Argentine population genetic structure: large variance in Amerindian contribution

Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies.     

An anthropological genetic perspective on creolization in the anglophone caribbean

Variable socio‐cultural influences developed in the colonial Caribbean as a result of competing European hegemonic rule. In this study, we examine how colonial regulations regarding social hierarchies and mate choice worked to influence the genetic landscape of contemporary African Caribbean populations. To this end, 420 individuals from Dominica, Grenada, St. Kitts, St. Lucia, St. Thomas, St. Vincent, Jamaica, and Trinidad were genotyped for 105 autosomal ancestry informative markers. Based on these data, population substructure and admixture were assessed using an exact test, a model‐based clustering method, and principal components analysis. On average, individual admixture estimates of the pooled African Caribbean sample were 77% (SD ± 18%) West African, 15% (SD ± 15%) European, and 7.7% (SD ± 8%) Native American. In general, ancestry estimates were significantly different between Dominica and all other islands. Genetic structure analyses indicated subdivision into two subpopulations on most islands. Finally, unlike all of the other Caribbean populations that clustered adjacent to African populations, the Dominican population was more intermediate between the three parental groups in the principal components plot. As a result of the significant French influence throughout Dominican history, Dominica did not have the same cultural influences that typified other Anglophone colonies. Consequently, there were different social hierarchies and resulting mate choices on Dominica compared with the other considered islands. This study highlights the complex socio‐cultural history of a broad region of the Caribbean and attests to the interplay between social and biological factors in shaping the genetic diversity present in present‐day communities. Am J Phys Anthropol 151:135–143, 2013. © 2013 Wiley Periodicals, Inc.     

Association of African Genetic Admixture with Resting Metabolic Rate and Obesity Among Women

Objective: To investigate the role of genetic admixture in explaining phenotypic variation in obesity‐related traits in a sample of African‐American women (n = 145) and to determine significant associations between obesity traits and admixture genetic markers. Research Methods and Procedures: Associations between genetic admixture and BMI, resting metabolic rate, fat mass, fat‐free mass, and bone mineral density were tested using linear regression considering the estimation of admixture by 1) a maximum‐likelihood approach (MLA) and 2) a Bayesian analysis. Results: Both the conservative MLA and the Bayesian approach support an association between African genetic admixture and BMI. Evidence for the associations of African genetic admixture with fat mass and fat‐free mass was supported by the Bayesian analysis; the MLA supported an association with bone mineral density. When the individual ancestry informative markers that were used to estimate admixture were tested for associations with BMI, significant associations were identified in chromosomes 1, 11, and 12. Discussion: These results provide evidence supporting the application of admixture mapping methods to the identification of genes that result in higher levels of obesity among African‐American women. Further research is needed to replicate and further explore these findings.     

distruct: a program for the graphical display of population structure

In analysis of multilocus genotypes from structured populations, individual coefficients of membership in subpopulations are often estimated using programs such as structure . distruct provides a general method for visualizing these estimated membership coefficients. Subpopulations are represented as colours, and individuals are depicted as bars partitioned into coloured segments that correspond to membership coefficients in the subgroups. distruct , available at http://www.cmb.usc.edu/~noahr/distruct.html , can also be used to display subpopulation assignment probabilities when individuals are assumed to have ancestry in only one group.     

Clumpak: a program for identifying clustering modes and packaging population structure inferences across K

The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population‐genetic data analysis. Application of model‐based clustering programs often entails a number of steps, in which the user considers different modelling assumptions, compares results across different predetermined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present Clumpak (Cluster Markov Packager Across K), a method that automates the postprocessing of results of model‐based population structure analyses. For analysing multiple independent runs at a single K value, Clumpak identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software Clumpp . Next, Clumpak identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in Clumpp and simplifying the comparison of clustering results across different K values. Clumpak incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. Clumpak , available at http://clumpak.tau.ac.il , simplifies the use of model‐based analyses of population structure in population genetics and molecular ecology.     

随机SNP在全基因组关联研究人群分层分析中的应用

在复杂疾病的全基因组关联研究中,人群分层现象会增加结果的假阳性率,因此考虑人群遗传结构、控制人群分层是很有必要的。而在人群分层研究中,使用随机选择的SNP的效果还有待进一步探讨。文章利用HapMap Phase2人群中无关个体的Affymetrix SNP 6.0芯片分型数据,在全基因组上随机均匀选择不同数量的SNP,同时利用f值和Fisher精确检验方法筛选祖先信息标记（Ancestry Informative Markers,AIMs）。然后利用HapMap Phase3中的无关个体的数据,以F-statistics和STRUCTURE分析两种方法评估所选出的不同SNP组合对人群的区分效果。研究发现,随机均匀分布于全基因组的SNP可用于识别人群内部存在的遗传结构。文章进一步提示,在全基因组关联研究中,当没有针对特定人群的AIMs时,可在全基因组上随机选择3000以上均匀分布的SNP来控制人群分层。     

