390 Ji 2012 Y=1
Han (Taiwan) 0.001 1117 Ji 2012 Y=1
Dingban Yao (Mengla, Yunnan) 0.000 10 Wen 2005 -
Xiban Yao (Fangcheng, Guangxi) 0.000 11 Wen 2005 -
Chukchi (Anadyr) 0.000 15 Derenko 2007 -
Dungan (Uzbekistan/Kyrgyzstan) 0.000 16 Comas 2004 -
Uyghur (Uzbekistan/Kyrgyzstan) 0.000 16 Comas 2004 -
Yukaghir (Upper Kolyma) 0.000 18 Volodko 2008 -
Huatou Yao (Fangcheng, Guangxi) 0.000 19 Wen 2005 -
Crimean Tatar (Uzbekistan/Kyrgyzstan) 0.000 20 Comas 2004 -
Iranian (Uzbekistan/Kyrgyzstan) 0.000 20 Comas 2004 -
Karakalpak (Uzbekistan/Kyrgyzstan) 0.000 20 Comas 2004 -
Turkmen (Uzbekistan/Kyrgyzstan) 0.000 20 Comas 2004 -
Yi (Hezhang County, Guizhou) 0.000 20 Li 2007 -
Yukaghir (Verkhnekolymsky & Nizhnekolymsky) 0.000 22 Fedorova 2013 -
Guoshan Yao (Jianghua, Hunan) 0.000 24 Wen 2005 -
Hindu (Chitwan, Nepal) 0.000 24 Fornarino 2009 -
Nganasan 0.000 24 Starikovskaya 2005 -
Bunu (Dahua & Tianlin, Guangxi) 0.000 25 Wen 2005 -
Buryat (Kushun, Nizhneudinsk, Irkutsk Oblast) 0.000 25 Starikovskaya 2005 -
Kubachi (Dagestan) 0.000 25 Marchani 2008 -
Kurd (northwestern Iran) 0.000 25 Derenko 2007 -
Kumyk (Dagestan) 0.000 26 Marchani 2008 -
Lanten Yao (Tianlin, Guangxi) 0.000 26 Wen 2005 -
Iu Mien (Mengla, Yunnan) 0.000 27 Wen 2005 -
Indonesian (Palembang, Sumatra) 0.000 28 Hill 2006 -
Andhra Pradesh (tribal) 0.000 29 Fornarino 2009 -
Batek (Malaysia) 0.000 29 Hill 2006 -
Tujia (Yanhe County, Guizhou) 0.000 29 Li 2007 -
Cun (Hainan) 0.000 30 Peng 2011 -
Nu (Gongshan, Yunnan) 0.000 30 Wen 2004 -
Tujia (Yongshun, Hunan) 0.000 30 Wen 2004 -
Lingao (Hainan) 0.000 31 Peng 2011 -
Wuzhou Yao (Fuchuan, Guangxi) 0.000 31 Wen 2005 -
Yi (Luxi, Yunnan) 0.000 31 Wen 2004 -
Chuvantsi (Markovo, Chukotka) 0.000 32 Volodko 2008 -
Mendriq (Malaysia) 0.000 32 Hill 2006 -
Mien (Shangsi, Guangxi) 0.000 32 Wen 2005 -
Pan Yao (Tianlin, Guangxi) 0.000 32 Wen 2005 -
Nogai (Dagestan) 0.000 33 Marchani 2008 -
Temuan (Malaysia) 0.000 33 Hill 2006 -
Bapai Yao (Liannan, Guangdong) 0.000 35 Wen 2005 -
Tibetan (Zhongdian, Yunnan) 0.000 35 Wen 2004 -
Aleut (Commander Islands) 0.000 36 Volodko 2008 -
Pumi (Ninglang, Yunnan) 0.000 36 Wen 2004 -
Yakut (Yakutia) 0.000 36 Derenko 2007 -
Sireniki Eskimo 0.000 37 Volodko 2008 -
Ket 0.000 38 Starikovskaya 2005 -
Eskimo (Naukan) 0.000 39 Volodko 2008 -
Hmong (Wenshan, Yunnan) 0.000 39 Wen 2005 -
Nganasan 0.000 39 Volodko 2008 -
Han (Beijing) 0.000 40 Jin 2009 -
Kim Mun (Malipo, Yunnan) 0.000 40 Wen 2005 -
Manchurian 0.000 40 Jin 2009 -
Thai 0.000 40 Jin 2009 -
Tharu (Morang, Nepal) 0.000 40 Fornarino 2009 -
Uzbek (Uzbekistan/Kyrgyzstan) 0.000 40 Comas 2004 -
Yi (Shuangbai, Yunnan) 0.000 40 Wen 2004 -
Tu Yao (Hezhou, Guangxi) 0.000 41 Wen 2005 -
Lowland Yao (Fuchuan, Guangxi) 0.000 42 Wen 2005 -
Vietnamese 0.000 42 Jin 2009 -
Indonesian (Ambon) 0.000 43 Hill 2007 -
Indonesian (Mataram, Lombok) 0.000 44 Hill 2007 -
Hui (Xinjiang) 0.000 45 Yao 2004 -
Indonesian (Alor) 0.000 45 Hill 2007 -
Naxi (Lijiang, Yunnan) 0.000 45 Wen 2004 -
Tofalar 0.000 46 Starikovskaya 2005 -
