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05-09-06, 17:43
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Diversity at eight polymorphic Alu insertion loci in Chinese populations shows evidence for European admixture in an ethnic minority population from Uyghuristan(Northwest China)

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05-09-06, 17:46
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Diversity at eight polymorphic Alu insertion loci in Chinese populations shows evidence for European admixture in an ethnic minority population from Uyghuristan(Northwest China)

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05-09-06, 18:30
I found it by searching with "DNA Uyghur" in the site that guy gave.
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uaa_admin
06-09-06, 09:57
Yuqirida tilgha elinghan maqalining toluq texti towendikiche:

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Diversity at eight polymorphic Alu insertion loci in Chinese populations shows evidence for European admixture in an ethnic minority population from Northwest China



Human Biology, Aug 2002 by Xiao, Feng-Xia, Yang, Jun-Fang, Cassiman, Jean-Jacques, Decorte, Ronny


Abstract We have analyzed eight human-specific Alu insertion polymorphisms in four Chinese populations belonging to three ethnic groups (98 Hans from Shanghai, 80 Hans from Guangzhou, 85 Uyghurs, and 60 Sibos). All populations exhibited high levels of average heterozygosity, and those in Uyghur and Sibo were higher than predicted by the island model of population structure. The degree of genetic differentiation among these populations is statistically significant, and lower than those observed in most parts of the world except for Europe and Sahul (Australia and New Guinea). Phylogenetic analysis of these data with published data from 29 worldwide populations shows that there is a close genetic affinity among all the East Asian populations except for the Uyghur, and that the Uyghur population was found to lie between the East Asian and the West Asian populations on the population tree. The greater heterozygosity and the significant genotype associations between unlinked loci observed for the Uyghurs support the scenario that the Uyghurs might have originated from an admixture between Europeans and East Asians. This study also provides further support for the "out-of-Africa" hypothesis of modern human evolution in East Asia.

Despite China's being one of the few regions of the world with abundant human fossils from Homo erectus to early Homo sapiens and to modern specimens (Brooks and Wood 1990; Li and Etler 1992), modern humans in this region are now believed to have originated in Africa (Vigilant et al. 1991; Chu et al. 1998; Jorde et al. 2000). However, the time and the actual migration routes by which modern humans spread from Africa to East Asia are still controversial (CavalliSforza et al. 1994). At least three different models for the prehistoric migrations of modem humans in this region have been proposed. The linguistic map in China suggested that the initial peopling took place in northeast Asia, followed by migration of populations to the south, where they mixed with the 'Australoid' setfled in Southeast Asia (Piazza 1998). The archaeological records supported the idea that northern and southern East Asian populations have originated independently from the two distinct populations since late Paleolithic times (Piazza 1998). Recent studies of East Asian populations, using nuclear microsatellite and Y-chromosome polymorphisms, have addressed such an issue and suggested that the first settlement of modern humans occurred in Southeast Asia, followed by a northward migration into northern China (Chu et al. 1998; Su et al. 1999). These studies also revealed substantial genetic differences between northern and southern Chinese people, consistent with previous observations based on protein polymorphisms (Zhao and Lee 1989; Etler 1992). These different models on the peopling of East Asia probably reflect different time spans of evolutionary history of modern humans in this region (Piazza 1998).

Alu sequences represent the largest family of short interspersed elements (SINEs) with more than 500,000 copies present in the human genome (Batzer et al. 1994). These mobile Alu elements are ancestrally derived from the 7SL RNA gene and mobilized throughout the primate genomes by retroposition in the last 65 million years (Rogers 1983; Ullu and Tschudi 1984). Approximately 500 Alu family members are present as a human-specific (HS) subfamily, which have been inserted in the human genome within the past 6 million years (Batzer and Deininger 1991). Some of them have retroposed so recently that they are polymorphic for presence or absence at a specific location within the human genome. Recently, Alu insertion polymorphisms have become a novel set of nuclear DNA markers for the study of human evolution. These repetitive Alu elements represent stable polymorphisms that are identical by descent from a common ancestor (Batzer et al. 1996; Stoneking et al. 1997). Particularly, the ancestral state of each Alu insertion is known with certainty to be the absence of an Alu element, facilitating accurate rooting of population trees (Batzer et al. 1996; Stoneking et al. 1997). Recent studies of worldwide populations using Alu polymorphic insertions have shown evidence for the support of "out-of-Africa" hypotheses for modern humans (Batzer et al. 1996; Stoneking et al. 1997). Other studies have dealt with more recent events in human evolution such as the settlements of the Americas and India (Novick et al. 1998; Majumder et al. 1999).

