Genetic Origins and Sex-Biased Admixture of the Huis

The Hui people are unique among Chinese ethnic minorities in that they speak the same language as Han Chinese (HAN) but practice Islam. However, as the second-largest minority group in China numbering well over 10 million, the Huis are under-represented in both global and regional genomic studies. Here, we present the first whole-genome sequencing effort of 234 Hui individuals (NXH) aged over 60 who have been living in Ningxia, where the Huis are mostly concentrated. NXH are genetically more similar to East Asian than to any other global populations. In particular, the genetic differentiation between NXH and HAN (F_ST = 0.0015) is only slightly larger than that between northern and southern HAN (F_ST = 0.0010), largely attributed to the western ancestry in NXH (∼10%). Highly differentiated functional variants between NXH and HAN were identified in genes associated with skin pigmentation (e.g., SLC24A5), facial morphology (e.g., EDAR), and lipid metabolism (e.g., ABCG8). The Huis are also distinct from other Muslim groups such as the Uyghurs (F_ST = 0.0187), especially, NXH derived much less western ancestry (∼10%) compared with the Uyghurs (∼50%). Modeling admixture history indicated that NXH experienced an episode of two-wave admixture. An ancient admixture occurred ∼1,025 years ago, reflecting the intensive west–east contacts during the late Tang Dynasty, and the Five Dynasties and Ten Kingdoms period. A recent admixture occurred ∼500 years ago, corresponding to the Ming Dynasty. Notably, we identified considerable sex-biased admixture, that is, excess of western males and eastern females contributing to the NXH gene pool. The origins and the genomic diversity of the Hui people imply the complex history of contacts between western and eastern Eurasians.     

The Admixture Linkage Disequilibrium and Genetic Linkage Inference on the Gradual Admixture Population

Through the theoretical analysis of the admixture linkage disequilibrium (ALD) in the gradual admixture (GA) model, in which admixture occurs in every generation, the ALD is found to be proportional to the difference in marker allele frequencies, p₁-p₂, between two subpopulations. Based on this property, we can employ a strict monotonic function (Δ_ker=Δ/(p₁-p₂), where Δ denotes the linkage disequilibrium (LD)) of the recombination fraction between the marker locus and the disease locus to infer the true genetic linkage. We construct a quasi likelihood ratio test (LRT) for the case-only data utilizing the information of unlinked markers in the human genome. The simulation results show that our tests can be used to fine map a disease locus. The effects of parameter values in the ALD mapping are also discussed.     

渐近混合群体的混合连锁不平衡及其遗传连锁推断

在渐近混合模型中,混合现象发生在每一世代,通过对其混合连锁不平衡的理论分析,发现混合连锁不平衡与两个子群体间的基因频率差成正比。基于这一点,构造了一个对重组率严格单调的函数（△ker=△／（p1-p2）,其中△代表连锁不平衡）,进而据此推断标记基因座与疾病基因座的遗传连锁。应用人类基因组上不连锁的标记基因提供的连锁不平衡信息,基于病人组数据构造了一个准似然比统计量。模拟结果显示,此检验可用于精确的基因定位。文章亦讨论了参数对检验的影响。     

Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes

Throughout its distribution across Eurasia, domestic pig (Sus scrofa) populations have acquired differences through natural and artificial selection, and have often interbred. We resequenced 80 Eurasian pigs from nine different Asian and European breeds; we identify 42,288 reliable SNPs on the Y chromosome in a panel of 103 males, among which 96.1% are newly detected. Based on these new data, we elucidate the evolutionary history of pigs through the lens of the Y chromosome. We identify two highly divergent haplogroups: one present only in Asia and one fixed in Europe but present in some Asian populations. Analyzing the European haplotypes present in Asian populations, we find evidence of three independent waves of introgression from Europe to Asia in last 200 years, agreeing well with the literature and historical records. The diverse European lineages were brought in China by humans and left significant imprints not only on the autosomes but also on the Y chromosome of geographically and genetically distinct Chinese pig breeds. We also find a general excess of European ancestry on Y chromosomes relative to autosomes in Chinese pigs, an observation that cannot be explained solely by sex-biased migration and genetic drift. The European Y haplotype is associated with leaner meat production, and we hypothesize that the European Y chromosome increased in frequency in Chinese populations due to artificial selection. We find evidence of Y chromosomal gene flow between Sumatran wild boar and Chinese pigs. Our results demonstrate how human-mediated admixture and selection shaped the distribution of modern swine Y chromosomes.     

