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Thread: Haplogroup C divided into two groups melanesian C a subgroup of what was Indian C5.

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    Haplogroup C divided into two groups melanesian C a subgroup of what was Indian C5.

    https://sites.google.com/site/haplogroupcproject/
    C1 (Formeraly CxC3)
    C1a1 - M8 Japanese
    C1a2 - V20 European+La Brana
    C1b - F1370, Middle East & southern Asia, esp. west India
    C1b2 - M38 Pacific Rim islands, eastern Indonesia
    C1c (tentative)- M347 Australian Aborigines (accidentally mislabeled as C1d)
    C2 (Formerly C3)
    C2a - M93 Japan
    C2b - L1373 Northern Asia, esp. central Asia
    C2b1 - P39 Amerindian (an exception to the Asian grp.)
    C2d - P62 Mongolia
    C2e - Z1338 eastern Asia
    Last edited by venustas; 08-11-2014 at 11:21 PM.
    Maternal Uncle y-line= F0R1b1-L21

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    That is interesting. So, Wallacean-Papuan-Oceanic Austronesian C-M38 (former C2) has turned out to be phylogenetically parallel to South Asian-Central Asian-Southwest Asian C-M356 (former C5). Those two groups together form a branch opposed to another branch that comprises Japanese C-M8 (former C1) and European (and La Braña) C-V20 (former C6). I think all these branches are very ancient (not significantly more recent than the origin of C-M130 as a whole), however, so each subclade (C-M38, C-M356, C-M8, or C-V20) should be considered independently as it was under the old schema (as C1, C2, C5, or C6).

    Also, I wish someone would figure out where the C-M130(xM8, M38, M217) Y-DNA from Indonesia belongs in the phylogeny. Such Y-DNA is quite common in populations of central Indonesia, especially the island of Flores.

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    Quote Originally Posted by everest59 View Post
    Now, C1b itself with no derived subgroup mutation (i.e. M356) has been found only in the Middle East. This part is tentative.
    Also, that one Scythian sample from Andronovo that tested +ve for C(x3) could easily be C1b as opposed to C1a. I am talking about this paper:
    http://hamagmongol.narod.ru/library/keyser_2009_e.pdf

    C1b is currently a South Asian haplogroup.
    According to Hua Zhong, Hong Shi, Xue-Bin Qi, Zi-Yuan Duan, Ping-Ping Tan, Li Jin, Bing Su, and Runlin Z. Ma (2011), "Extended Y Chromosome Investigation Suggests Postglacial Migrations of Modern Humans into East Asia via the Northern Route," Mol. Biol. Evol. 28(1):717–727 (doi:10.1093/molbev/msq247), their team has found C1b1-M356 in the following samples from the PRC:

    Xibe (Xinjiang)
    2/61 = 3.3% D-M174
    2/61 = 3.3% C-M130(xC2-M217, C1b1-M356)
    2/61 = 3.3% C1b1-M356
    18/61 = 29.5% C2-M217
    1/61 = 1.6% J2b2-M241
    11/61 = 18.0% N-M231
    24/61 = 39.3% O-M175
    1/61 = 1.6% R1a1a-M17

    Uyghur (Xinjiang [judging from the map in Figure 1, probably Urumqi])
    4/50 = 8.0% D-M174
    1/50 = 2.0% C1b1-M356
    3/50 = 6.0% C2-M217
    3/50 = 6.0% G2a-P15(xG2a1a-P16)
    1/50 = 2.0% J1-M267
    4/50 = 8.0% J2a-M410(xJ2a1a-M322, J2a1b-M67, J2a1d-M319)
    2/50 = 4.0% L1c-M357
    3/50 = 6.0% N-M231
    7/50 = 14.0% O-M175
    1/50 = 2.0% Q1a1a1-M120
    2/50 = 4.0% Q1a1b-M25
    12/50 = 24.0% R1a1a-M17
    3/50 = 6.0% R1b-M343(xR1b1b-M335, R1b1a1-M73, R1b1a2-M269)
    1/50 = 2.0% R1b1a1-M73
    1/50 = 2.0% R1b1a2-M269
    2/50 = 4.0% R2a-M124

