imvivi001 发表于 2017-7-16 08:10

多年前关于欧亚人群常染的论文,至今仍有很大的参考价值

Am J Hum Genet. 2009 Dec 11; 85(6): 934–937.
doi:10.1016/j.ajhg.2009.10.024
PMCID: PMC2790568

Genetic Landscape of Eurasia and “Admixture” in Uyghurs

作者:李辉,1 Kelly Cho,1 Judith R. Kidd,1 and Kenneth K. Kidd1,∗
1Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
Kenneth K. Kidd: ude.elay@ddik.htennek

Main Text
To the Editor: In the papers1,2 by Xu and Jin, the genetic structure of Uyghurs was described by 8150 ancestry-informative markers (AIMs). These markers estimated the admixture rate of the Uyghur population to be around 50% East Asian ancestry by comparing Uyghurs to East Asians and Europeans. However, we suspect that the estimate of Xu and Jin may be considerably biased by insufficient reference population coverage. In their study, Xu and Jin used the STRUCTURE program3,4 as the major method for estimating the admixture rate; however, results from the STRUCTURE program are strictly the probabilities of assignment to different estimated clusters and therefore are influenced by both the marker selection and the populations used to estimate allele frequencies in those other clusters. The results of Xu and Jin are unlikely to be biased due to marker selection because they used a large number of AIMs selected to distinguish Europeans from East Asians. However, the population coverage in their analysis was relatively sparse. They only analyzed Japanese, northern Chinese, and a very small sample (n = 10) of Mongols for the East Asian reference. For Europeans, they included some southern European populations, Russians, and Adygei. It is doubtful that this sparse population coverage can yield precise results. Although the cluster assignments can be interpreted as admixture under many circumstances, these reference populations may not serve as relevant ancestral populations for an admixture analysis of Uyghurs. We also note that, for populations in the middle of a clinal distribution, STRUCTURE cannot readily distinguish recent admixture from a historical cline established by an expanding population as in the original spread of modern humans out of Africa and across Eurasia.5
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In our study, we typed 68 AIMs on 1766 individuals from 34 populations representing all subdivisions of Eurasia (Figure 1 and Table S1 available online; allele frequency data also in ALFRED). All samples were collected with informed consent by participants using protocols approved by all relevant institutional review boards. The SNPs were selected at random from a group of ∼300 markers having a high global FST and already tested on many populations, including some reported here. However, the selection paid no attention to the pattern of variation across Eurasia. This “randomness” is illustrated by the Eurasian FST values for these 68 markers, which range from 0.028 to 0.681 in a highly skewed distribution with a median value of ∼0.15 (Figure S1). Our set of populations contained several population samples for those regions around Uyghurs, such as Kazakhs, Mongols, Tibetan Khams, etc. to the east of Uyghurs and Hazaras, Khanty, etc. to the west. This comprehensive population coverage allowed more reliable estimates of relationships among the populations. We used STRUCTURE 2.2 and SURFER 8.0 programs to illustrate the population similarities (Figure 1). The analyses showed a very clear west-east cline when K = 2. The median border estimated from these 68 SNPs divided Central Asia along the Ob River, the Kazakh highland, the western side of the Pamir Mountains, and the southwestern side of the Himalayas. Although the small number of markers examined cannot result in an accurate median border, the Uyghur population fell east of the median border with 31.2% assignment to the western cluster. Even the Hazaras and Khanty were to the east of the median border. This result matched the results of more anthropological studies on Eurasian population structures with the Hazaras around the median.6 Other anthropological studies also estimated Uyghurs to have ∼30% western proportions,7,8 closer to our estimate.

imvivi001 发表于 2017-7-16 08:17

Table S1. Allele Frequencies of 68 AIMs of the Eurasian Populations(欧洲西欧亚与部分中亚部分1)
RS#