It is obvious that an extensive study of Chinese populations using Alu insertion polymorphisms might be helpful to clarify the controversial issues of the peopling of East Asia. However, genetic data on Alu insertion polymorphisms is still insufficient for populations from mainland China. In the present study, we have analyzed genetic variation at eight Alu insertion polymorphic loci in four populations of China from three ethnic groups. The aim of this study is to better understand the relationships of these populations as well as their genetic affinities with other populations in East Asia.

Materials and Methods

Population Samples. China consists of a Han majority (93.3%) and 55 official minorities (6.7%). In this study, 323 unrelated individuals from four populations of China belonging to three ethnic groups were analyzed. The geographic locations of the four populations are illustrated in Figure 1. The samples of 98 Hans from Shanghai (East China) and 80 Hans from Guangzhou (Southeast China) were previously described (Xiao et al. 1998). Bloodstain samples of 85 Uyghurs and single-hair samples of 60 Sibos were collected from Yining in the Xinjiang autonomous region (Northwest China). The Uyghurs, living in a region of Central Asia along the Silk Road in ancient China, represent the second largest minority in China. The Sibos, currently residing in Yining, are descendants of approximately 3000 Sibos (1000 Sibo warriors and their families), who migrated from Shenyang (Northeast China) to Yining in 1764 during the Qing dynasty. The Han populations speak different dialects of a Sino-Tibetan language (Chinese), whereas Uyghurs are Turkic speakers and Sibos are Tungusic speakers. Both of the latter two languages belong to the Altaic language family.

DNA from bloodstain samples was extracted by using the QIAamp Tissue kit (Qiagen, Hilden). DNA extraction from hair samples was done according to published protocols (Higuchi et al. 1988). To overcome an inhibitory effect of a high salt concentration in the polymerase chain reaction (PCR), buccal samples from the Shanghai population were desalted on a Microcon100 filter (Amicon, Beverly, MA). All samples were obtained anonymously through local physicians and with consent of the participants.

Analysis of Alu Insertion Polymorphisms. Eight human-specific nuclear polymorphic Alu insertions, TPA25, PV92, APO, ACE, FXIIIB, DI, A25, and B65, were analyzed in the four population samples. Primer sequences for all loci have been described previously (Arcot et al. 1995a; Arcot et al. 1995b; Batzer et al. 1996). The loci TPA25, PV92, DI, and FXIIIB were, respectively, amplified in a single locus PCR reaction as published by Batzer et al. (1996).

Results

Genetic Variation within and between Populations. A total of 323 individuals from four Chinese populations were typed for the eight Alu insertion polymorphic loci. For each locus, the frequency of the Alu element in each population was recorded (Table 1). All loci were polymorphic in all populations, with the lowest level of polymorphism at A25. Exact tests showed that all loci in each population met HWE expectations except for FXIIIB in the Shanghai (p = 0.036) and DI in the Guangzhou populations (p = 0.023). In addition, exact tests also showed that there were significant genotype associations in the Uyghurs in 4 out of 28 locus pairs (TPA25 / APO, p = 0.025; PV92 / ACE, p = 0.003; ACE / B65, p = 0.018, and DI / B65, p = 0.018). However, when a Bonferroni correction for multiple testing was applied, all the tests for HWE expectations and genotype associations were not statistically significant.