Admixture and patterns of linkage disequilibrium in a free-living vertebrate population

Linkage disequilibrium (LD), a measure of nonrandom association of alleles at different loci, is of great interest to evolutionary geneticists as it can be used to help identify loci that explain phenotypic variation. Surveys of the extent of LD across genomes have been carried out in a number of systems, most notably humans and model organisms. However, studies of natural populations of vertebrates have rarely been performed. Here, we describe an investigation of LD in a free-living island population of red deer Cervus elaphus. Relatively high levels of LD extended several tens of centimorgans, and significant LD was frequently detected between unlinked markers. The magnitude of LD varied depending on how the population was sampled. It also varied across different chromosomes, and was shown to be a function of sample size, intermarker distance and marker heterozygosity. A recent admixture event in the population led to an ephemeral increase in LD. Association mapping may be possible in this population, although a high 'baseline' level of LD could lead to false positive associations between marker loci and a trait of interest.     

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.     

单管直扩38重祖先信息InDels体系的构建及其在微流控芯片系统的应用

本文基于插入-缺失多态性(insertion-deletion polymorphism,InDel)遗传标记,从相关文献和dbSNP库中筛选出38个在东亚、欧洲、非洲人群中具有等位基因频率差异的祖先来源InDel位点,同时整合Amelogenin位点和Y染色体STR(DYS439)位点,以辅助未知样本的性别鉴定,采用PCR-CE技术构建了可以区分三大洲际人群的单管直接扩增复合检测体系,该体系可与微流控芯片系统相结合,1.7 h内完成DNA样本自动化扩增和电泳分型,利用公共数据库1000Genomes中16个人群1 607名个体的分型数据对筛选的38个InDel位点进行初步评估;同时对构建的38-plex InDels体系的灵敏度、准确性、直接扩增能力进行验证评估;检测5种不同人群的779份样本和215份唾液卡、血卡的直接扩增样本,采用聚类分析和主成分分析方法,评价体系的推断准确性.结果表明该38-plex InDels复合检测体系分型准确,灵敏度达157 pg,能够对唾液卡和血卡直接扩增,可以区分三大洲际人群及其混合人群,能够准确推断待测样本的族群来源、估算祖先成分,且通过集成细胞裂解步骤将有望2h实现"样本进-结果出"式快速自动化InDel分型.     

African ancestry of the population of Buenos Aires

The population of Argentina today does not have a “visible” black African component. However, censuses conducted during most of the 19th century registered up to 30% of individuals of African origin living in Buenos Aires city. What has happened to this African influence? Have all individuals of African origin died, as lay people believe? Or is it possible that admixture with the European immigrants made the African influence “invisible?” We investigated the African contribution to the genetic pool of the population of Buenos Aires, Argentina, typing 12 unlinked autosomal DNA markers in a sample of 90 individuals. The results of this analysis suggest that 2.2% (SEM = 0.9%) of the genetic ancestry of the Buenos Aires population is derived from Africa. Our analysis of individual admixture shows that those alleles that have a high frequency in populations of African origin tend to concentrate among 8 individuals in our sample. Therefore, although the admixture estimate is relatively low, the actual proportion of individuals with at least some African influence is approximately 10%. The evidence we are presenting of African ancestry is consistent with the known historical events that led to the drastic reduction of the Afro‐Argentine population during the second half of the 19th century. However, as our results suggest, this reduction did not mean a total disappearance of African genes from the genetic pool of the Buenos Aires population. Am J Phys Anthropol 128:164‐170, 2005. © 2005 Wiley‐Liss, Inc.     

Brief communication: Admixture analysis with forensic microsatellites in Minas Gerais,Brazil: The ongoing evolution of the capital and of an African‐derived community

We report the estimated allele frequencies for 13 and 14 microsatellite loci in two populations of Minas Gerais, Brazil as follows: Belo Horizonte (the capital) and Marinhos (an African‐derived community). Analysis of the African, Amerindian, and European genetic contributions to both populations, together with historical information, revealed distinct differences between the two populations. Estimates for Belo Horizonte revealed a higher‐European (66%) than African (32%) contribution, and a minimal Amerindian contribution. These results are consistent with the peopling of the city mainly by people from the Minas Gerais hinterland, a people highly admixed but with more European ancestry. Estimates for Marinhos confirmed the high‐African component of the population. However, a temporal analysis of two datasets—CURRENT (representing the population living in Marinhos today) and ORIGINAL (representing families, who have lived in Marinhos since the onset of the 20th century),—identified a diminishing of the population's African ancestry from 92% in the ORIGINAL group to 67% in the CURRENT group. This change is here interpreted as a consequence of the growing migration into the village of people with more European ancestry and subsequent admixture with the local population. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.     

