Directional mating and a rapid male population expansion in a hybrid Uruguayan population.

The Uruguayan population has been considered as mainly European descent, with a negligible Native American or African contributions. Based on serological and molecular markers, recent studies demonstrate that these two populations had an important influence in the conformation of the present one. To the Northeastern region of Uruguay, a 20% Native American contribution was estimated using autosomal markers and a 62% Native American female origin based on mitochondrial markers. In this paper, we analyze four Y chromosome markers, two biallelic loci (M3 and YAP) and two microsatellites (DYS389I and DYS391), to characterize the male genetic contribution of a sample from the Northeastern city of Tacuarembó. We take different approaches to estimate the origin of male contributions to the population of Tacuarembó; Native American contribution ranges between 1.60% and 8.31%, confirming strong directional mating, which was also detected before with mitochondrial markers. Furthermore, the male population of Tacuarembó presents the characteristic of a population that suffered a bottleneck and a posterior expansion, confirmed using two microsatellite-based statistics to analyze the past population growth; patrilocality and migration could be responsible of those characteristics.     

Genetic background of people in the Dominican Republic with or without obese type 2 diabetes revealed by mitochondrial DNA polymorphism

People in the Dominican Republic are considered to be genetically heterogeneous owing to the post-Colombian admixture of Native American, African, and European populations. To characterize their genetic background, nucleotide sequences of the D-loop region of human mitochondrial DNA (mtDNA) were examined in 33 healthy women and 50 gender-matched patients with obese type 2 diabetes (OD) from the Dominican Republic. Phylogenetic analysis of 198 mtDNA lineages including Native Americans, Africans, and Europeans enabled us to assess relative genetic contributions of the three ancestral fractions to the two groups in the Dominican Republic. In the OD group, the majority (64.0%) of the mtDNA lineages were from African ancestry, whereas the Native American fraction was predominant (51.5%) in the healthy group, with both showing smallest amounts (14.0% and 9.1%, respectively) of European contribution. This difference in maternal genetic background between the two groups was similarly demonstrated by phylogenetic analysis at the population level based on net nucleotide diversities between populations. These findings may imply ethnic-specific predisposition to OD, a possible association of an unidentified factor from African ancestry with OD in the Dominican Republic population.The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers AB174901–AB174983.     

Gender bias in the multiethnic genetic composition of central Argentina

A sample of central Argentina (Córdoba) was genotyped for the first hypervariable region (HVS-I) plus a set of coding region mitochondrial DNA (mtDNA) single nucleotide polymorphisms (SNPs) (N = 102) and compared with a data set of Y-chromosome short tandem repeats (Y-STRs; N = 100) previously genotyped in the same individuals. We additionally compiled a database containing more than 4,000, 6,800, and 12,000 HVS-I sequences of Native American, sub-Saharan African, and European origin, respectively. The Y-Chromosome Haplotype Reference Database (YHRD) was used as a reference for the Y-STR profiles from Córdoba. The Native American component is highly prevalent on the maternal side (approximately 41%) in contrast to the Y-chromosome paternal contribution (approximately 2%), indicating a strong gender bias in the colonization and admixture processes that occurred in the recent history of Argentina, in agreement with historical records. The demographic input of African slaves in Córdoba was very high in the eighteenth century (approximately 40% of the total population) but decreased dramatically after a few decades; therefore, the minor traces of sub-Saharan Y-chromosome and mtDNA lineages observed in our sample fit well with these historical records. The European Y-chromosome component of Córdoba (approximately 97%; in contrast to the 57% observed in the mtDNA side) also mirrors the substantial immigration experienced by Argentina during the beginning of the last century, predominantly from Italy and Spain.     

Assessing individual interethnic admixture and population substructure using a 48–insertion‐deletion (INSEL) ancestry‐informative marker (AIM) panel

Estimating the proportions of different ancestries in admixed populations is very important in population genetics studies, and it is particularly important for detecting population substructure effects in case‐control association studies. In this work, a set of 48 ancestry‐informative insertion‐deletion polymorphisms (INDELs) were selected with the goal of efficiently measuring the proportions of three different ancestries (sub‐Saharan African, European, and Native American) in mixed populations. All selected markers can be easily analyzed via multiplex PCR and detected with standard capillary electrophoresis. A total of 593 unrelated individuals representative of European, African, and Native American parental populations were typed, as were 380 individuals from three Brazilian populations with known admixture patterns. As expected, the interethnic admixture estimates show that individuals from southern Brazil present an almost exclusively European ancestry; Afro‐descendant communities in the Amazon region, apart from the major African contribution, present some degree of admixture with Europeans and Native Americans; and a sample from Belém, in the northeastern Amazon, shows a significant contribution of the three ethnic groups, although with a greater European proportion. In summary, a panel of ancestry‐informative INDELs was optimized and proven to be a valuable tool for estimating individual and global ancestry proportions in admixed populations. The ability to accurately infer interethnic admixtures highlights the usefulness of this marker set for assessing population substructure in association studies, particularly those conducted in Brazilian and other Latin American populations sharing trihybrid ancestry patterns. Hum Mutat 31:184–190, 2010. © 2009 Wiley‐Liss, Inc.     

