Examination of ancestry and ethnic affiliation using highly informative diallelic DNA markers: application to diverse and admixed populations and implications for clinical epidemiology and forensic medicine

We and others have identified several hundred ancestry informative markers (AIMs) with large allele frequency differences between different major ancestral groups. For this study, a panel of 199 widely distributed AIMs was used to examine a diverse set of 796 DNA samples including self-identified European Americans, West Africans, East Asians, Amerindians, African Americans, Mexicans, Mexican Americans, Puerto Ricans and South Asians. Analysis using a Bayesian clustering algorithm (STRUCTURE) showed grouping of individuals with similar ethnic identity without any identifier other than the AIMs genotyping and showed admixture proportions that clearly distinguished different individuals of mixed ancestry. Additional analyses showed that, for the majority of samples, the predicted ethnic identity corresponded with the self-identified ethnicity at high probability (P > 0.99). Overall, the study demonstrates that AIMs can provide a useful adjunct to forensic medicine, pharmacogenomics and disease studies in which major ancestry or ethnic affiliation might be linked to specific outcomes.Electronic Supplementary Material Supplementary material is available for this article at     

Estimating ethnic admixture from pedigree data

This paper introduces a likelihood method of estimating ethnic admixture that uses individuals, pedigrees, or a combination of individuals and pedigrees. For each founder of a pedigree, admixture proportions are calculated by conditioning on the pedigree-wide genotypes at all ancestry-informative markers. These estimates are then propagated down the pedigree to the nonfounders by a simple averaging process. The large-sample standard errors of the founders' proportions can be similarly transformed into standard errors for the admixture proportions of the descendants. These standard errors are smaller than the corresponding standard errors when each individual is treated independently. Both hard and soft information on a founder's ancestry can be accommodated in this scheme, which has been implemented in the genetic software package Mendel. The utility of the method is demonstrated on simulated data and a real data example involving Mexican families of mixed Amerindian and Spanish ancestry.     

African-American mitochondrial DNAs often match mtDNAs found in multiple African ethnic groups

Background  

Mitochondrial DNA (mtDNA) haplotypes have become popular tools for tracing maternal ancestry, and several companies offer this service to the general public. Numerous studies have demonstrated that human mtDNA haplotypes can be used with confidence to identify the continent where the haplotype originated. Ideally, mtDNA haplotypes could also be used to identify a particular country or ethnic group from which the maternal ancestor emanated. However, the geographic distribution of mtDNA haplotypes is greatly influenced by the movement of both individuals and population groups. Consequently, common mtDNA haplotypes are shared among multiple ethnic groups. We have studied the distribution of mtDNA haplotypes among West African ethnic groups to determine how often mtDNA haplotypes can be used to reconnect Americans of African descent to a country or ethnic group of a maternal African ancestor. The nucleotide sequence of the mtDNA hypervariable segment I (HVS-I) usually provides sufficient information to assign a particular mtDNA to the proper haplogroup, and it contains most of the variation that is available to distinguish a particular mtDNA haplotype from closely related haplotypes. In this study, samples of general African-American and specific Gullah/Geechee HVS-I haplotypes were compared with two databases of HVS-I haplotypes from sub-Saharan Africa, and the incidence of perfect matches recorded for each sample.     

Combining genetics and population history in the study of ethnic diversity in the People's Republic of China