Heterozygosity and associated standard error for each locus for each population are given in Table 2. All populations exhibited high levels of diversity at most of the loci, some of which have values approaching the theoretical maximum heterozygosity of 0.5 for a biallelic marker. The heterozygosity for APO and A25 were relatively low in all populations. The average heterozygosity over all eight loci for each population was substantial and varied from 0.329 in the Shanghai and Guangzhou populations to 0.364 in the Uyghurs (Table 2).

The GST value for each locus (Table 2) was calculated in order to measure the degree of gene differentiation between these populations. They ranged from a low of 0 for TPA25 to a high of 0.095 for PV92; for PV92 and ACE the values were statistically significantly different from 0, as determined by exact tests of the allele frequencies. The tests showed significant differences in the frequencies of the Alu element between the four populations at these two loci (data not shown). The GST value for all loci was 0.020, which could mean that 2.0% of the total variance in allele frequency differences at these loci was due to differences between the populations and 98.0% was due to differences within the populations. This value was highly significantly different from 0 by Fisher's exact test of the allele frequencies for all the loci (data not shown).

Determination of Population Relationships. To investigate the relationship of the four Chinese populations as well as the relationship with global populations, we analyzed the data of the present study together with the data on the same eight loci from 29 worldwide populations reported by Stoneking et al. (1997). The allele frequency for each locus in each population was used to calculate the Nei's standard distances (Nei 1972) between the populations. Based on this distance matrix, a neighbor-joining (NJ) tree relating the 33 global populations was constructed (Figure 2).

On the tree, all the African populations clustered together, as did the Sahul (Australia and New Guinea) and the European populations. The tree showed that all the East Asian populations except Uyghurs clustered together, which is supported by 38% of the bootstrap value. The bootstrap values observed within the cluster of the East Asians were very small, which reflected that information based on the eight Alu polymorphic loci was insufficient to resolve the relationships between these geographically close populations. The Western Asian populations did not cluster together on the tree.

Two North American Natives (Alaska and Greenland) were placed clearly outside the cluster of the East Asians. The Uyghur population lay between the West Asians and the cluster consisting of East Asians and North American Natives, indicating that the Uyghurs have a genetic composition intermediate between those of Europeans and East Asians. It has been suggested that such a pattern in Uyghurs was probably due to an admixture of already differentiated Europeans and East Asians rather than to an intermediate position in a general Eurasian cline (Zhao and Lee 1989; Comas et al. 1998). The admixture proportion (m) in the Uyghurs was estimated from the distance matrix between the populations calculated from the frequencies of the Alu element at the eight loci by the triangle method of Cavalli-Sforza et al. (1994, p. 57). Three European (French, Breton, and Swiss) and the four other Chinese (Shanghai, Guangzhou, Sibo, and Southern Chinese Han) populations were used as the putative source populations for the calculation. The proportion of European admixture in the Uyghurs found by this method was 36.3%.

As the ancestral state of these Alu insertion polymorphisms is known with certainty to be the absence of an Alu element, we rooted the tree with a hypothetical ancestral population in which the frequency of the Alu element at each locus was set to zero. Inclusion of this ancestral population placed the root within the cluster of African populations as indicated by the arrow in Figure 2. This provides additional evidence for the support of the "out-of-Africa" hypothesis of modern humans (Cann et al. 1987; Bowcock et al. 1994).

The population relationship was also calculated using a principal component analysis (Cavalli-Sforza et al. 1994) of the allele frequencies at the eight loci (Figure 3). The first two principal components, which account for 83% of the variation in allele frequencies, were used to plot the positions of the populations. All the African populations are closest to the Ancestral population in the first PC, which would be consistent with the African origin of modern humans. The second PC placed the population relationships similar to those observed in the NJ tree. However, geographic clusters of the East Asian populations were not as evident as in the NJ tree, in which the India-Christian group was close to the East Asian populations, whereas the Filipinos were close to the two West Asian populations (India-Hindu and Tamil), as were the Uyghurs. The Pakistani and United Arab Emirates (UAE) populations were found to lie between the Europeans and other West Asians, showing more concordance with geography than the NJ tree. The Uyghurs approximately fell between the East Asians and the West Asians, which supports the admixture scenario for this population. When the hypothetical ancestral population, with the allele frequency at each locus set to zero, was removed, the same pattern of population distributions was observed.