Estimates of interethnic admixture in the Brazilian population using a panel of 24 X‐linked insertion/deletion markers

Objectives. In this study, we aimed to identify ancestry informative haplotypes and make interethnic admixture estimates using X‐chromosome markers. Methods. A significant sample (461 individuals) of European, African, and Native American populations was analyzed, and four linkage groups were identified. The data obtained were used to describe the ancestral contribution of populations from four different geographical regions of Brazil (745 individuals). Results. The global interethnic admixture estimates of the four mixed populations under investigation were calculated applying all the 24 insertion/deletion (INDEL) markers. In the North region, a larger Native Americans ancestry was observed (42%). The Northeast and Southeast regions had smaller Native American contribution (27% in both of them). In the South region, there was a large European contribution (46%). Conclusions. The estimates obtained are compatible with expectations for a colonization model with biased admixture between European men (one X chromosome) and Native American and African women (two X chromosomes), so the 24 X‐INDEL panel described here can be a useful to make admixture interethnic estimates in Brazilian populations. Am. J. Hum. Biol., 2010. © 2010 Wiley‐Liss, Inc.     

Joining the Pillars of Hercules: mtDNA Sequences Show Multidirectional Gene Flow in the Western Mediterranean

Phylogenetic analysis of mitochondrial DNA (mtDNA) performed in Western Mediterranean populations has shown that both shores share a common set of mtDNA haplogroups already found in Europe and the Middle East. Principal co‐ordinates of genetic distances and principal components analyses based on the haplotype frequencies show that the main genetic difference is attributed to the higher frequency of sub‐Saharan L haplogroups in NW Africa, showing some gene flow across the Sahara desert, with a major impact in the southern populations of NW Africa. The AMOVA demonstrates that SW European populations are highly homogeneous whereas NW African populations display a more heterogeneous genetic pattern, due to an east‐west differentiation as a result of gene flow coming from the East. Despite the shared haplogroups found in both areas, the European V and the NW African U6 haplogroups reveal the traces of the Mediterranean Sea permeability to female migrations, and allowed for determination and quantification of the genetic contribution of both shores to the genetic landscape of the geographic area. Comparison of mtDNA data with autosomal markers and Y‐chromosome lineages, analysed in the same populations, shows a congruent pattern, although female‐mediated gene flow seems to have been more intense than male‐mediated gene flow.     

Heterogeneity of the genome ancestry of individuals classified as White in the state of Rio Grande do Sul, Brazil.

One hundred nineteen individuals classified as White, living in different localities of the Brazilian state of Rio Grande do Sul, were studied in relation to the HVS-I region of the mitochondrial DNA (mtDNA). The male fraction of the sample (N = 74) was also tested for seven Y-chromosome polymorphisms. In a specific population (Veranópolis), a city characterized by a large influence of the Italian immigration of the 19th century, the results from the maternal and paternal sides indicated almost complete European ancestry. However, another sample identified as White, from different localities of Rio Grande do Sul, presented significant fractions of Native American (36%) and African (16%) mtDNA haplogroups. These results indicate that Brazilian populations are remarkably heterogeneous; while some present an overwhelming majority of transplanted European genomes, with a complete correspondence between physical appearance and ancestry, others reflect a history of extensive admixture with dissociation between physical appearance and ancestry.     

Admixture and Population Stratification in African Caribbean Populations

Throughout biomedical research, there is growing interest in the use of ancestry informative markers (AIMs) to deconstruct racial categories into useful variables. Studies on recently admixed populations have shown significant population substructure due to differences in individual ancestry; however, few studies have examined Caribbean populations. Here we used a panel of 28 AIMs to examine the genetic ancestry of 298 individuals of African descent from the Caribbean islands of Jamaica, St. Thomas and Barbados. Differences in global admixture were observed, with Barbados having the highest level of West African ancestry (89.6%± 2.0) and the lowest levels of European (10.2%± 2.2) and Native American ancestry (0.2%± 2.0), while Jamaica possessed the highest levels of European (12.4%± 3.5) and Native American ancestry (3.2%± 3.1). St. Thomas, USVI had ancestry levels quite similar to African Americans in continental U.S. (86.8%± 2.2 West African, 10.6%± 2.3 European, and 2.6%± 2.1 Native American). Significant substructure was observed in the islands of Jamaica and St. Thomas but not Barbados (K=1), indicating that differences in population substructure exist across these three Caribbean islands. These differences likely stem from diverse colonial and historical experiences, and subsequent evolutionary processes. Most importantly, these differences may have significant ramifications for case-control studies of complex disease in Caribbean populations.     