    Han (Shanxi)
    1/56 = 1.8% C1b1-M356
    10/56 = 17.9% C2-M217
    1/56 = 1.8% J2a1a-M322
    12/56 = 21.4% N-M231
    27/56 = 48.2% O-M175
    1/56 = 1.8% Q1a1a1-M120
    1/56 = 1.8% Q1a1b-M25
    1/56 = 1.8% Q1a2-M346
    2/56 = 3.6% R1a1a-M17

    Each of the samples with C1b1-M356 also contains at least one representative of R1a1a-M17, so ascribing the presence of C1b1-M356 in the PRC to Andronovo influence may be plausible, but note that this team has found C1b1-M356 in two individuals and R1a1a-M17 in only one individual among their samples of the Xibe (who are essentially modern Manchu-speaking people in Xinjiang). Perhaps C1b1-M356 might have been pushed eastward or southeastward by an originally R1a1a-M17 Andronovo population.

    On the other hand, the so-called C* that I have mentioned previously has been found mostly in northeastern, south-central, and southwestern China (Heilongjiang, Hulunbuir, Hubei, Guizhou, Guangxi, Yunnan) among speakers of Tungusic, Sinitic, Tujia, Kam-Sui (Daic), and Hmong-Mien languages, and usually not in association with R1a1a-M17 (except in a sample of Han from Guizhou). It also has been found alongside R1a1a-M17 in the Hui of Ningxia and the Xibe of Xinjiang in northwestern China; note that the ethnic core of the Xibe in Xinjiang are 18th-century migrants from northeastern China, and the Hui (Chinese-speaking Muslims) are an ethnoreligious group formed during historical times.

    C*-M130(xC2-M217, C1b1-M356) from Hua Zhong et al. (2011):

    Yao (Guangxi)
    9/55 = 16.4% C-M130(xC2-M217, C1b1-M356)
    1/55 = 1.8% C2-M217
    44/55 = 80.0% O-M175
    1/55 = 1.8% Q1a1a1-M120

    Mulao (Guangxi)
    1/11 = 9.1% C-M130(xC2-M217, C1b1-M356)
    1/11 = 9.1% C2-M217
    9/11 = 81.8% O-M175

    Hui (Ningxia)
    2/62 = 3.2% D-M174
    2/62 = 3.2% E-SRY4064
    5/62 = 8.1% C-M130(xC2-M217, C1b1-M356)
    6/62 = 9.7% C2-M217
    1/62 = 1.6% G1-M285
    1/62 = 1.6% G2a-P15(xG2a1a-P16)
    1/62 = 1.6% H1-M370(xH1a-M52)
    1/62 = 1.6% J1-M267
    5/62 = 8.1% J2a-M410(xJ2a1a-M322, J2a1b-M67, J2a1d-M319)
    2/62 = 3.2% J2a1b-M67
    1/62 = 1.6% L1c-M357
    5/62 = 8.1% N-M231
    22/62 = 35.5% O-M175
    2/62 = 3.2% Q1a1a1-M120
    1/62 = 1.6% R1-M173(xR1a1a-M17, R1b-M343)
    2/62 = 3.2% R1a1a-M17
    1/62 = 1.6% R1b1a2-M269
    2/62 = 3.2% R2a-M124

    Tujia (Hubei)
    2/26 = 7.7% C-M130(xC2-M217, C1b1-M356)
    6/26 = 23.1% C2-M217
    3/26 = 11.5% N-M231
    15/26 = 57.7% O-M175

    Shui (Guizhou)
    4/29 = 13.8% D-M174
    2/29 = 6.9% C-M130(xC2-M217, C1b1-M356)
    2/29 = 6.9% C2-M217
    21/29 = 72.4% O-M175

    Han (Yunnan)
    1/19 = 5.3% D-M174
    1/19 = 5.3% C-M130(xC2-M217, C1b1-M356)
    2/19 = 10.5% C2-M217
    15/19 = 78.9% O-M175

    Han (Guizhou)
    1/58 = 1.7% D-M174
    2/58 = 3.4% C-M130(xC2-M217, C1b1-M356)
    2/58 = 3.4% C2-M217
    3/58 = 5.2% N-M231
    48/58 = 82.8% O-M175
    1/58 = 1.7% Q1a2-M346
    1/58 = 1.7% R1a1a-M17