Reconstructing the Human Genetic History of Mainland Southeast Asia: Insights from Genome-Wide Data from Thailand and Laos

Thailand and Laos, located in the center of Mainland Southeast Asia (MSEA), harbor diverse ethnolinguistic groups encompassing all five language families of MSEA: Tai-Kadai (TK), Austroasiatic (AA), Sino-Tibetan (ST), Hmong-Mien (HM), and Austronesian (AN). Previous genetic studies of Thai/Lao populations have focused almost exclusively on uniparental markers and there is a paucity of genome-wide studies. We therefore generated genome-wide SNP data for 33 ethnolinguistic groups, belonging to the five MSEA language families from Thailand and Laos, and analyzed these together with data from modern Asian populations and SEA ancient samples. Overall, we find genetic structure according to language family, albeit with heterogeneity in the AA-, HM-, and ST-speaking groups, and in the hill tribes, that reflects both population interactions and genetic drift. For the TK speaking groups, we find localized genetic structure that is driven by different levels of interaction with other groups in the same geographic region. Several Thai groups exhibit admixture from South Asia, which we date to ∼600–1000 years ago, corresponding to a time of intensive international trade networks that had a major cultural impact on Thailand. An AN group from Southern Thailand shows both South Asian admixture as well as overall affinities with AA-speaking groups in the region, suggesting an impact of cultural diffusion. Overall, we provide the first detailed insights into the genetic profiles of Thai/Lao ethnolinguistic groups, which should be helpful for reconstructing human genetic history in MSEA and selecting populations for participation in ongoing whole genome sequence and biomedical studies.     

汉族群体23个Y染色体双等位基因标记遗传多态性研究

为了筛选在汉族群体中具有多态性的Y染色体双等位基因标记并获取其群体遗传学数据。采用片段长度差异等位基因特异性PCR和PAGE技术对武汉地区160名男性汉族无关个体的23个Y染色体双等位基因标记（M7,M9,M50,M88,M89,M95,M111,M117,M119,M121,M122,M134,M159,M164,M175,M214,LINE1,MSY2,RPS4Y711,SRY＋465,IMS-JST164520,IMS-JST021354和IMS-JST003305）进行分型。除M50、M159和M164外,其余20个标记在武汉汉族群体中均具有遗传多态性,其基因多样性（GD）范围为0.0126～0.4855,共检出35种不同单体群组合（Hg1～35）,单体群多样性（HD）为0.9471。表明20个Y染色体双等位基因标记组成的单体群具有较高的遗传多样性,在法医学应用和群体进化研究中具有较高的实用价值。     

Ancient DNA evidence supports the contribution of Di‐Qiang people to the han Chinese gene pool

Han Chinese is the largest ethnic group in the world. During its development, it gradually integrated with many neighboring populations. To uncover the origin of the Han Chinese, ancient DNA analysis was performed on the remains of 46 humans (～1700 to 1900 years ago) excavated from the Taojiazhai site in Qinghai province, northwest of China, where the Di‐Qiang populations had previously lived. In this study, eight mtDNA haplogroups (A, B, D, F, M*, M10, N9a, and Z) and one Y‐chromosome haplogroup (O3) were identified. All analyses show that the Taojiazhai population presents close genetic affinity to Tibeto‐Burman populations (descendants of Di‐Qiang populations) and Han Chinese, suggesting that the Di‐Qiang populations may have contributed to the Han Chinese genetic pool. Am J Phys Anthropol, 2011. © 2010 Wiley‐Liss, Inc.     