Evenk (New Barag Left Banner) 0.000 47 Kong 2003 -
Kyrgyz (Sary-Tash) 0.000 47 Yao 2004 -
Mongolian (Ulan Bator) 0.000 47 Derenko 2007 -
Uyghur (Xinjiang) 0.000 47 Yao 2004 -
Hindu (New Delhi) 0.000 48 Fornarino 2009 -
Korean (Arun Banner) 0.000 48 Kong 2003 -
Kyrgyz (Talas) 0.000 48 Yao 2004 -
Mongol (New Barag Left Banner) 0.000 48 Kong 2003 -
Oirat Mongol (Xinjiang) 0.000 49 Yao 2004 -
Aini (Xishuangbanna, Yunnan) 0.000 50 Wen 2004 -
Eskimo (Chaplin) 0.000 50 Volodko 2008 -
Indonesian (Waingapu, Sumba) 0.000 50 Hill 2007 -
Jahai (Malaysia) 0.000 51 Hill 2006 -
Korean (northern China) 0.000 51 Jin 2009 -
Senoi (Malaysia) 0.000 52 Hill 2006 -
Kazakh (Xinjiang) 0.000 53 Yao 2004 -
Teleut (Kemerovo) 0.000 53 Derenko 2007 -
Chuvash (Morgaushsky, Chuvashia) 0.000 55 Bermisheva 2002 -
Uyghur (Kazakhstan) 0.000 55 Yao 2004 -
Tibetan (Qinghai) 0.000 56 Wen 2004 -
Khakassian (Khakassia) 0.000 57 Derenko 2007 -
Semelai (Malaysia) 0.000 61 Hill 2006 -
Komi-Zyryan (Sysolsky, Komi Republic) 0.000 62 Bermisheva 2002 -
Mansi 0.000 63 Pimenoff 2008 -
Tujia (western Hunan) 0.000 64 Wen 2004 -
Chukchi 0.000 66 Starikovskaya 2005 -
Bai (Dali, Yunnan) 0.000 68 Wen 2004 -
Saami (Finland) 0.000 69 Tambets 2004 -
Tatar (Aznakayevo, Tatarstan) 0.000 71 Malyarchuk 2010 -
Telenghit (Altai Republic) 0.000 71 Derenko 2007 -
Tubalar (Turochaksky & Choysky, Altai Republic) 0.000 72 Starikovskaya 2005 -
Komi-Permyak (Komi-Permyak Autonomous Okrug) 0.000 74 Bermisheva 2002 -
Siberian Eskimo 0.000 79 Starikovskaya 2005 -
Persian (eastern Iran) 0.000 82 Derenko 2007 -
Shor (Kemerovo) 0.000 82 Derenko 2007 -
Yukaghir (Lower Kolyma-Indigirka) 0.000 82 Volodko 2008 -
Altai Kizhi 0.000 90 Derenko 2007 -
Tuvan 0.000 95 Starikovskaya 2005 -
Eskimo (Canada) 0.000 96 Volodko 2008 -
Mansi 0.000 98 Starikovskaya 2005 -
Saami (Sweden) 0.000 98 Tambets 2004 -
Udmurt (Malopurginsky, Udmurtia & Tatyshlinsky, Bashkortostan) 0.000 101 Bermisheva 2002 -
Gelao (Daozhen County, Guizhou) 0.000 102 Liu 2011 -
Mordvinian (Staroshaygovsky, Mordovia) 0.000 102 Bermisheva 2002 -
Tuvinian 0.000 105 Derenko 2007 -
Khanty 0.000 106 Pimenoff 2008 -
Yakut 0.000 117 Kong 2003 -
Evenk (Ust-Maysky, Oleneksky, & Zhigansky, Yakutia) 0.000 125 Fedorova 2013 -
Tharu (Chitwan, Nepal) 0.000 133 Fornarino 2009 -
Mari (Zvenigovsky, Mari El) 0.000 136 Bermisheva 2002 -
Han (Southwest China; pool of 44 Sichuan, 34 Chongqing, 33 Yunnan, & 26 Guizhou) 0.000 137 Ji 2012 -
Yakut (northern Yakutia) 0.000 148 Fedorova 2013 -
Dolgan (Anabarsky, Volochanka, Ust-Avam, and Dudinka) 0.000 154 Fedorova 2013 -
Chinese (Shenyang, Liaoning) 0.000 160 Umetsu 2005 -
Aleut (Aleutian Islands) 0.000 163 Volodko 2008 -
Cham (Bình Thuận, Vietnam) 0.000 168 Peng 2010 -
Tatar (Almetyevsky and Yelabuzhsky, Tatarstan) 0.000 228 Bermisheva 2002 -
Saami (Norway) 0.000 278 Tambets 2004 -
Japanese (Tōkai) 0.000 282 Umetsu 2005 -
Tibetan (Tibet) 0.000 289 Ji 2012 -
Li (Hainan) 0.000 346 Peng 2011 -
Eskimo (Greenland) 0.000 385 Volodko 2008 -