Genetic origins in a South American clefting population

It has been proposed that susceptibility to clefting in South America is related to Amerindian ancestry, where clefting is present at a higher frequency than in the other admixed populations (Caucasian and African) that make up the diverse racial mix of current South Americans. To clarify the genetic origins and establish a method for genetic mapping, mitochondrial DNA variation and Y-chromosome markers were studied in a South American population affected with clefting. Two-hundred and seventeen subjects and matched controls were selected through the Latin-American Collaborative Study of Congenital Malformations (ECLAMC). The case group showed a higher frequency of Native American haplogroups and a lower frequency of African haplogroups (p < 0.00001). In addition, the case group showed a much higher frequency of the specific native American haplogroup D than the control group (p < 0.00001). For the Y-chromosome markers, the case group showed a lower frequency of the African-specific marker, YAP (p = 0.002), and a higher frequency of the Native American-specific marker, DYS199 (p < 0.00001). Even though differences were found in the frequencies of the markers studied, the contribution of each founder population was similar for both groups. Results suggest a strong Native American maternal contribution and a strong Caucasian (Spanish and Portuguese) paternal contribution to the population studied. The implications of this finding include the possibility of using admixture mapping approaches to this population.     

African,Native American,and European mitochondrial DNAs in Cubans from Pinar del Rio Province and implications for the recent epidemic neuropathy in Cuba

Genetic predisposition, particularly specific mitochondrial DNA (mtDNA) backgrounds, has been proposed as a contributing factor in the expression of an epidemic of bilateral optic neuropathy that has affected residents of Cuba since 1991. To substantiate or refute the possibility that specific subsets of mtDNAs could participate in disease expression, we took advantage of the heterogeneous ethnic origin of the Cuban population and the recent identification of a number of mtDNA polymorphisms that appear to be specific for Africans, Native Americans, and Europeans. The screening of both carefully selected people with epidemic neuropathy and control subjects from the Pinar del Rio Province for these polymorphisms revealed that African, Native American, and European mtDNA haplotypes were equally represented among case and control subjects, and suggested that ～ 50% of Cuban mtDNAs originated from Europeans, 46% from Africans, and 4% from Native Americans. These findings demonstrate that mutations arising in spic mtDNAs are unlikely to play a role in the epidemic neuropathy and indicate that analysis of mtDNA haplotypes can be a valuable tool for assessing the relative maternal contribution of Africans, Native Americans, and Europeans in a mixed population. © 1995 Wiley-Liss, Inc.     

Admixture estimates based on ABO,Rh and nine STRs in two Venezuelan regions

Background: The Venezuelan population is the product of Native American, African and European admixture. Few admixture studies have been made in Venezuela using short tandem repeats (STRs).

Aim: The study estimated the contribution of each parental group in two Venezuelan regions: the Northern-Central and the Central-Western Regions.

Subjects and methods: Frequencies for ABO and Rh were estimated by maximum likelihood, and by direct count for nine STRs, for 211 individuals. Admixture was estimated using Chakraborty's gene identity method. Neighbour-joining dendrograms were obtained with Nei's DS distance calculated between the two regions, the parental populations and other Venezuelan and Latin American populations. A principal component analysis (PCA) was also performed.

Results: For the Northern-Central Region, the estimate of admixture was 37.7% for the European component, 37.7% for the African and 24.6% for the Native American. For the Central-Western region, the estimate of admixture was 58.5% for the European, 16.5% for the African and 25.0% for the Native American component.

Conclusions: (i) All systems were in Hardy–Weinberg equilibrium, except the Rh blood group of the Central-Western Region; (ii) the European contribution is high in both groups; (iii) in the dendrogram and PCA, the studied populations appear close to other admixed populations, and their relative position with regard to the three parental populations coincides with the admixture analysis.     