江苏常熟地区汉族人群47个微单倍型的遗传多态性及遗传结构分析

目的 探索江苏常熟地区汉族人群在47个常染色体微单倍型基因座的遗传多态性,评估应用效能及法庭科学参数。方法 采用MHSeqTyper47混合DNA鉴定试剂盒进行基因座复合扩增及文库构建,使用MiSeq FGx测序平台进行测序,测得的数据应用MHTyper数据分析软件进行分析,对获得的样本遗传信息进行评估,结合千人基因组数据（1000 Genomes Project phase 3,1KG）评估群体间遗传分化指数及遗传距离,并计算法庭科学参数。结果 江苏常熟地区汉族人群与1KG中的中国北京群体的遗传分化和遗传距离最小,并得到最接近的有效等位基因数（A_e）,累积随机匹配概率（combined matching probability,CMP）与1KG中东亚参考人群的5个群体均接近,为1.25×10^-36,累积非父排除概率达0.999 999 999 964 1。结论 本研究报告了47个微单倍型基因座在江苏常熟地区汉族人群中的等位基因频率及遗传多态性信息,为47个微单倍型在法医学应用中提供了数据基础。另外,比较了1KG参考人群与江苏常熟地区汉族人群的多态性差异,并揭示了47个微单倍型在江苏常熟地区汉族人群中的遗传结构。总的来说,1KG中的东亚人群参考数据更符合江苏常熟地区汉族人群的遗传特征。     

Demographic Inference Reveals African and European Admixture in the North American Drosophila melanogaster Population

Drosophila melanogaster spread from sub-Saharan Africa to the rest of the world colonizing new environments. Here, we modeled the joint demography of African (Zimbabwe), European (The Netherlands), and North American (North Carolina) populations using an approximate Bayesian computation (ABC) approach. By testing different models (including scenarios with continuous migration), we found that admixture between Africa and Europe most likely generated the North American population, with an estimated proportion of African ancestry of 15%. We also revisited the demography of the ancestral population (Africa) and found—in contrast to previous work—that a bottleneck fits the history of the population of Zimbabwe better than expansion. Finally, we compared the site-frequency spectrum of the ancestral population to analytical predictions under the estimated bottleneck model.     

Fine-Scale Genetic Structure in the United Arab Emirates Reflects Endogamous and Consanguineous Culture,Population History,and Geography

The indigenous population of the United Arab Emirates (UAE) has a unique demographic and cultural history. Its tradition of endogamy and consanguinity is expected to produce genetic homogeneity and partitioning of gene pools while population movements and intercontinental trade are likely to have contributed to genetic diversity. Emiratis and neighboring populations of the Middle East have been underrepresented in the population genetics literature with few studies covering the broader genetic history of the Arabian Peninsula. Here, we genotyped 1,198 individuals from the seven Emirates using 1.7 million markers and by employing haplotype-based algorithms and admixture analyses, we reveal the fine-scale genetic structure of the Emirati population. Shared ancestry and gene flow with neighboring populations display their unique geographic position while increased intra- versus inter-Emirati kinship and sharing of uniparental haplogroups, reflect the endogamous and consanguineous cultural traditions of the Emirates and their tribes.     

环境因子对雉鸡甘肃亚种种群遗传多样性的影响(英文)

采用聚合酶链式反应(PCR)和直接测序的方法,测定了雉鸡甘肃亚种9个种群118个样本的线粒体DNA(mtDNA)控制区(D-loop)1150个碱基长度的基因序列,43个变异位点产生51个单倍型。环境因子与种群遗传变异的相关性研究表明,序列变异与经度(r=0.725,P<0.05)、年平均温度(r=0.833,P<0.05)呈显著正相关,核苷酸多样性与经度(r=0.686,P<0.05)、年平均温度(r=0.844,P<0.05)呈显著正相关。片段化与低温是导致雉鸡甘肃亚种遗传多样性的主要因素。序列变异及核苷酸多样性与温度的变异系数呈显著负相关(r序列=-0.679,P<0.05;r核苷酸=-0.669,P<0.05)。温度越稳定地区雉鸡甘肃亚种的遗传多样性越高。     