Subclades

Haplogroup Y has been divided into two primary subclades, Y1 and Y2. In a study published in 2016, mtDNA haplogroup Y1a was observed in an Ulchi sampled in Nizhniy Gavan, Lower Amur, whereas mtDNA haplogroup Y2a1 was observed in an Igorot from Mountain Province, Luzon Island, Philippines (sampled in Singapore) and in a Hawaiian.[11]

Y1 predominates in the Northeast Asian range of haplogroup Y, which is centered on the Sea of Okhotsk. Y1* has been observed in two Uyghurs, a Minnan Han Chinese in Taiwan, and a Khamnigan. Y1a* has been observed in a Nivkh, in a Buryat in Zabaikal, in Mongolia, in a Daur and a Han Chinese in China, and in Tibet. Y1a with an additional T16189C mutation is common among the Nivkhs and among several Tungusic peoples (Hezhen in the PRC, Ulchi, Udegey, Even in the basins of the Kolyma and Indigirka rivers). Y1a1 has been observed in at least five Uyghurs, a Kyrgyz, a Buryat in Buryat Republic, a Hezhen in China, an Udegey, three Evenks in Taimyr, and two Yakuts in central Sakha Republic. Y1a2 has been observed in Koryaks and in an Even in Kamchatka. Y1a appears to be a relatively young haplogroup, with an age of 6,000 (95% CI 3,300 <-> 8,800) years estimated from 13 complete genomes (Ulchi x 6, Nivkh x 3, Koryak x 2, Even x 1, Mongolian x 1); however, this estimate may be relevant only for the TMRCA of Y1a2 and most Y1a* and Y1a-T16189C haplotypes, as it is not certain that any of the Y1a mtDNAs that have been analyzed belong to the Y1a1 clade.[2] (However, YFull has estimated the TMRCA of the entire Y1a clade, including all tabulated members of Y1a1 and Y1a* as well as Y1a+T16189C and Y1a2, to be 7,200 [95% CI 4,000 <-> 11,900] ybp,[12] so the addition of members of the Y1a1 subclade apparently does not significantly affect the estimate of the time to most recent common ancestor of the Y1a clade.) Y1b has been observed in a Tatar from Buinsk, Y1b1 has been observed in China, and Y1b1a has been observed in China and in Japan. The age of the entire Y1 clade has been estimated from 17 complete genomes (including the 13 aforementioned members of the Y1a clade plus one Japanese, one Chinese, and one Tatar member of the Y1b clade plus one Khamnigan member of Y1*) to be 12,400 (95% CI 5,900 <-> 19,100) ybp.[2]

Y2a predominates in the Southeast Asian range of haplogroup Y, which is centered on the Philippines and Sumatra. However, Y2b has been observed in Japan and in a Buryat, and Y2* has been observed in Chinese, Japanese, and Khamnigan samples.

