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venustas
08-11-2014, 11:18 PM
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

Ebizur
08-11-2014, 11:51 PM
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.

Ebizur
11-20-2014, 08:44 AM
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.

parasar
11-20-2014, 05:01 PM
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%3Adoi%2F10.1371%2Fjournal.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

Ebizur
11-23-2014, 09:01 AM
To add for C-M130(xC2-M217, C1b1-M356):
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.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

Ebizur
11-25-2014, 08:22 AM
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 (https://sites.google.com/site/yhaptree/k-series).

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.)