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C-M130 reveals the prehistoric migration routes of African exodus and early settlement in East Asia
Topic Started: May 9 2010, 06:44:03 AM (2,235 Views)
natsuya
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Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia

Hua Zhong et al.

The regional distribution of an ancient Y-chromosome haplogroup C-M130 (Hg C) in Asia provides an ideal tool of dissecting prehistoric migration events. We identified 465 Hg C individuals out of 4284 males from 140 East and Southeast Asian populations. We genotyped these Hg C individuals using 12 Y-chromosome biallelic markers and 8 commonly used Y-short tandem repeats (Y-STRs), and performed phylogeographic analysis in combination with the published data. The results show that most of the Hg C subhaplogroups have distinct geographical distribution and have undergone long-time isolation, although Hg C individuals are distributed widely across Eurasia. Furthermore, a general south-to-north and east-to-west cline of Y-STR diversity is observed with the highest diversity in Southeast Asia. The phylogeographic distribution pattern of Hg C supports a single coastal ‘Out-of-Africa’ route by way of the Indian subcontinent, which eventually led to the early settlement of modern humans in mainland Southeast Asia. The northward expansion of Hg C in East Asia started ~40 thousand of years ago (KYA) along the coastline of mainland China and reached Siberia ~15 KYA and finally made its way to the Americas.

Link: http://www.nature.com/jhg/journal/vaop/ncurrent/abs/jhg201040a.html
SI: http://www.nature.com/jhg/journal/vaop/ncurrent/suppinfo/jhg201040s1.html?url=/jhg/journal/vaop/ncurrent/abs/jhg201040a.html
The whole paper: http://viewer.zoho.com/docs/sRbQt
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ren
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It seems that C3 might have a southern origin. I was wondering about the origins of C3 a while back. It seems to have been a separate phenomenon from the ancestors of the Neolithic explosion that seems to have come out NW China proper. C3 might've had a coastal distribution that was cut up by NO's expansion.




Thanx, our man in Taiwan! black man mentioned the paper and gave us the XLS but did not provide the paper.

http://s6.zetaboards.com/man/single/?p=8020645&t=528039
Edited by ren, May 10 2010, 01:38:37 AM.
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natsuya
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You're welcome, Ren.

I notice the paper indicates:

"Interestingly, besides Hg C1, Japanese also have M217-derived individuals who have a close relationship with the Han Chinese (Figures 3a and b), rather than with the Altaic-speaking populations."

I really wonder when these C3* moved from China to Japan.

It's possible that part of C3* were brought to Japan by Microlithic hunter-gatherers, and part of C3* were carried to Japan by early farmers from the coastline of China.

And how would Ainu C3* fit in the picture? Close to Siberian C3*?

MJ Network of C3*:

http://konglong.5d6d.com/userdirs/8/6/konglong/attachments/month_1005/100513211553d82886dae8179a.png
Edited by natsuya, May 13 2010, 05:00:36 PM.
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ren
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Hey can you give us a PDF version of the file? The present format is hard to magnify and view in detail.

I didn't find any C3* among the Japanese and I can't see any reference to Ainu in Figure 1.
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natsuya
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You can download the paper just click on the "save" in the Zoho Viewer.

http://viewer.zoho.com/docs/sRbQt
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Ebizur
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I do not see the point in making such a fuss about haplogroup C3 among Japanese, because it is neither common nor especially diverse among them. Of all eastern Asian peoples, Y-DNA haplogroup C in general seems to be rarest among populations of Japan, Tibet, and Thailand.

Japanese (Karafet et al. 1999)
1/118 = 1% BT-SRY10831.1(xC-M130, DE-YAP, K-M9)
6/118 = 5% C-M130
55/118 = 47% DE-YAP(xE-SRY4064)
54/118 = 46% K-M9(xN1c-Tat, M2a-SRY9138, P-DYS257)
2/118 = 2% P-DYS257(xQ1a3a-DYS199, R1a1-SRY10831.2)

Nonaka's sample of Japanese from the Kanto region of southeastern Honshu, which includes Tokyo and is the most densely populated region of Japan (it is not a very large area, but it contains at least one third of the entire population of the country), is the best proxy for the Japanese population as a whole among published samples of Japanese, for which rather insignificant regions, such as Kyushu, Tokushima (eastern Shikoku), or Okinawa, have been oversampled:

Japanese/Kanto region (Nonaka et al. 2007)
2/137 = 1.5% C1-M105
3/137 = 2.2% C3-M217(xC3a-M93, C3b-P39, C3c-M48/M77/M86)
(5/137 = 3.6% C-M130 total)