Genomic data have increasingly been used to complement linguistic, archeological, and anthropological evidence in reconstructing the origins and migratory patterns of modern humans. East Asia is a particular hotspot of human migration, especially mainland China, where a large number of human fossils have been unearthed and more than 20% of the world's population now resides. There are 56 officially recognized ethnic populations (minzu) in China. In the present study we investigated the ancestry and genetic diversity of nine populations: the majority Han of Liaoning Province; the Miao, Yao, Kucong, and Tibetan communities of Yunnan Province in southwest China; and four Muslim populations, the Hui, Bonan, Dongxiang, and Sala from central and northern China. We used both biparental and uniparental markers to determine patterns of diversity at autosomal, mitochondrial, and Y-chromosome loci. The study populations displayed several paternal origins but restricted maternal ancestries. From the Y-chromosome data in particular, major demographic changes, such as the Neolithic population expansion and more recent historical events including migration along the Silk Road, could be inferred. Specific aspects of the internal structure and organization of the study populations, including endogamy and consanguinity, were uncovered using autosomal markers. However, we encountered interpretive problems in terms of the definition of the present-day ethnic study populations in China, which appear to reflect past and present political as well as genetic influences.     

Modernity and ethnic affiliation in Israeli schools: A dependence approach*

In this article, we argue that there is an important, but as yet unidentified, process involved in the maintenance and reconstruction of ethnic identity. We call this process ‘ethnic reorganization’. We argue that this process is useful for understanding the ethnic survival of indigenous peoples in colonized societies, as well as for illuminating the processes of ethnic renascence among both indigenous and immigrant groups. We find it especially useful in accounting for both the persistence and the transformation of American Indian ethnicity in the United States. Ethnic reorganization occurs when an ethnic minority undergoes a reorganization of its social structure, redefinition of ethnic group boundaries, or some other change in response to pressures or demands imposed by the dominant culture. From this viewpoint, ethnic reorganization is a mechanism that facilitates ethnic group survival, albeit in a modified form. We specify several types of ethnic reorganization. These include: social reorganization, economic reorganization, political reorganization, and cultural reorganization. We argue that ethnic reorganization represents a central mechanism of ethnic change. We present evidence of these forms of ethnic reorganization among many different American Indian societies faced with demographic and cultural extinction.     

Industrialization and ethnic change in the modern world

Despite the large recent attention given to ethnicity within the social sciences, the sources of modern ethnic change have remained opaque. Drawing upon social theory from Marx and Gellner, I argue here that industrialization incentivizes ethnic homogenization by lowering the relative value of land. Using carbon emissions per capita as a proxy for industrialization, I show that cross-country changes in ethno-linguistic fractionalization between 1961 and 1985 are negatively correlated with industrialization, and that this result is robust to the use of a variety of control variables, sub-samples and alternative measures of industrialization such as cement production, urbanization and agriculture as a percentage of GDP. In particular, I find no evidence for the direct role of the state in promoting ethnic homogenization, which adds to other recent evidence on how economic incentives may trump political ones as regards identity change, at least in the short- to medium term.     

Demographic behaviour of adults of mixed ethnic ancestry: Jews in Israel

We examine demographic behaviour of Jewish adults of mixed ethnic ancestry, relative to those of the two major Jewish ethnic groups in Israel. Research has shown that for measures of socioeconomic status, such as educational attainment, outcomes for multi-ethnics are in between – and very close to the middle of – those associated with the two major ethnic groups. We find that, in contrast, the marriage and fertility behaviour of multi-ethnic adults is nearly identical to that of the more socially advantaged ethnic group and quite distinct from that of the less advantaged ethnic group. Through multivariate analyses, we explore factors associated with families of origin, including socioeconomic status and cultural indicators of family norms, which are associated with these patterns. We discuss interpretations of our findings.     

Ancestral and instrumental in the politics of ethnic and religious conflict

ABSTRACT

Ethnicity, like race, religion, and nationality, is a feature of group identity that is contested. There are literatures devoted to each, and in each there are those who see the origins of identity and affiliation in ancestry and deeply rooted affect and those who see these as socially constructed and instrumentally used by elites. Yet all recognize that the ancestral is socially constructed and that social constructions make use of existing cultural features, and that the vertical cleavages of race, religion, ethnicity, and nationality dominate the horizontal ones of class. This generates implications for institutional changes, for the pursuit of extraterritorial interests, for the selection of explanatory narratives for conflict when multiple attributions are possible, for intra-communal conflict, and for policies for ethnic conflict regulation.     