Gene Flow between Populations. To estimate the relative amount of gene flow experienced by each population studied, we plotted the heterozygosity of each population against the distance of the population from the centroid (the overall mean allele frequencies of the populations) (Harpending and Ward 1982). This model assumes a linear relationship between the heterozygosity of a population and the distance of the population from the centroid. In a population that has received more gene flow than average, the heterozygosity will be higher than predicted by the model; in a more isolated population, the heterozygosity will be lower than predicted. In Figure 4A, the two minority populations, especially the Uyghurs, showed a greater heterozygosity than predicted, whereas the two Han populations had a lower heterozygosity than predicted. This implies that the two minority populations have received more gene flow than average, while the two Han groups are more isolated.

We also performed this centroid analysis by pooling the data of the present study with the 29 worldwide populations (Stoneking et al. 1997) included in the phylogenetic analysis (Figure 4B). All six African and two West Asian populations (Tamil and India-Christians) showed greatly higher heterozygosities than predicted, while all four Chinese populations exhibited lower values than predicted. The greater African heterozygosities have been interpreted as evidence supporting the "out-of-Africa" hypotheses and a larger effective population size in Africa (Stoneking et al. 1997). Inclusion of the four Chinese populations in the centroid analysis showed again a greater heterozygosity in African populations, which led to the further support for the African origin of modern humans in East Asia.
Discussion

Recently, Alu insertion polymorphisms have been used to study the relationships of human populations (Batzer et al. 1996; Stoneking et al. 1997). In the present study, we report the allele frequencies of eight polymorphic Alu insertions in four Chinese populations from three ethnic groups. Significant departures from HWE expectations were observed for 2 of 32 exact tests (6.3%). This is slightly higher than the 5% expected from chance alone, and may still represent normal statistical fluctuations. Significant genotype associations were detected in the Uyghurs in 4 out of 28 locus pairs (14.3%). This is higher than the 5% expected by chance alone, probably reflecting genetic substructure or admixture in this population. This observation is consistent with the population history, which suggests a substantial gene flow from Europe (Zhao and Lee 1989).

A significant variability between the four populations was observed with the GsT value of 0.020, confirming the genetic heterogeneity of the Chinese nation (Zhao and Lee 1989; Etler 1992; Chu et al. 1998; Su et al. 1999). However, the GST value obtained for the four Chinese populations was lower than those observed in most parts of the world except for Europe (GST = 0.011) and Sahul (Australia and New Guinea; GST = 0.001) (Stoneking et al. 1997). Substantial internal migrations in the history of Chinese populations (Cavalli-Sforza et al. 1994) probably reduced the extent of gene differentiation between these populations. The GST value based on the eight Alu polymorphic loci was found to be higher than that observed for four nuclear microsatellite loci in the same population set (GST = 0.011, unpublished data). This could be attributed to the high microsatellite mutation rates producing the high level of within-population diversity relative to the total diversity (Jin and Chakraborty 1995).

The NJ tree in Figure 2 showed that the East Asian populations, except Uyghurs, form a single cluster, supporting a single origin for East Asians (Chu et al. 1998; Su et al. 1999). However, this cluster is only supported by 38% of the bootstrap value. Moreover, very small bootstrap values were observed within the cluster of the East Asians. To resolve the relationship between these closely related populations between which migrations could be substantial, the number of Alu polymorphic loci should be increased. In addition, the current study involved only four populations from China. A study of large quantities of Alu polymorphisms on a representative sample of Chinese populations across the country is necessary to provide a genetic perspective for the origin of East Asians.