北京地区汉族人群21号染色体上5个STR基因座的遗传多态性

阐明21号染色体上唐氏综合征关键区域内或附近的5个STR基因座（D21S1413、D21S1446、D21S1437、D21S1411、D21S1412）在北京地区汉族人群中的结构特征和群体遗传学数据。Chelex法提取血DNA,PCR扩增后,应用聚丙烯酰胺凝胶电泳和银染法或基因片段扫描检测法进行STR分型,测序后确定STR基因座的主型和进行等位基因的命名。结果该5个STR基因座具有简单重复序列和遗传多态性,杂合度和多态信息含量高。它为唐氏综合征的基因诊断和产前基因诊断提供理论依据,也为这些遗传标记在我国人群中进行亲子鉴定和个体识别提供概率计算依据。Abstract: To elucidate the genetic polymorphisms of five STR loci on chromosome 21 in Chinese Han population and construct a preliminary database,EDTA-blood specimens were collected from unrelated individuals in Beijing. The DNAs were extracted with Chelex method and were amplified by PCR. The PCR products were analyzed by the PAG electrophoresis or by the approach of the automated fluorescent detection. The five STR loci consist of simple repeat motif and its distributions of genotypes are agreement with Hardy–Weinberg equation. Its polymorphism information content is all over 0.50. The obtained data can not only be used as evidences for genetic diagnosis of Down Syndrome, but also for calculating the probabilities in the paternity test and individual identification.     

Unbiased and Locally Efficient Estimation of Genetic Effect on Quantitative Trait in the Presence of Population Admixture

Summary Population admixture can be a confounding factor in genetic association studies. Family‐based methods ( Rabinowitz and Larid, 2000 , Human Heredity 50, 211–223) have been proposed in both testing and estimation settings to adjust for this confounding, especially in case‐only association studies. The family‐based methods rely on conditioning on the observed parental genotypes or on the minimal sufficient statistic for the genetic model under the null hypothesis. In some cases, these methods do not capture all the available information due to the conditioning strategy being too stringent. General efficient methods to adjust for population admixture that use all the available information have been proposed ( Rabinowitz, 2002 , Journal of the American Statistical Association 92, 742–758). However these approaches may not be easy to implement in some situations. A previously developed easy‐to‐compute approach adjusts for admixture by adding supplemental covariates to linear models ( Yang et al., 2000 , Human Heredity 50, 227–233). Here is shown that this augmenting linear model with appropriate covariates strategy can be combined with the general efficient methods in Rabinowitz (2002) to provide computationally tractable and locally efficient adjustment. After deriving the optimal covariates, the adjusted analysis can be carried out using standard statistical software packages such as SAS or R . The proposed methods enjoy a local efficiency in a neighborhood of the true model. The simulation studies show that nontrivial efficiency gains can be obtained by using information not accessible to the methods that rely on conditioning on the minimal sufficient statistics. The approaches are illustrated through an analysis of the influence of apolipoprotein E (APOE) genotype on plasma low‐density lipoprotein (LDL) concentration in children.     

云南泸西汉族17个Y-STR基因座多态性及遗传关系分析

调查云南泸西县汉族群体17个Y-STR基因座的多态性分布, 探讨其群体遗传学及法医学应用价值。应用AmpF?STR?Yfiler荧光标记复合扩增系统扩增156名汉族无关男性个体的17个Y-STR基因座, 用ABI3100遗传分析仪进行基因检测, 计算等位基因及单倍型频率, 并结合已公开发表的国内外其他16个群体的遗传学资料, 分析各群体间的遗传距离。云南泸西汉族男性群体中, 共观察到154种单倍型, 其中152种为仅观察到1次的单倍型, 2种单倍型观察到2次, 单倍型多样性(HD)值为0.9998, 基因多样性(GD)值在0.3901(DYS437)—0.9632(DYS385a/b)。17个群体遗传距离分析提示, 国内人群云南泸西汉族与湖南汉族的遗传距离最小(0.005), 与闽南汉族的遗传距离最大(0.035); 在中国周边群体中,云南泸西汉族与新加坡华人的遗传距离最小(0.015), 与日本人和马来西亚印度人群的遗传距离最大(0.060)。结果表明, 17个Y-STR基因座在云南泸西汉族中具有较高的遗传多态性, 适用当地的法医学应用。与其他民族群体的遗传多样性比较, 对了解各群体的起源、迁徙及相互关系有重要意义。     