Formation of ethnic and racial identities: narratives by young Asian-American professionals

This article examines Asian-American professionals’ ethnic and pan-ethnic attachments and identities through fifteen autobiographical essays. Classical assimilation theory predicts that well-educated Asian-American professionals will be highly acculturated into the white middle class, with little retention of their ethnic subculture; yet many of our essayists had strong, bicultural orientations. Their high level of social assimilation, reflected in their friendships and intimate relationships with whites, indicates that Asian Americans can socially assimilate without relinquishing their culture. Most of the 1.5 and second-generation essayists tried to hide their ethnic culture and non-white characteristics during their early school years. Yet, they experienced a painful but gradual establishment of an ethnic identity, usually beginning in their college years. Some contributors also expressed varying degrees of pan-Asian identity and a moderate level of Third World racial identity.     

The fragility of “white Irish” as a minority ethnic identity in England

This paper is a methodological reflection on the experiences of a white Irish woman researching ethnicity in England. Ethnic identity is described as a performance between two social actors that requires the collusion of both parties in order to be socially accepted. The history and disputes around the white Irish ethnic group category in England are discussed. Through the use of fieldnotes and interview extracts, I discuss how I became aware that my ethnic identity was not always recognized by participants, and in some cases the distinction between white Irish and white British was denied. At the micro level, this affects my rapport with individual participants, while at the macro level it resonates with historical relationships between Ireland and England. I argue that such experiences can lead to an existential threat to a person’s ethnic identity and therefore that the status of white Irish identity in England can be fragile.     

The management of otherness beyond the state: integration policies and inclusive citizenship as a government paradigm in the Basque Country

The ethnic identity of second-generation immigrant youth has important implications for their association with, and integration in, receiving countries. This paper deals with the ethnic identity formation of second-generation Turkish immigrant youth in Germany, with particular attention paid to the notion of reactive ethnicity. While much of the literature discusses the ethnic retention of this specific group as unwillingness to integrate, this paper frames their ethnic identity formation as reactive ethnicity, which emerges in reaction to social exclusion. Utilizing a case study of Turkish students of disadvantaged schools, the article illustrates that reactive ethnicity is strongly linked to perceived discrimination and that it acquires characteristics of resistance when the dominant group denigrates and invalidates the immigrants' culture.     

Ethnic identity on display: West Indian youth and the creation of ethnic boundaries in high school

The black immigrant population in New York City has grown exponentially since 1990, such that West Indians now compose the majority of the black population in several neighbourhoods. This article examines how this ethnic density manifests among youth in high school, and how it has influenced ethnic identity formation among second-generation West Indians. My findings are based on twenty-four interviews and eight months of participant observation in two Brooklyn high schools from 2003 to 2004. The results show that in both schools, Caribbean island identities have become a ‘cool’ commodity within peer groups. Further, although it was important to express pride in one's island identity, these young people often blurred their national origin boundaries by drawing on Jamaican popular culture as way of projecting a unified ‘West Indian identity’. The research also uncovers evidence of a de-stigmatization of Haitianness as a way to incorporate them as cultural insiders into the larger Caribbean collective.     

Ethnic identity and Chicano literature: How ethnicity affects reading and reading affects ethnic consciousness

This article interrogates the impact of readers’ ethnicity (Latino and non-Latino) on meanings crafted from Chicano literature. This article addresses the effect of Chicano literature on ethnic identity and worldview formation. The data source is participant observation and interviews with eighteen students in a college-level Chicano literature seminar in the United States. Latino students found that the literature spoke to their experience as Latinos, inciting a sense of membership in a community that merits inclusion in a college course. This connection with the literature transmuted into ethnic validation for nearly all Latino students. Non-Latinos, hindered from relating to the course content on an ethnic level, discovered alternate entryways into the texts that allowed for identification on other particular levels. Non-Latinos ascertained how ethnic distinctions partially shape human experience and that this understanding is critical to cross-cultural appreciation and empathy. Non-Latinos additionally perceived that a common humanity tunnels beneath ethnic difference.     