Tree

This phylogenetic tree of haplogroup Y subclades is based on the paper by Mannis van Oven and Manfred Kayser Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation[1] and subsequent published research.[citation needed]

  • Y
    • Y1
      • Y1a
      • Y1b
    • Y2
      • Y2a
      • Y2b

See also

Wikimedia Commons has media related to Haplogroup Y (mtDNA).

Phylogenetic tree of human mitochondrial DNA (mtDNA) haplogroups

  Mitochondrial Eve (L)    
L0 L1–6  
L1 L2   L3     L4 L5 L6
M N  
CZ D E G Q   O A S R   I W X Y
C Z B F R0   pre-JT   P   U
HV JT K
H V J T

References

  1. ^ a b van Oven, Mannis; Manfred Kayser (13 Oct 2008). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation. 30 (2): E386–E394. doi:10.1002/humu.20921. PMID 18853457. S2CID 27566749. Archived from the original on 4 December 2012. Retrieved 2009-05-20.
  2. ^ a b c Rem I. Sukernik, Natalia V. Volodko, Ilya O. Mazunin, Nikolai P. Eltsov, Stanislav V. Dryomov, and Elena B. Starikovskaya, "Mitochondrial Genome Diversity in the Tubalar, Even, and Ulchi: Contribution to Prehistory of Native Siberians and Their Affinities to Native Americans." American Journal of Physical Anthropology 148:123–138 (2012). DOI 10.1002/ajpa.22050
  3. ^ M. A. Bermisheva, I. A. Kutuev, V. A. Spitsyn et al., "Analysis of Mitochondrial DNA Variation in the Population of Oroks", Russian Journal of Genetics, Vol. 41, No. 1, 2005, pp. 66–71. Translated from Genetika, Vol. 41, No. 1, 2005, pp. 78–84.
  4. ^ a b Tanaka M, Cabrera VM, González AM, et al. (2004). "Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan". Genome Research. 14 (10A): 1832–1850. doi:10.1101/gr.2286304. PMC 524407. PMID 15466285.
  5. ^ Tajima A, Hayami M, Tokunaga K, 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. doi:10.1007/s10038-004-0131-x. PMID 14997363.
  6. ^ Noboru Adachi, Ken-ichi Shinoda, Kazuo Umetsu, and Hirofumi Matsumura, "Mitochondrial DNA Analysis of Jomon Skeletons From the Funadomari Site, Hokkaido, and Its Implication for the Origins of Native American", American Journal of Physical Anthropology 138:255–265 (2009)
  7. ^ Inoue et al. 2016
  8. ^ Diversity of Mitochondrial DNA Lineages in South Siberia by Derenko1 et al., Annals of Human Genetics Volume 67 Issue 5 Page 391 - September 2003
  9. ^ Yong-Gang Yao, Qing-Peng Kong, Cheng-Ye Wang et al., "Different Matrilineal Contributions to Genetic Structure of Ethnic Groups in the Silk Road Region in China", Mol. Biol. Evol. 21(12):2265–2280. 2004
  10. ^ Mannis van Oven, Johannes M Hämmerle, Marja van Schoor et al., "Unexpected island effects at an extreme: reduced Y-chromosome and mitochondrial DNA diversity in Nias", Molecular Biology and Evolution (2010) doi:10.1093/molbev/msq300
  11. ^ Swapan Mallick, Heng Li, Mark Lipson, et al., "The Simons Genome Diversity Project: 300 genomes from 142 diverse populations." Nature 538, 201–206 (13 October 2016) doi:10.1038/nature18964
  12. ^ Cite error: The named reference YFull was invoked but never defined (see the help page).
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