丹麦

匈牙利

芬兰

俄罗斯

阿迪盖

阿系犹太

撒玛利亚人

哈扎拉

汉特

rs963171

WARS2 C_8013966

0.167

0.182

0.206

0.271

0.269

0.095

0.012

0.346

0.439

rs1994859

SFRS4 C_2558108

0.167

0.218

0.343

0.292

0.25

0.241

0.5

0.464

0.75

rs279025

NECAP2 C_8861049

0.206

0.331

0.333

0.365

0.222

0.278

0.138

0.412

0.52

rs12075

IGSF4B C_2493442

0.353

0.409

0.443

0.406

0.557

0.394

0.61

0.769

0.51

rs1404402

TMEM9 C_1942792

0.28

0.287

0.343

0.255

0.25

0.266

0.638

0.115

0.53

rs2065160

ANON01 C_1648531

0.147

0.14

0.157

0.094

0.148

0.106

0.012

0.344

0.5

imvivi001 发表于 2017-7-16 08:19

Table S1. Allele Frequencies of 68 AIMs of the Eurasian Populations(欧洲西欧亚与部分中亚部分2)

RS#
丹麦匈牙利芬兰俄罗斯阿迪盖阿系犹太撒玛利亚人哈扎拉汉特rs1032982SEC15L2 C_32538140.240.3060.1360.3150.1670.1970.4120.10.09rs6713532POMC C_294121250.1860.2010.4170.2720.260.2560.1790.50.66rs1876482ANON02 C_116409690.0590.040.0830.1460.0560.050.1220.5280.418rs896788RNF144A C_17510840.1470.1690.10.1560.2040.1140.1380.3440.6rs1016120TMEM163 C_26887090.2550.4770.2350.4260.3770.570.90.5770.521

imvivi001 发表于 2017-7-16 08:27

Table S1. Allele Frequencies of 68 AIMs of the Eurasian Populations(东亚欧部分1)


LocationRS#羌族蒙古族
客家人缅甸人广府人韩国人日本人阿美族老挝人柬埔寨大洋洲micronesianFst1p12brs96
31710.5210.5770.50.330.5430.5770.5290.3590.3930.4790.30.1301p35.3ars199
48590.7950.7730.8050.870.8620.8890.8880.7050.860.820.6080.2441p36.13ers27
90250.5770.6140.6710.590.6120.620.7760.6880.6140.7290.5830.1481q21
(东亚标志性,不知道美洲土著的数据)rs12
0750.910.8861(标准的东亚人,呵呵)0.9580.940.9070.9480.950.8980.9380.8750.2651q32.1brs140
44020.2310.2060.1340.1670.1790.2170.2450.1880.2050.1040.2920.0831q32.1frs206
51600.7410.6670.7930.8020.8530.8240.760.850.7610.7080.5410.3522p13.2ars103
29820.0380.0390.0610.02100.0380.02100.01300.1490.1162p23.3crs671
35320.6030.6460.5750.650.6640.620.7060.4250.5180.6040.5140.0962p24rs187
64820.7180.6560.7750.5830.7540.7410.8160.8970.6620.7290.7940.4082p25.1grs89
67880.7380.6810.6340.630.6320.5370.7040.7440.5890.5620.4860.215