An anthropological approach to the demography of central Brazil Gê societies

In this paper, the author considers the spatial and social dynamics of the Akwen Xerente population and demonstrates the necessity of relying on both demographic and anthropological information. This population is characterised by a complex combination of distinct processes which at the same time maintain the ethnic identity and redistribute individuals among villages. Individuals moves in different villages following a rule of uxorilocal residence and as the result of the formation of new villages after conflicts between political factions, whereas the social belonging of the individual is organised by exogamous moieties and patrilineal clans. This work shows that these different dimensions of the organisation of the Xerente society can only be understood when considering together a group of villages: in this case, the village is not a functional unit.     

Relation of risk of systemic lupus erythematosus to west African admixture in a Caribbean population

Risk of systemic lupus erythematosus (SLE) is higher in people of west African descent than in Europeans. The objective of this study was to distinguish between genetic and environmental explanations for this ethnic difference by examining the relationship of disease risk to individual admixture (defined as the proportion of the genome that is of west African ancestry); 124 cases of SLE and 219 matched controls resident in Trinidad were studied. Analysis of admixture was restricted to 52 cases and 107 controls who reported no Indian or Chinese ancestry. These individuals were typed with a panel of 26 single-nucleotide polymorphisms and five insertion/deletion polymorphisms chosen to have large allele frequency differentials between west African, European and Native American populations. A Bayesian model for population admixture, individual admixture and locus ancestry was fitted by Markov chain simulation. Mean west African admixture (M) was 0.81 in cases and 0.74 in controls (P=0.01). The risk ratio for SLE associated with unit change in M was estimated as 32.5 with a 95% confidence interval (CI) of 2.0-518. Adjustment for measures of socioeconomic status (household amenities in childhood and years of education) altered this risk ratio only slightly (adjusted risk ratio: 28.4, 95% CI 1.7-485). These results support an additive genetic model for the ethnic difference in risk of SLE between west Africans and Europeans, rather than an environmental explanation or an "overdominant" model in which risk is higher in heterozygous than in homozygous individuals. This conclusion lays a basis for localizing the genes underlying this ethnic difference in risk of SLE by admixture mapping.     

Ethnic Variation in Inflammatory Profile in Tuberculosis

Distinct phylogenetic lineages of Mycobacterium tuberculosis (MTB) cause disease in patients of particular genetic ancestry, and elicit different patterns of cytokine and chemokine secretion when cultured with human macrophages in vitro. Circulating and antigen-stimulated concentrations of these inflammatory mediators might therefore be expected to vary significantly between tuberculosis patients of different ethnic origin. Studies to characterise such variation, and to determine whether it relates to host or bacillary factors, have not been conducted. We therefore compared circulating and antigen-stimulated concentrations of 43 inflammatory mediators and 14 haematological parameters (inflammatory profile) in 45 pulmonary tuberculosis patients of African ancestry vs. 83 patients of Eurasian ancestry in London, UK, and investigated the influence of bacillary and host genotype on these profiles. Despite having similar demographic and clinical characteristics, patients of differing ancestry exhibited distinct inflammatory profiles at presentation: those of African ancestry had lower neutrophil counts, lower serum concentrations of CCL2, CCL11 and vitamin D binding protein (DBP) but higher serum CCL5 concentrations and higher antigen-stimulated IL-1 receptor antagonist and IL-12 secretion. These differences associated with ethnic variation in host DBP genotype, but not with ethnic variation in MTB strain. Ethnic differences in inflammatory profile became more marked following initiation of antimicrobial therapy, and immunological correlates of speed of elimination of MTB from the sputum differed between patients of African vs. Eurasian ancestry. Our study demonstrates a hitherto unappreciated degree of ethnic heterogeneity in inflammatory profile in tuberculosis patients that associates primarily with ethnic variation in host, rather than bacillary, genotype. Candidate immunodiagnostics and immunological biomarkers of response to antimicrobial therapy should be derived and validated in tuberculosis patients of different ethnic origin.     