    Xibe (Xinjiang)
    2/61 = 3.3% D-M174
    2/61 = 3.3% C-M130(xC2-M217, C1b1-M356)
    2/61 = 3.3% C1b1-M356
    18/61 = 29.5% C2-M217
    1/61 = 1.6% J2b2-M241
    11/61 = 18.0% N-M231
    24/61 = 39.3% O-M175
    1/61 = 1.6% R1a1a-M17

    The age of STR variation among members of this group has been estimated to be 5,500 [±1,600] years using the "evolutionary mutation rate" (cf. Hua Zhong, Hong Shi, Xue-Bin Qi, Chun-Jie Xiao, Li Jin, Runlin Z Ma, and Bing Su (2010), "Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia"). It is certainly a very recently expanded clade despite its "C*" designation.
    Last edited by Ebizur; 11-20-2014 at 09:30 AM.

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    Quote Originally Posted by Ebizur View Post
    According to Hua Zhong, Hong Shi, Xue-Bin Qi, Zi-Yuan Duan, Ping-Ping Tan, Li Jin, Bing Su, and Runlin Z. Ma (2011), "Extended Y Chromosome Investigation Suggests Postglacial Migrations of Modern Humans into East Asia via the Northern Route," Mol. Biol. Evol. 28(1):717–727 (doi:10.1093/molbev/msq247), their team has found C1b1-M356 in the following samples from the PRC:

    Xibe (Xinjiang)
    2/61 = 3.3% D-M174
    2/61 = 3.3% C-M130(xC2-M217, C1b1-M356)
    2/61 = 3.3% C1b1-M356
    18/61 = 29.5% C2-M217
    1/61 = 1.6% J2b2-M241
    11/61 = 18.0% N-M231
    24/61 = 39.3% O-M175
    1/61 = 1.6% R1a1a-M17

    Uyghur (Xinjiang [judging from the map in Figure 1, probably Urumqi])
    4/50 = 8.0% D-M174
    1/50 = 2.0% C1b1-M356
    3/50 = 6.0% C2-M217
    3/50 = 6.0% G2a-P15(xG2a1a-P16)
    1/50 = 2.0% J1-M267
    4/50 = 8.0% J2a-M410(xJ2a1a-M322, J2a1b-M67, J2a1d-M319)
    2/50 = 4.0% L1c-M357
    3/50 = 6.0% N-M231
    7/50 = 14.0% O-M175
    1/50 = 2.0% Q1a1a1-M120
    2/50 = 4.0% Q1a1b-M25
    12/50 = 24.0% R1a1a-M17
    3/50 = 6.0% R1b-M343(xR1b1b-M335, R1b1a1-M73, R1b1a2-M269)
    1/50 = 2.0% R1b1a1-M73
    1/50 = 2.0% R1b1a2-M269
    2/50 = 4.0% R2a-M124

    Han (Shanxi)
    1/56 = 1.8% C1b1-M356
    10/56 = 17.9% C2-M217
    1/56 = 1.8% J2a1a-M322
    12/56 = 21.4% N-M231
    27/56 = 48.2% O-M175
    1/56 = 1.8% Q1a1a1-M120
    1/56 = 1.8% Q1a1b-M25
    1/56 = 1.8% Q1a2-M346
    2/56 = 3.6% R1a1a-M17

    Each of the samples with C1b1-M356 also contains at least one representative of R1a1a-M17, so ascribing the presence of C1b1-M356 in the PRC to Andronovo influence may be plausible, but note that this team has found C1b1-M356 in two individuals and R1a1a-M17 in only one individual among their samples of the Xibe (who are essentially modern Manchu-speaking people in Xinjiang). Perhaps C1b1-M356 might have been pushed eastward or southeastward by an originally R1a1a-M17 Andronovo population.

    On the other hand, the so-called C* that I have mentioned previously has been found mostly in northeastern, south-central, and southwestern China (Heilongjiang, Hulunbuir, Hubei, Guizhou, Guangxi, Yunnan) among speakers of Tungusic, Sinitic, Tujia, Kam-Sui (Daic), and Hmong-Mien languages, and usually not in association with R1a1a-M17 (except in a sample of Han from Guizhou). It also has been found alongside R1a1a-M17 in the Hui of Ningxia and the Xibe of Xinjiang in northwestern China; note that the ethnic core of the Xibe in Xinjiang are 18th-century migrants from northeastern China, and the Hui (Chinese-speaking Muslims) are an ethnoreligious group formed during historical times.

