Bozur
Amicus
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Post by Bozur on Dec 16, 2011 13:59:31 GMT -5
July 02, 2010 Admixture in Uyghurs (again)
Gene Expression points me to this letter which suggests that Western Eurasian admixture in Uyghurs has been overestimated in previous studies. They base their claim on the alleged low population coverage of previous studies. I don't buy their argument, mainly because of Behar et al. (2010) which has as good a coverage of Eurasia as one might hope for, and finds (expectedly) Uyghurs to be about a 50-50 Caucasoid/Mongoloid mix. The same is also true for Hazara, shown by the authors as majority Mongoloid, but revealed by Behar et al. (2010) to be about 50-50 as well.
The authors make another claim: STRUCTURE cannot distinguish recent admixture from a cline of other origin, and these analyses cannot prove admixture in the Uyghurs; however, historical records indicate that the present Uyghurs were formed by admixture between Tocharians from the west and Orkhon Uyghurs (Wugusi-Huihu, according to present Chinese pronunciation) from the east in the 8th century CE.14 The Uyghur Empire was originally located in Mongolia and conquered the Tocharian tribes in Xinjiang. Tocharians such as Kroran have been shown by archaeological findings to appear phenotypically similar to northern Europeans,15 whereas the Orkhon Uyghur people were clearly Mongolians. The two groups of people subsequently mixed in Xinjiang to become one population, the present Uyghurs. We do not know the genetic constitution of the Tocharians, but if they were similar to western Siberians, such as the Khanty, admixture would already be biased toward similarity with East Asian populations. First of all, the authors forget about the eastern Iranian peoples (Sakas) who most surely were present among the ancestors of the Uyghurs. Second, there is no reason to think that Tocharians were similar to the Khanty, a population with a substantial presence of northern Eurasian Y-haplogroup N does not make a link with Uyghurs likely.
Am J Hum Genet. 2009 December 11; 85(6): 934–937.
Genetic Landscape of Eurasia and “Admixture” in Uyghurs
Hui Li et al. dienekes.blogspot.com/2010/07/admixture-in-uyghurs-again.htmlwww.ncbi.nlm.nih.gov/pmc/articles/PMC2790568/
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Bozur
Amicus
Posts: 5,515
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Post by Bozur on Dec 16, 2011 15:10:38 GMT -5
June 30, 2009 Uyghurs as an admixed not source population (Xu et al. 2009)
This paper is interesting not so much because it estimates admixture in Uyghurs (click on the post label for previous studies on the topic), but because it explicitly rejects the hypothesis that they are a source ("donor") population.
If a population has substantial genetic variation which overlaps with that of two other groups, then there are two possible interpretations: It represents the population from which the other two groups sprang, or at least contributed genes to both of them It represents a mixture of the two other groups What this paper does, is to show that Uyghurs are best explained as a mixture of Caucasoids and Mongoloids (#2) rather than #1.
Molecular Biology and Evolution, doi:10.1093/molbev/msp130
Haplotype Sharing Analysis Showing Uyghurs Are Unlikely Genetic Donors
Shuhua Xu et al.
Abstract
The Uyghur are a group of people primarily residing in Xinjiang of China which is geographically located in Central Asia, from where modern humans were presumably spread in all directions reaching Europe, east and northeast Asia about 40 kya. A recent study suggested that the Uyghur are ancestry donors of the East Asian gene pool. However, an alternative hypothesis, i.e. the Uyghur is an admixture population with both East Asian (EAS) and European (EUR) ancestries is also supported by our previous studies. To test the two competing hypotheses, here we conducted a haplotype sharing analysis based on empirical and simulated data of high density single nucleotide polymorphisms (SNPs). Our results showed that more than 95% of Uyghur (UIG) haplotypes could be found in either East Asian (EAS) or European (EUR) populations, which contradicts the expectation of the null models assuming that UIG are donors. Simulation studies further indicated that the proportion of UIG private haplotypes observed in empirical data is only expected in alternative models assuming that UIG is an admixture population. Interestingly, the estimated ancestry contribution of 44%:56% (EAS:EUR) based on haplotype sharing analysis is consistent with our previous estimation with STRUCTURE analysis. Although the history of Uyghurs could be complex, our method is explicit and conservative in rejecting the null hypothesis. We concluded that the gene pool of modern Uyghurs is more likely a sole recipient with contribution from both EAS and EUR.
dienekes.blogspot.com/2009/06/uyghurs-as-admixed-not-source.html
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Bozur
Amicus
Posts: 5,515
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Post by Bozur on Dec 16, 2011 16:12:06 GMT -5
August 30, 2008 Admixture mapping in Uyghurs
This is a followup to this earlier study. Note that the "European" label for the Caucasoid component in Uyghurs is inappropriate, since this is composed of href="http://dienekes.blogspot.com/2008/02/huge-paper-on-human-genetic.html">two distinct "European" and "Caucasoid Central Asian" elements.