imvivi001 发表于 2017-7-16 08:30

居然还有更具标志性的变异,快看

Table S1. Allele Frequencies of 68 AIMs of the Eurasian Populations(东亚欧部分2)
LocationGeneRS#维吾尔哈萨克康区羌族蒙古族客家人缅甸人广府人韩国人日本人阿美族老挝人柬埔寨大洋洲
Micron-esiansFst
(注:此Fst2q21.3aTMEM163rs10161200.4890.4570.4330.410.4920.50.590.50.5370.3920.550.5130.6460.403是针对本表2q33.1fALS2CR12rs14061210.4430.40.5690.6280.4190.4510.480.4910.5090.3330.2620.5380.5830.458全体欧亚人群2q33.2bPARD3Brs7230210.5420.6250.740.70.6840.8050.8090.7190.7740.7650.5880.6650.7080.5970.0932q34bLANCL1rs7253790.3380.2090.2730.1730.2340.1830.1770.2410.2220.2060.2180.1580.1250.1390.0462q34bLANCL1rs13504620.410.2380.550.4580.5080.6340.4390.50.4720.620.6540.6270.7080.4860.1072q36.3cSKIPrs13438450.5130.4880.6210.70.6040.780.750.7190.6320.6370.70.6480.6250.50.0773p12FOXP1rs117139960.6830.6160.8960.9250.8190.9750.990.9480.9910.9380.90.930.860.8380.0813q11.2bARL13Brs20488610.330.4640.3850.4490.3910.390.4790.4380.3890.3330.4880.470.480.1670.1603q11.2cEPHA6rs23172120.30.4620.50.4790.5490.4880.6460.5710.6060.50.4860.4960.6040.4410.1634p16.1aMISTrs20143030.2250.1140.0830.260.0830.0980.10.1030.0370.0290.0380.1370.2290.0280.0504q31.3dKIAA1727rs8695380.4090.2380.320.3910.3890.4270.3750.4210.3960.3630.2750.3860.3540.2920.0794q32.3cTLL1rs1871450.2620.3140.5190.220.2540.3540.3750.2370.2590.1270.2950.3350.2080.5830.0625p13.3a
够标志性吧,呵呵SLC45A2rs168919820.7670.7560.96610.918110.9830.9910.981110.9320.3575q12.1cKIF2rs20328760.4020.420.4680.5510.40.4510.420.4040.4350.3530.3120.3350.240.2360.1835q21.1cST8SIA4rs10377960.5120.5620.5650.50.4920.5240.490.5090.5740.530.5390.4320.4790.2860.3945q21.3dFBXL17rs9884360.1590.1410.260.20.1330.1710.1770.1550.1570.1760.0380.2030.1960.0830.048

imvivi001 发表于 2017-7-16 08:33

上表已经清楚表明,东亚大多数族系(包括蒙古族与中南半岛的族系)都是充分的南北混合的族系,这种混合非常深入,显然不是历史时期开始的,应该是非常久远~~

imvivi001 发表于 2017-7-16 08:35

揭晓:本轮入围最具东亚风情的族群或族系,他们是:

LocationGeneRS#维吾尔哈萨克康区羌族蒙古族客家人缅甸族广府人韩国朝鲜族日本和族阿美族老挝柬埔寨Micron
esiansFst5p13.3aSLC45A2rs168919820.7670.7560.96610.918110.9830.9910.981110.9320.357


            ~~~~~~~~~~~~~~~~~~~~~~~{:8_192:}

imvivi001 发表于 2017-7-16 14:50



尽管这个当年的admixture软件的设计者可能还不太懂得美术基本常识,以至于K值图的色系搞得一塌糊涂,令读者非常难以辨认。但是本文作者另外补充的Contour Plot图倒是非常管用,够直观。看得出来,当时他们的分析与目前的admix分析大体上是一致的。
可以看到一个有趣的现象,东亚的常染分布其实主要是东西轴向演化,狭义上的‘东亚’或远东成分,基本在东经105°线以东,相比之下,与纬度的关联性不大。
与此同时,南亚成分则围绕喜马拉雅山脉向北蔓延。难怪本文作者提出远古时期存在一条“环喜马拉雅东进路线的西线”(“early modern humans entered East Asia in the south along two routes, the western route from Myanmar to Yunnan and the eastern route from Vietnam to Guangdong.10,12,13”),这条“环喜马拉雅东进路线的西线”向北一直蔓延到西北的甘青地区,这个与我们目前在土族身上观察到的南亚成分相吻合,但是具体成因,似可继续探究~

imvivi001 发表于 2017-7-16 15:05

52291

尽管这个当年的admixture软件的设计者可能还不太懂得美术基本常识,以至于K值图的色系搞得一塌糊涂,令读者非常难以辨认。但是本文作者另外补充的Contour Plot图倒是非常管用,够直观。看得出来,当时他们的 ...
imvivi001 发表于 2017-7-16 14:50 http://www.ranhaer.org/images/common/back.gif

Contour Plot图上面好像有一个失误,比如把中南半岛的全部以及台湾岛土著都归为与岛屿东南亚一样了,这显然与最新的检测结果不一致,因为我们现在知道,台湾土著以及越南京族的常染与大陆傣族几乎没有区别,但是岛屿东南亚不单是有较多的南亚成分,其澳美巴布亚成分也颇为明显~
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