    C*-M130(xC2-M217, C1b1-M356) from Hua Zhong et al. (2011):

    Yao (Guangxi)
    9/55 = 16.4% C-M130(xC2-M217, C1b1-M356)
    1/55 = 1.8% C2-M217
    44/55 = 80.0% O-M175
    1/55 = 1.8% Q1a1a1-M120

    Mulao (Guangxi)
    1/11 = 9.1% C-M130(xC2-M217, C1b1-M356)
    1/11 = 9.1% C2-M217
    9/11 = 81.8% O-M175

    Hui (Ningxia)
    2/62 = 3.2% D-M174
    2/62 = 3.2% E-SRY4064
    5/62 = 8.1% C-M130(xC2-M217, C1b1-M356)
    6/62 = 9.7% C2-M217
    1/62 = 1.6% G1-M285
    1/62 = 1.6% G2a-P15(xG2a1a-P16)
    1/62 = 1.6% H1-M370(xH1a-M52)
    1/62 = 1.6% J1-M267
    5/62 = 8.1% J2a-M410(xJ2a1a-M322, J2a1b-M67, J2a1d-M319)
    2/62 = 3.2% J2a1b-M67
    1/62 = 1.6% L1c-M357
    5/62 = 8.1% N-M231
    22/62 = 35.5% O-M175
    2/62 = 3.2% Q1a1a1-M120
    1/62 = 1.6% R1-M173(xR1a1a-M17, R1b-M343)
    2/62 = 3.2% R1a1a-M17
    1/62 = 1.6% R1b1a2-M269
    2/62 = 3.2% R2a-M124

    Tujia (Hubei)
    2/26 = 7.7% C-M130(xC2-M217, C1b1-M356)
    6/26 = 23.1% C2-M217
    3/26 = 11.5% N-M231
    15/26 = 57.7% O-M175

    Shui (Guizhou)
    4/29 = 13.8% D-M174
    2/29 = 6.9% C-M130(xC2-M217, C1b1-M356)
    2/29 = 6.9% C2-M217
    21/29 = 72.4% O-M175

    Han (Yunnan)
    1/19 = 5.3% D-M174
    1/19 = 5.3% C-M130(xC2-M217, C1b1-M356)
    2/19 = 10.5% C2-M217
    15/19 = 78.9% O-M175

    Han (Guizhou)
    1/58 = 1.7% D-M174
    2/58 = 3.4% C-M130(xC2-M217, C1b1-M356)
    2/58 = 3.4% C2-M217
    3/58 = 5.2% N-M231
    48/58 = 82.8% O-M175
    1/58 = 1.7% Q1a2-M346
    1/58 = 1.7% R1a1a-M17

    Xibe (Xinjiang)
    2/61 = 3.3% D-M174
    2/61 = 3.3% C-M130(xC2-M217, C1b1-M356)
    2/61 = 3.3% C1b1-M356
    18/61 = 29.5% C2-M217
    1/61 = 1.6% J2b2-M241
    11/61 = 18.0% N-M231
    24/61 = 39.3% O-M175
    1/61 = 1.6% R1a1a-M17

    The age of STR variation among members of this group has been estimated to be 5,500 [±1,600] years using the "evolutionary mutation rate" (cf. Hua Zhong, Hong Shi, Xue-Bin Qi, Chun-Jie Xiao, Li Jin, Runlin Z Ma, and Bing Su (2010), "Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia"). It is certainly a very recently expanded clade despite its "C*" designation.
    To add for C-M130(xC2-M217, C1b1-M356):
    http://www.plosone.org/article/info%...l.pone.0050269
    "90% of the C-M130 samples reported here (66 out of 74) were positive for C5-M356 while the rest were negative for both C3-M217 and C5-M356" Arunkumar et. al