Genetic diversity and population demography of narrow‐ridged finless porpoises from South Korea on the basis of mitochondrial DNA variation: Implications for its conservation in East Asia

The narrow‐ridged finless porpoise, Neophocaena asiaeorientalis, is a small cetacean inhabiting the coastal waters of Taiwan, East China, Korea, and Japan, and is threatened by anthropogenic pressures. We analyzed the mitochondrial control region of N. asiaeorientalis from Korean waters to better understand the genetic diversity, population structure, and demographic history through comparison with previously reported sequences from Japan and China. The network and phylogenetic analyses illustrated that few common haplotypes were centrally located, and that most of the unique haplotypes were on the edges of the branches. Moreover, the estimates of fixation indices and gene flow revealed significant genetic differentiation among the regions in East Asia. The mismatch distribution suggested a population expansion in the late Pleistocene. We propose that the current genetic variation in N. asiaeorientalis in East Asia was shaped by historical demographic expansion during the late Pleistocene. The N. asiaeorientalis of Korean waters has the highest diversity observed with the sampling available at this time. However, the abundance of N. asiaeorientalis in Korean waters has rapidly declined and the species needs protection from bycatch.     

DXS6804/DXS9896/GATA144D04基因座在中国汉族群体中的遗传多态性及其法医学应用

为了调查X染色体上DXS6804、DXS9896和GATA144D04等3个STR基因座在中国汉族群体的遗传多态性及其法医学应用价值,来用PCR和聚丙烯酰胺凝胶电泳对X染色体3个STR基因座进行分型,并检验女性基因型频率分布是否符合Hardy Weinberg平衡,计算法医学常用各种概率。DXS6804、DXS9896和GATA144D04的非父排除率分别为0 5990、0 6220、0 4280,表明3个STR基因座在中国汉族群体均具有遗传多态性,χ2检验表明女性的基因型频率分布符合Hardy Weinberg平衡。X染色体上的基因座DXS6804、DXS9896和GATA144D04在中国汉族群体中具有较高的遗传多态性,可应用于法医学检验和群体遗传学分析。     

DXS6804/DXS9896/GATA144D04基因座在中国汉族群体中的遗传多态性及其法医学应用Genetic

为了调查X染色体上DXS6804、DXS9896和 GATA144D04等3个STR基因座在中国汉族群体的遗传多态性及其法医学应用价值,来用PCR和聚丙烯酰胺凝胶电泳对X染色体3个STR基因座进行分型,并检验女性基因型频率分布是否符合Hardy-Weinberg平衡,计算法医学常用各种概率。DXS6804、DXS9896和 GATA144D04的非父排除率分别为0.5990、0.6220、0.4280,表明3个STR基因座在中国汉族群体均具有遗传多态性,χ2检验表明女性的基因型频率分布符合Hardy-Weinberg平衡。X染色体上的基因座DXS6804、DXS9896和 GATA144D04在中国汉族群体中具有较高的遗传多态性,可应用于法医学检验和群体遗传学分析。 Abstract： To investigate the genetic polymorphisms of three short tandem repeats loci of chromosome X in Chinese Han population in Chengdu area and its use in forensic science. Three X-chromosome linked short tandom repeat loci were analyzed by PCR followed by polyacrylamide gel electrophoresis. Hardy-Weinberg equilibrium was tested and forensic interested value was calculated .The power of exlcution of DXS6804、DXS9896和 GATA144D04 is 0.5990、0.6220、0.4280,respectively. The result showed that all the three STR loci were polymorphic among 100 unrelated females and 120 unrelated males from Chinese Han population. χ2 tests demonstrated that genotype frequencies in females did not depart from Hardy-Weinberg equilibrium. Three X-chromosome linked short tandem repeat loci have high polymorphism, they can be applied to forensic medicine and population genetics.