The Uyghur population is living in a region of Central Asia along the Silk Road trade route. Previous studies of the Uyghur population based on classical and mtDNA control-region sequence polymorphisms revealed genetic admixture with European populations (Zhao and Lee 1989; Comas et al. 1998). The NJ tree and PC analysis in this study indicated that the Uyghurs have a genetic composition intermediate between those of Europeans and East Asians. Such a pattern for the Uyghurs could be due to either an admixture of Europeans and East Asians or an intermediate position in a general Eurasian gradient. However, the greater heterozygosity of the Uyghurs (Figure 4A) could reflect admixture (Batter et al. 1996). In addition, the significant genotype associations between unlinked loci observed for the Uyghurs could be argued as evidence for admixture. The results of this study therefore support the scenario that the Uyghurs might have originated from an admixture between Europeans and East Asians. Further studies of the Y-chromosome haplotypes and mtDNA sequences in the Uyghurs of our study have provided additional evidence for the admixture scenario (Xiao et al. in preparation). The proportion of European admixture in the Uyghurs found by the method of Cavalli-Sforza (1994) in this study is m = 0.36, which is lower than the estimates from classical markers (m = 0.53; Zhao and Lee 1989) and mtDNA sequence polymorphisms (m = 0.55; Comas et al. 1998). However, a more profound study of the mtDNA sequence types in the Uyghur population sampled in East Kazakhstan, only 18 km from the boundary with China, showed that approximately 35% of the sequences could be attributed to European origins (Comas et al. 1998).

The mechanism for the generation of admixture of East Asian and European genes in Central Asia is less clear. Based on the recent discovery of mummified bodies in Xinjiang and linguistic evidence, the presence of Europeans in this region can be established to be as early as 4000 years ago (Han 1986). During the Han Dynasty (206 B.C.-A.D. 220) and the Tang Dynasty (A.D. 618-A.D. 907), the Silk Road trade route was established from Xian (capital of the Han and Tang dynasties) through Central Asia to the Mediterranean Sea. Traveling over the Silk Road, many European traders settled within China (Jian 1983). During the 3rd and 4th centuries A.D., Turkic nomads of Siberian origin occupied Central Asia and replaced the Indo-European people in this region. The presence of European admixture in the Uyghurs might be mainly attributed to earlier European founders in Central Asia, and enhanced by the subsequent settlement of European traders along the Silk Road in ancient China.

The relative amount of gene flow experienced by each population was estimated using the island model of Harpending and Ward (1982). The two minority populations, especially the Uyghurs, showed a greater heterozygosity than predicted by the model, implying that they have received more gene flow. A great extent of European admixture could be a main reason for the greater heterozygosity in the Uyghurs. Furthermore, repeated invasions of Mongolian nomads from the north over thousands of years (Cavalli-Sforza et al. 1994) could also have contributed to the increased heterozygosity in these two northern populations. In addition, since China was politically unified in 221 B.C. Chinese minorities have partly integrated into Han society and adopted Han language and culture. As a result, a certain degree of gene flow occurred from the local Han populations to these minorities. This gene flow could have contributed to an even greater heterogeneity in the Uyghurs and Sibos.

In conclusion, this study provides evidence for the genetic heterogeneity of the Chinese nation. The constructed NJ tree shows that there is a close genetic affinity among the East Asian populations. The Uyghur population might have originated from an admixture between Europeans and East Asians. This study also provides further support for the "out-of-Africa" hypothesis of modem humans in East Asia.

Acknowledgments We wish to thank all DNA donors who made this study possible. This work was supported by the Fund for Scientific Research (Flanders, Belgium) through grant G.0241.98. FX is the recipient of a doctoral scholarship from the University of Leuven (reference: DB/99/38).

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FENG-XIA XIAO,1,2 JUN-FANG YANG,3 JEAN-JACQUES CASSIMAN,1 AND RONNY DECORTE1

1Center for Human Genetics, University of Leuven, Leuven, Belgium.

2Research Center, Hospital Sainte-Justine, Montreal, Quebec, Canada.

3Department of Internal Medicine, People's Hospital of Yining, Xinjiang, P. R. China

Human Biology, August 2002, v. 74, no. 4, pp. 555-568.