TETRASAT: a program for the population analysis of allotetraploid microsatellite data

Microsatellite markers are quite popular due to their degree of polymorphism and efficiency; however, the utility of such markers for analysing allotetraploid species is often hampered by an inability to determine allele copy number for partial heterozygotes. tetrasat is a program that uses an iterative substitution process to account for all probable combinations of allele copy numbers in populations with partial heterozygote samples. The program subsequently calculates allele frequencies, and mean Hardy–Weinberg expected heterozygosity (H_E), Shannon–Weiner Diversity Index (H′) and Nei's measure of population differentiation (G_ST) are reported for each locus and population. Of equal importance is the calculation of statistical variability generated by the missing data and allele substitution process, which allows for assessment of the strength of conclusions drawn from the statistics.     

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.     

Admixture and skin color in the transplanted Tlaxcaltecan population of Saltillo,Mexico

Ethnohistoric accounts and serological analyses have documented the genetic effects of transplantation and admixture of several subpopulations of Tlaxcaltecans in Saltillo, Mexico. Interpopulational affinities are assessed using skin reflectance readings taken at the upper inner arm site with a Photovolt Model 670 reflectance spectrophotometer for these groups, focusing on the barrios of La Minita and Chamizal. Genetic distance analyses based on blood groups and skin reflectance data are in close agreement and reflect differential rates of admixture for these groups. Admixture estimates for a dihybrid model (Indian-Spanish) were derived from skin reflectances and show a slight tendency for underestimation of Spanish admixture when compared to blood group estimates. Application of a trihybrid model incorporating West African admixture shows similar estimates based on blood groups, immunoglobulins, and skin color.     

Brief communication: Evolution of a specific O allele (O1vG542A) supports unique ancestry of Native Americans

In this study, we explore the geographic and temporal distribution of a unique variant of the O blood group allele called O1v^G542A, which has been shown to be shared among Native Americans but is rare in other populations. O1v^G542A was previously reported in Native American populations in Mesoamerica and South America, and has been proposed as an ancestry informative marker. We investigated whether this allele is also found in the Tlingit and Haida, two contemporary indigenous populations from Alaska, and a pre‐Columbian population from California. If O1v^G542A is present in Na‐Dene speakers (i.e., Tlingits), it would indicate that Na‐Dene speaking groups share close ancestry with other Native American groups and support a Beringian origin of the allele, consistent with the Beringian Incubation Model. If O1v^G542A is found in pre‐Columbian populations, it would further support a Beringian origin of the allele, rather than a more recent introduction of the allele into the Americas via gene flow from one or more populations which have admixed with Native Americans over the past five centuries. We identified this allele in one Na‐Dene population at a frequency of 0.11, and one ancient California population at a frequency of 0.20. Our results support a Beringian origin of O1v^G542A, which is distributed today among all Native American groups that have been genotyped in appreciable numbers at this locus. This result is consistent with the hypothesis that Na‐Dene and other Native American populations primarily derive their ancestry from a single source population. Am J Phys Anthropol 151:649–657, 2013. © 2013 Wiley Periodicals, Inc.     

Genetic genealogy comes of age: Perspectives on the use of deep‐rooted pedigrees in human population genetics

In this article, we promote the implementation of extensive genealogical data in population genetic studies. Genealogical records can provide valuable information on the origin of DNA donors in a population genetic study, going beyond the commonly collected data such as residence, birthplace, language, and self‐reported ethnicity. Recent studies demonstrated that extended genealogical data added to surname analysis can be crucial to detect signals of (past) population stratification and to interpret the population structure in a more objective manner. Moreover, when in‐depth pedigree data are combined with haploid markers, it is even possible to disentangle signals of temporal differentiation within a population genetic structure during the last centuries. Obtaining genealogical data for all DNA donors in a population genetic study is a labor‐intensive task but the vastly growing (genetic) genealogical databases, due to the broad interest of the public, are making this job more time‐efficient if there is a guarantee for sufficient data quality. At the end, we discuss the advantages and pitfalls of using genealogy within sampling campaigns and we provide guidelines for future population genetic studies. Am J Phys Anthropol 150:505–511, 2013. © 2013 Wiley Periodicals, Inc.     

Sister-chromatid exchange analysis in a rural population of Mexico exposed to pesticides.

Cytogenetic damage was evaluated by means of the analysis of sister-chromatid exchange (SCE) in a rural population of Tlaxcala, Mexico, in occupational contact with pesticides. We studied 170 men, 94 exposed and 76 not exposed. It was shown that SCE followed a normal distribution and Student's t test did not present differences between the two groups (P = 0.4). The frequency of SCE was not correlated with the duration of exposure of the rural workers (r = -0.06), the multiple covariance analysis applied to the data of duration of exposure, tobacco intake and alcohol ingestion demonstrated a lack of statistical significance. In the exposed people we observed no symptoms provoked by these compounds.