11/137 = 8.0% D2*-M55(xD2a-M116a)
18/137 = 13.1% D2a-M116a(xD2a1-M125, D2a2-M151)
2/137 = 1.5% D2a1-M125(xD2a1b-022457)
35/137 = 25.5% D2a1b-022457
(66/137 = 48.2% D2-M55 total)

3/137 = 2.2% O1a-M119(xO1a1a-M101, O1a2-M50)
9/137 = 6.6% O2b*-SRY465(xO2b1-47z)
33/137 = 24.1% O2b1-47z
(42/137 = 30.7% O2b-SRY465 total)
2/137 = 1.5% O3-M122(xO3a1-M121, O3a2-M164, O3a3-021354, O3a4-002611)
3/137 = 2.2% O3a4-002611
5/137 = 3.6% O3a3-021354(xO3a3b-M7, O3a3c-M134)
4/137 = 2.9% O3a3c-M134(xO3a3c1-M117)
6/137 = 4.4% O3a3c1-M117(xO3a3c1a-M162)
(20/137 = 14.6% O3-M122 total)
(65/137 = 47.4% O-M175 total)

1/137 = 0.7% Q1a1-M120

H Zhong et al. 2010 have suggested that most of the extant C3-M217 representatives in Japan may be more closely related to Han Chinese representatives of C3-M217 than to C3-M217 representatives in other populations of eastern Asia. However, according to their median-joining networks,

1. One C3* haplotype is shared equally among "Japanese," "Altaic," "Tibeto-Burman," "Southern Han," and "Northern Han"
2. One C3* haplotype that is similar to #1 is shared equally between "Japanese" and "Tibeto-Burman"
3. One C3* haplotype that is similar to #2 and #1 is shared equally among "Japanese," "Korean," and "Northern Han"
4. One C3* haplotype that is rather distinct from the previous three is shared equally between "Japanese" and "Northern Han"
5. One C3* haplotype that is similar to #4 is found mainly in "Northern Han," but also has some representation among "Southern Han" and "Japanese"
6. One C3* haplotype that is close to the center of the median-joining network is found mainly in "Hmong-Mien/Daic/Austro-Asiatic (of southern China)," but also has some representation among "Japanese"
7. The modal haplotype of C3* lies near the tip of a rather long branch that appears to stem from a haplotype found in "Northern Han," but most extant members of this branch are "Altaic" or "Tibetan." The modal haplotype itself is found mainly in "Altaic," but it also has a few representatives in "Japanese," "Tibetan," and "Northern Han."
8. Five different C3* haplotypes, all but one of which appear at the very edges of the median-joining network, have been found only in "Japanese" (perhaps as singletons).
9. Three different haplotypes that belong to two different branches found at the edges of the median-joining network for haplogroup C3c have been found only in "Japanese" as singletons.
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ren
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natsuya
May 14 2010, 01:28:22 PM
You can download the paper just click on the "save" in the Zoho Viewer.

http://viewer.zoho.com/docs/sRbQt
Oh sorry. That was stupid of me.
natsuya, lemme give you access to the Advanced Member section. It's where members request and post articles they have access to. When you are interested, you can post studies you find interesting or answer others' requests.
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Ebizur
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A median-joining network of haplogroup C-M130 haplotypes from Redd et al. 2002, followed by what appears to be a median-joining network of haplogroup C-M130(xC3-M217) haplotypes from Hammer et al. 2005:

Posted Image
Posted Image

For the median-joining network from the paper by Hammer et al. 2005,
Quote:
 
the position of the M8 mutation is denoted by a black line and the open circle represents a single central Asian haplotype. Microsatellite haplotypes are represented by circles with area proportional to the number of individuals with that haplotype. Branch lengths are proportional to the number of one-repeat mutations separating the two haplotypes. Haplotypes are color-coded by geographic region (see key), with haplotype sharing indicated by pie chart divisions.
Attached to this post:
Attachments: Redd2002HaploC.jpg (83.55 KB)
Attachments: HaploCHammer2005.jpg (16.3 KB)
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Ebizur
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Appendices 3 and 4 of the study by Nonaka et al. 2007 provide the prefectural origin of each of their Japanese Y-DNA samples:

C1-M105
1/5 Wakayama
1/6 Fukushima
1/11 Nagano
1/12 Shizuoka
1/13 Saitama
1/45 Chiba

Wakayama is located on the Kii Peninsula, immediately south of the prefectures of Osaka, Nara, and Mie. Fukushima is the southernmost part of the Tohoku ("Northeast") region of Honshu. Nagano and Shizuoka are technically considered to belong to the Chubu ("Central") region of Honshu, but they abut the western edge of the Kanto region. The prefectures of Saitama and Chiba are located in the Kanto region of southeastern Honshu.