From the paper: Figure 3A shows summary plot of individual admixture proportions based on the highest-probability run of ten STRUCTURE runs. The results show that individuals from the same population often share membership coefficients in the inferred cluster, with the exception that one Japanese outlier shows obvious admixture. Mongola, Adygei, and Russian individuals show some degree of admixture as well. Most of the EAS admixture in the Adygei from the Caucasus seems mostly spurious, as the Adygei have a substantial "Central Asian" Caucasoid component (38%) rather than Mongoloid admixture (2%).
Note that, as in the previous study, the Uyghur individuals seem to have similar proportions of "Western" and "Eastern" genes, due to the fact that the blend which produced them is fairly old and there are really no individuals in which either of the two components predominate.
The American Journal of Human Genetics, doi:10.1016/j.ajhg.2008.08.001
A Genome-wide Analysis of Admixture in Uyghurs and a High-Density Admixture Map for Disease-Gene Discovery
Shuhua Xu and Li Jin Abstract
Following up on our previous study, we conducted a genome-wide analysis of admixture for two Uyghur population samples (HGDP-UG and PanAsia-UG), collected from the northern and southern regions of Xinjiang in China, respectively. Both HGDP-UG and PanAsia-UG showed a substantial admixture of East-Asian (EAS) and European (EUR) ancestries, with an empirical estimation of ancestry contribution of 53:47 (EAS:EUR) and 48:52 for HGDP-UG and PanAsia-UG, respectively. The effective admixture time under a model with a single pulse of admixture was estimated as 110 generations and 129 generations, or admixture events occurred about 2200 and 2580 years ago for HGDP-UG and PanAsia-UG, respectively, assuming an average of 20 yr per generation. Despite Uyghurs' earlier history compared to other admixture populations, admixture mapping, holds promise for this population, because of its large size and its mixture of ancestry from different continents. We screened multiple databases and identified a genome-wide single-nucleotide polymorphism panel that can distinguish EAS and EUR ancestry of chromosomal segments in Uyghurs. The panel contains 8150 ancestry-informative markers (AIMs) showing large frequency differences between EAS and EUR populations (FST > 0.25, mean FST = 0.43) but small frequency differences (7999 AIMs validated) within both populations (FST < 0.05, mean FST < 0.01). We evaluated the effectiveness of this admixture map for localizing disease genes in two Uyghur populations. To our knowledge, our map constitutes the first practical resource for admixture mapping in Uyghurs, and it will enable studies of diseases showing differences in genetic risk between EUR and EAS populations.
www.cell.com/AJHG/abstract/S0002-9297(08)00439-4dienekes.blogspot.com/2008/08/admixture-mapping-in-uyghurs.html
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Bozur
Amicus
Posts: 5,515
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Post by Bozur on Dec 16, 2011 16:27:37 GMT -5
March 25, 2008 Origins of the Uighur
Interesting bit from the paper: Notably, the distribution of admixture proportions among UIG individuals is relatively even, with 48.7% the lowest admixture from European ancestry and the highest 62.2%. The standard deviation is only 3.8%, which is much smaller than the estimation for the African-American (AfA) population,58 suggesting a much longer history of admixture events for the Uyghur population compared with the AfA population.
The American Journal of Human Genetics, doi:10.1016/j.ajhg.2008.01.017
Analysis of Genomic Admixture in Uyghur and Its Implication in Mapping Strategy
Shuhua Xu et al.
Abstract
The Uyghur (UIG) population, settled in Xinjiang, China, is a population presenting a typical admixture of Eastern and Western anthropometric traits. We dissected its genomic structure at population level, individual level, and chromosome level by using 20,177 SNPs spanning nearly the entire chromosome 21. Our results showed that UIG was formed by two-way admixture, with 60% European ancestry and 40% East Asian ancestry. Overall linkage disequilibrium (LD) in UIG was similar to that in its parental populations represented in East Asia and Europe with regard to common alleles, and UIG manifested elevation of LD only within 500 kb and at a level of 0.1 < style="font-weight: bold;">we estimated that the admixture event of UIG occurred about 126 [107∼146] generations ago, or 2520 [2140∼2920] years ago assuming 20 years per generation. In spite of the long history and short LD of Uyghur compared with recent admixture populations such as the African-American population, we suggest that mapping by admixture LD (MALD) is still applicable in the Uyghur population but ∼10-fold AIMs are necessary for a whole-genome scan. dienekes.blogspot.com/2008/03/origins-of-uighur.htmlwww.cell.com/AJHG/abstract/S0002-9297(08)00166-3
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Post by uz on Dec 16, 2011 16:28:24 GMT -5
BOZUR IS ON A ROLL TODAY !!! ;D
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