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    Quote Originally Posted by parasar View Post
    To add for C-M130(xC2-M217, C1b1-M356):
    http://www.plosone.org/article/info%...l.pone.0050269
    "90% of the C-M130 samples reported here (66 out of 74) were positive for C5-M356 while the rest were negative for both C3-M217 and C5-M356" Arunkumar et. al
    The following data also should be relevant:

    Indo-European speakers from Kathmandu, Nepal (Gayden et al. 2007)
    3/77 = 3.9% C-M216(xC1a1-M8, C1b1-M356, C1b2-M38, C1c1-M210, C2-M217)
    2/77 = 2.6% C2-M217(xC2a-M93, C2b1b1-M77, C2e1a1a1-M407)
    1/77 = 1.3% C1b1-M356

    1/77 = 1.3% H1-M69(xH1a-M52, H1b1-Apt)
    4/77 = 5.2% H1a-M52(xM82)
    4/77 = 5.2% H1a1-M82

    3/77 = 3.9% J2a-M410(xJ2a1a-M322, J2a1b-M67, J2a1c-M68, J2a1d-M319, J2a1e-M339, J2a1f-M419, J2a1h2a1a-M137, J2a1h2a1b-M318, J2a2a1-M340)
    5/77 = 6.5% J2b2-M241(xM99)

    1/77 = 1.3% N-M231(xN1c1-Tat, N1c2a-M128, N1c2b-P43)
    1/77 = 1.3% N1c1-Tat (P21+)

    1/77 = 1.3% O3a-M324(xO3a1a-M121, O3a1b-M164, O3a2b-M7, O3a2c1-M134, O3a3-M300)
    2/77 = 2.6% O3a2c1-M134(xO3a2c1a-M117)
    13/77 = 16.9% O3a2c1a-M117 (However, note that M117 is included in this study's list of "biallelic markers [that] were genotyped but were not polymorphic" in the studied samples. I presume that this must be a typographical error.)

    1/77 = 1.3% Q-M242(xQ1a1a1-M120, Q1a1b-M25, Q1a2-M346, Q1b1-M378)

    27/77 = 35.1% R1a1a-M198
    8/77 = 10.4% R2a-M124

    However, note how rare C1b1-M356 is in this sample from Kathmandu: C1b1-M356 accounts for only 1/4 = 25% of the C-M216(xC2-M217) Y-chromosomes instead of 90%.

    Also note these samples from the valleys of the Yangtze river system in western Sichuan (cf. Chuan-Chao Wang, Ling-Xiang Wang, Rukesh Shrestha, Manfei Zhang, Xiu-Yuan Huang, Kang Hu, Li Jin, and Hui Li (2014), "Genetic Structure of Qiangic Populations Residing in the Western Sichuan Corridor," PLoS ONE 9(8): e103772. doi:10.1371/journal.pone.0103772):

    Horpa/Danba County, Sichuan
    1/18 = 5.6% C-M130(xC1a1-M105, C1b2-M38, C1c-M347, C2-M217)

    8/18 = 44.4% D1a1-N1(xN2)
    1/18 = 5.6% D1c-P99(xD1c1-P47)

    2/18 = 11.1% O2a1a-M88

    1/18 = 5.6% O3a2b-M7
    1/18 = 5.6% O3a2c1-M134(xO3a2c1a-M117)
    4/18 = 22.2% O3a2c1a-M117

    Khampa/Xinlong County, Garzê Tibetan Autonomous Prefecture, Sichuan
    1/46 = 2.2% C-M130(xC1a1-M105, C1b2-M38, C1c-M347, C2-M217)

    4/46 = 8.7% D1a1-N1(xN2)
    1/46 = 2.2% D1c-P99(xD1c1-P47)
    10/46 = 21.7% D1c1-P47

    1/46 = 2.2% F-M89(xG-M201, I-M258, J-M304, K-M9)

    1/46 = 2.2% N1c1a-M178

    4/46 = 8.7% O1a1-P203

    1/46 = 2.2% O2-M268(xO2a-PK4, O2b-M176)
    2/46 = 4.3% O2a-PK4(xO2a1-M95)
    1/46 = 2.2% O2a1-M95(xO2a1a-M88)
    1/46 = 2.2% O2b-M176