Copyright (C) 2002 Wayne State University Press, Detroit, Michigan 48201-1309

Copyright Wayne State University Press Aug 2002
Provided by ProQuest Information and Learning Company. All rights Reserved

Unregistered
06-09-06, 10:10
I have also read an article about DNA tests.
The DNA of Uighurs, Kazak,Kiyrgiz are very much similar to Turkish and British.
Greeks, French, German,Italians have similar DNA.
I was a bit surprised when I read that the Turkish has quite different DNA from the Greeks but very much similar to the British and Uighurs.

Unregistered
06-09-06, 10:26
I have also read an article about DNA tests.
The DNA of Uighurs, Kazak,Kiyrgiz are very much similar to Turkish and British.
Greeks, French, German,Italians have similar DNA.
I was a bit surprised when I read that the Turkish has quite different DNA from the Greeks but very much similar to the British and Uighurs.




Uyghurlarning DNA analizi heqqidiki u eser bir kitap, bu bir bapi qalghan qisminimu shu aderestin köchürüp qoyghan bolsanglar!

Unregistered
06-09-06, 11:17
*******In addition, since China was politically unified in 221 B.C. Chinese minorities have partly integrated into Han society and adopted Han language and culture. As a result, a certain degree of gene flow occurred from the local Han populations to these minorities. This gene flow could have contributed to an even greater heterogeneity in the Uyghurs and Sibos.

In conclusion, this study provides evidence for the genetic heterogeneity of the Chinese nation. The constructed NJ tree shows that there is a close genetic affinity among the East Asian populations. The Uyghur population might have originated from an admixture between Europeans and East Asians. This study also provides further support for the "out-of-Africa" hypothesis of modem humans in East Asia. *******

Yukarki makalining bu uzundiki yekuni tihimu kizkken.
Hitaylar uyghurlar 221 B.C yillardilam hitayning bir kismitti dimekqikenghu?

Unregistered
06-09-06, 14:30
In addition, since China was politically unified in 221 B.C. Chinese minorities have partly integrated into Han society and adopted Han language and culture. As a result, a certain degree of gene flow occurred from the local Han populations to these minorities. This gene flow could have contributed to an even greater heterogeneity in the Uyghurs and Sibos.


Bu xitaylaraning dimekchi bolghini Xitay miladidin burunqi 221-yildin bashlapla siyasi jehette birlikke kelgenmish (Sherqiy Türkistanni 18-esirde bésip alghini yadida yoq iken). Shunga, Uyghurlarning DNA sidiki asiya genesi, xitaylar bilen arilishishtin kelgenmish (Bu mangqurtlargha Uyghurlarning bir bölikining hazirqi Mongholiye tewesidiki Urxun derya wadiliridin köchüp kelgenliki we bir qisim yerlik kawakziye irqidiki Toxarilar bilen arilishishidin hazirqi Uyghurlar wujutqa kelgenlikidek pakit ayding emestek).

Dimekchi bolghini, Sherqiy Türkistan ezeldin Xitayning birqismi we Uyghurlar ezeldin xitayning qolida yashighan digen xitay showinizm idiyesini ilgiri sürmekchi. Körünüp turuptu, meyli xitayning siyasioni we ilmiy xadimlirida bolsun, hemmisi chong xitaychiliq idiyesidin saqit emes.

Unregistered
06-09-06, 15:22
Xunqe uzun tarihka ige Hitay nime uqun terekkiyatta egexip yaxaxka mahir bolup, likin terekkiyatni baxlap mingix kolidin kelmeydu. Buningdiki eng assalik sewep ular neqqe ming yillik yalghanqilik medinyitige ige eng mexhur millet.
Muxu dunyada yalghanqini sinaydighan birdin bir nerse "science (ilim-pen)", xuning uqun hitaylar muxu nuhtida mengguluk yingilguqi mehluklar. Xuning uqun uning dunya hojaynigha aylinix hiyali hergiz emelge axmaydu. Qunki hitay ozidiki bu medinyetni tuyuksiz ozgertelmeydu.