The terms of the debate: Untangling language about ethnicity and ethnic movements

Theoretical debates on ethnicity suffer from a general confusion about the divergent meanings which academics ascribe to key terms. ‘Primordialist’ approaches include biological, psychological and cultural explanations, whose conflation tends to confuse proponents and critics alike. ‘Instrumentalist’ approaches conflate all ethnic movements within a profile of political opportunism, failing to recognize the varying degrees to which underlying social‐institutional incompatibilities may contribute to ethnic conflict. ‘Constructivist’ approaches vacillate between a focus on the influence of intellectual ethnic discourse and an understanding of ethnic identity as developing out of wider bodies of social experience. Greater attention to the varying contribution of ‘deep’ culture to ethnic conflict can clarify why these subschools find such differences among ethnic movements, which can indeed be understood to vary along a spectrum of political functions: at one pole, ethnic movements seek to inflate ethnic sentiment for political purposes; at the other, they seek rather to reconstruct the existing political position of a distinct cultural formation. This distinction can permit more appropriate policy‐making towards the resolution of ethnic conflict, yet raises new challenges to the biases of the researcher.     

Ancestral components of admixed genomes in a Mexican cohort

For most of the world, human genome structure at a population level is shaped by interplay between ancient geographic isolation and more recent demographic shifts, factors that are captured by the concepts of biogeographic ancestry and admixture, respectively. The ancestry of non-admixed individuals can often be traced to a specific population in a precise region, but current approaches for studying admixed individuals generally yield coarse information in which genome ancestry proportions are identified according to continent of origin. Here we introduce a new analytic strategy for this problem that allows fine-grained characterization of admixed individuals with respect to both geographic and genomic coordinates. Ancestry segments from different continents, identified with a probabilistic model, are used to construct and study "virtual genomes" of admixed individuals. We apply this approach to a cohort of 492 parent-offspring trios from Mexico City. The relative contributions from the three continental-level ancestral populations-Africa, Europe, and America-vary substantially between individuals, and the distribution of haplotype block length suggests an admixing time of 10-15 generations. The European and Indigenous American virtual genomes of each Mexican individual can be traced to precise regions within each continent, and they reveal a gradient of Amerindian ancestry between indigenous people of southwestern Mexico and Mayans of the Yucatan Peninsula. This contrasts sharply with the African roots of African Americans, which have been characterized by a uniform mixing of multiple West African populations. We also use the virtual European and Indigenous American genomes to search for the signatures of selection in the ancestral populations, and we identify previously known targets of selection in other populations, as well as new candidate loci. The ability to infer precise ancestral components of admixed genomes will facilitate studies of disease-related phenotypes and will allow new insight into the adaptive and demographic history of indigenous people.     

Marriage and family formation among the white and ethnic minority populations in Britain

Recent UK Labour Force Survey data are used to investigate marriage and family formation among the white and ethnic minority populations in Britain. The different age‐sex structures of the white and ethnic minority groups are analysed and the increasing number of UK‐born or ‘second‐generation’ persons identified. Large differentials are seen between ethnic minority groups in the propensity to cohabit, marry and experience marital disruption. Average spousal age differences and the propensity to form interethnic unions are also distinctive. Resulting patterns of family and household composition are described. In particular, the data suggest important divergences between individuals of Indian and those of Pakistani and Bangladeshi ethnic origin, such that we cannot talk about the demography of the South Asian population as a whole. Comparisons of marriage patterns among ‘first‐’ and ‘second‐generation’ individuals within each ethnic group suggest some assimilation in marriage patterns among the Indian, Pakistani and Bangladeshi populations towards those of the white population.