    1/46 = 2.2% O3a-M324(xO3a1-L127/KL1, O3a2-P201)
    7/46 = 15.2% O3a1c-JST002611
    1/46 = 2.2% O3a2b-M7
    3/46 = 6.5% O3a2c1-M134(xM117)
    5/46 = 10.9% O3a2c1a-M117

    2/46 = 4.3% Q1a1a1-M120/N14

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    From the supplementary materials of Yan S, Wang C-C, Zheng H-X, Wang W, Qin Z-D, et al. (2014) "Y Chromosomes of 40% Chinese Descend from Three Neolithic Super-Grandfathers":

    YCH251 (Han Chinese from Hunan, PRC) C-M130(xM105, M38, M217, M347)

    This individual's Y-DNA is positive for at least 132 SNPs that are not positive in any studied representative of C2-M217:

    F441
    F725, F736, F741, F778, F796
    F808, F821, F870, F873, F884
    F973, F988
    F1033, F1037, F1059
    F1109, F1151, F1171
    F1220, F1259
    F1315, F1331, F1370
    F1459, F1469, F1493
    F1580, F1585, F1593
    F1606, F1617, F1640, F1686, F1689
    F1716, F1782
    F1914, F1959, F1990
    F2010, F2022, F2031, F2085, F2098
    F2143, F2181, F2182
    F2204, F2248, F2286, F2298
    F2324, F2330, F2333, F2335, F2351, F2364, F2381
    F2403, F2413, F2476
    F2526, F2533, F2544, F2545, F2559, F2582
    F2610, F2611, F2617, F2641, F2642, F2693, F2694
    F2720, F2738, F2776
    F2825, F2832, F2843, F2848, F2873, F2874
    F2915, F2946, F2959
    F3007
    F3100, F3101, F3107, F3114, F3120, F3137, F3184
    F3219, F3244
    F3351, F3378, F3381, F3391, F3393
    F3442, F3444, F3493
    F3509, F3566, F3582
    F3600, F3636, F3648
    F3842, F3859, F3860, F3863, F3874, F3882
    F3915, F3922, F3962, F3966, F3974
    F4019, F4020, F4067
    F4111, F4116, F4137
    F4222, F4265
    F4338, F4340

    Of these 132 SNPs listed above, two have been placed on the ISOGG tree already: C1-F3393 and C1b-F1370.

    In an attempt to discover a synonymous SNP in the K series, I compared the definitions of the remaining 130 F-series SNPs from the list above with the definitions of the K series SNPs that have been listed on the current version of the ISOGG tree as phylogenetically equivalent to C1b1a-P92. I have considered the definitions of the K series SNPs to be as they are listed on this web page by JeongAhn.

    The result was that none of the definitions matched. Assuming that everything is correct, this must mean one of two things: either there is no relevant overlap between the F series and the K series in regard to the portions of the Y-chromosome that have been sequenced, or YCH251 belongs to C1b-F1370(xC1b1a-K105/K43/K45/K59/K61/K69/K78/K83/K88/K90/K94/K99/K108/K129/K134/K141/K146/K147/K156/K161/K162/K181/K184/K185/K186/K187/K188/K205/K245/K246/K249/K252/K260/K261/K267/K280/K293/K310/K317/K319/K320/K323/K327/K331/K358/K377/K396/K398/K401/K402/K414/K415/K417/K426/K427/K435).

    Does anyone have a list of definitions of the Z series SNPs that I could use for comparison?

    (As an aside, in the process of my comparison, I have discovered a discrepancy. The current version of the ISOGG tree lists F930/K105 as synonymous SNPs that mark C1b1a, but the definition of F930 given in Table S6 of Yan et al. 2014 does not match the definition of K105 given on JeongAhn's website: F930 is supposed to be a c > T transition, and K105 is supposed to be a C > A transversion. The locus is identical (7262706/7202706), but the F930+ mutant is supposed to have T at this locus according to Table S6 of Yan et al. 2014, whereas the K105+ mutant is supposed to have A at this locus according to the table of K series SNPs on JeongAhn's website. Table S6 of Yan et al. 2014 has presented F930 as a mutation within a subclade of O3-M122, and not within C-M130. ISOGG, Yan et al., or JeongAhn must have made an error here...or am I totally off-base?

    By the way, YCH251 is indicated to be negative for F930, too.)

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