C3-M217(xC3a-M93, C3b-P39, C3c-M48/M77/M86)
1/4 Fukuoka (or perhaps 1/3 Hokkaido - there appears to have been some confusion in the use of the abbreviations for Fukuoka and Hokkaido)
1/4 Ishikawa
1/4 Kagawa (NE Shikoku)
1/5 Ibaraki
1/6 Niigata
1/11 Nagano
2/45 Chiba

The prefectures of Ibaraki and Chiba are located in the Kanto region.

In conclusion, of the 5/137 = 3.6% C-M130 that Nonaka et al. 2007 have found in their samples from the important Kanto region of southeastern Honshu, three (two C3 and one C1) have been found in Chiba Prefecture, one (C3) has been found in Ibaraki Prefecture, and one (C1) has been found in Saitama Prefecture.
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ren
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Can't decide if C3 was broken by the Neolithic expansion or was part of it with O.
Any ideas from you guys? JCA? You seem to be very active on the C issue.
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Ebizur
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All that I can say with any certainty at present is that the variance of O-M175 in northern East Asia is greater than the variance of C-M130 in northern East Asia (cf. T. Katoh et al. 2004, Table 2). Since the variance of C-M130 in northern East Asia is not much less than the variance of all extant derivatives of C-M130 in total, this might be taken as an indication that O-M175 has originated earlier than C-M130. However, the phylogenetic position of C-M130 in the Y-SNP tree and the marginal geographical distribution of C-M130 (essentially, it has been found more frequently in males who inhabit areas that are less suited for supporting human populations or that have been more isolated from major centers of human population growth and cultural development) have made many people suppose that it should represent an older layer of population (probably the first layer of Homo sapiens sapiens) in the areas where it is found.

Please remember that, assuming that the present Y-SNP tree is accurate, an older age for O-M175 in comparison to C-M130 would entail that NO-M214, MNOPS-M526, K-M9, IJK-L15, and F-M89 also are all older than C-M130. The inclusion of C-M130 haplotypes from Indochina and the Malay Archipelago should reduce the difference in variance between C-M130 and O-M175 to some extent. I suspect that the fairly low STR variance of extant C-M130 Y-chromosomes might be a result of re-expansion after a bottleneck caused by interaction with an expanding population of MNOPS-M526 (or perhaps K-M9 in general; I am not aware of any data regarding the M526 status of Australian aboriginal K-M9 individuals).
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black man
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ren
May 21 2010, 02:09:29 AM
Can't decide if C3 was broken by the Neolithic expansion or was part of it with O.
Any ideas from you guys? JCA? You seem to be very active on the C issue.
There are many non-Han northerners and southerners in paragroup C3*. But I don't have the time to check all haplotypes.

In previous studies they only reported between 5 and 10%. But these authors report relatively high frequencies estimations, between 10 and 20%, for hg C3 in northern Han (and frequencies up to about 10% for southern Han). If the data are correct, hg C3 can no longer be accepted as a relatively unambiguously North Asian marker. I.e., the authors should have distinguished between Manchu-Tungus and other "Altaic" C3 in figure 4.

On the other hand, didn't Sino-Tibetans expand from a relatively southern region (Sichuan)? Then M217 in northern Han and Qinghai Tibetans could also be interpretated as aboriginal "Altaic" marker.

I didn't count the haplotypes but at the first glance it seemed to me as if haplotypes are often shared between the Han (dark blue and white) and the yellow ("Altaic") groups but rarely between the red (Austro-Asiatic, Miao-Yao and Daic) and the yellow groups. So maybe the red group descends from pre-Sinitic populations in prehistoric northern China.

M48 in Tibetans and Japanese now appears to be North Asian because it is almost absent in Han (despite of the increased sample sizes).

M407 is found in Han, Manchus and Uigurs, as this team reports. PReviously, Sengupta et al. reported these haplotypes for carriers the same SNP marker:
DYS19 DYS388 DYS389 AB (389II) DYS389 CD (389I) DYS390 DYS391 DYS392 DYS393 DYS439 DYSA7.2 (Add 2 to get DYS461)
Yakut C3a2 15 12 15 13 23 10 15 14 12 10
Han C3a2 16 12 15 14 23 10 11 15 14 10
Yakut C3a2 17 12 16 14 23 10 11 13 13 11

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C* is present in the Ningxia Hui, Xibe, Tujia, Guangxi Yao, Yunnan Han, Guizhou Han and some Guangxi and Guizhou Daic populations according to Zhong Hua et al. I.e. coastal central East Asia possibly lacks this paragroup.
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