Admixture estimates based on ABO, Rh and nine STRs in two Venezuelan regions

BACKGROUND: The Venezuelan population is the product of Native American, African and European admixture. Few admixture studies have been made in Venezuela using short tandem repeats (STRs). AIM: The study estimated the contribution of each parental group in two Venezuelan regions: the Northern-Central and the Central-Western Regions. SUBJECTS AND METHODS: Frequencies for ABO and Rh were estimated by maximum likelihood, and by direct count for nine STRs, for 211 individuals. Admixture was estimated using Chakraborty's gene identity method. Neighbour-joining dendrograms were obtained with Nei's DS distance calculated between the two regions, the parental populations and other Venezuelan and Latin American populations. A principal component analysis (PCA) was also performed. RESULTS: For the Northern-Central Region, the estimate of admixture was 37.7% for the European component, 37.7% for the African and 24.6% for the Native American. For the Central-Western region, the estimate of admixture was 58.5% for the European, 16.5% for the African and 25.0% for the Native American component. CONCLUSIONS: (i) All systems were in Hardy-Weinberg equilibrium, except the Rh blood group of the Central-Western Region; (ii) the European contribution is high in both groups; (iii) in the dendrogram and PCA, the studied populations appear close to other admixed populations, and their relative position with regard to the three parental populations coincides with the admixture analysis.     

Admixture estimates for the population of Havana City

Background: The Cuban population is essentially a result of the admixture between Spanish, West African and, to a lesser degree, Amerindian tribes that inhabited the island.

Aim: The study analysed the genetic structure of the three principal ethnic groups from Havana City, and the contribution of parental populations to its genetic pool.

Subjects and methods: According to genealogical information and anthropological traits, 206 subjects were classified as Mulatto, of Spanish decent or of African descent. Seventeen Ancestry Informative Markers, with high difference in frequency between parental populations, were selected to estimate individual and group admixture proportions. The statistical analyses were performed using the ADMIX, ADMIX95 and STRUCTURE 2.1 packages.

Results: The results demonstrate a high level of European and African admixture in Mulattos (57–59% European; 41–43% West African). The European contribution was higher in those of Spanish descent (85%) while in those of African descent, the West African contribution ranged between 74% and 76%. Genetic structure was only detected in Mulattos and those of African descent. An Amerindian contribution was not detectable in the studied sample.

Conclusion: Our findings indicate the existence of admixture and genetic structure in the population of Havana City. This study represents one of the first steps towards understanding Cuban population admixture in order to produce successful experimental designs for admixture mapping.     

Pattern of mtDNA Variation in Three Populations from São Tomé e Príncipe

We have analysed the matrilineal genetic composition of three self‐reported ethnic groups from São Tomé e Príncipe (Gulf of Guinea), an African archipelago whose settlement begun in the late fifteenth century. Sequence data from the hypervariable segments I (HVS‐I) and II (HVS‐II) were obtained for 30 Angolares, 35 Forros and 38 Tongas. The repertory of mtDNA lineages in São Tomé e Príncipe denoted a fully African maternal pool, primarily arisen from a Central/Southwestern substratum. The absence of any lineages of putative European descent means that the European impact at the mitochondrial pool was virtually nil. Angolares showed a clear reduction of mtDNA diversity and a slight genetic differentiation relative to Tongas or Forros, whereas the latter two groups did not present any signs of genetic boundaries between each other. The data obtained here reinforce the depiction of genetic substructuring in São Tomé e Príncipe previously derived from Y‐chromosome STRs. In addition, the crossing of mtDNA and Y‐STR information led to the inference that the female mediated gene flow within the archipelago was less restricted than the male, a pattern that could be framed in the cultural traditions and socio‐historical interactions among the groups.     

Inferring Continental Ancestry of Argentineans from Autosomal, Y-Chromosomal and Mitochondrial DNA

We investigated the bio-geographic ancestry of Argentineans, and quantified their genetic admixture, analyzing 246 unrelated male individuals from eight provinces of three Argentinean regions using ancestry-sensitive DNA markers (ASDM) from autosomal, Y and mitochondrial chromosomes. Our results demonstrate that European, Native American and African ancestry components were detectable in the contemporary Argentineans, the amounts depending on the genetic system applied, exhibiting large inter-individual heterogeneity. Argentineans carried a large fraction of European genetic heritage in their Y-chromosomal (94.1%) and autosomal (78.5%) DNA, but their mitochondrial gene pool is mostly of Native American ancestry (53.7%); instead, African heritage was small in all three genetic systems (<4%). Population substructure in Argentina considering the eight sampled provinces was very small based on autosomal (0.92% of total variation was between provincial groups, p = 0.005) and mtDNA (1.77%, p = 0.005) data (none with NRY data), and all three genetic systems revealed no substructure when clustering the provinces into the three geographic regions to which they belong. The complex genetic ancestry picture detected in Argentineans underscores the need to apply ASDM from all three genetic systems to infer geographic origins and genetic admixture. This applies to all worldwide areas where people with different continental ancestry live geographically close together.     

Genetic admixture in three mexican mestizo populations based on D1S80 and HLA‐DQA1 Loci

This study compares genetic polymorphisms at the D1S80 and HLA‐DQA1 loci in three Mexican Mestizo populations from three large states (Nuevo León, Jalisco, and the Federal District). Allele frequency distributions are relatively homogenous in the three samples; only the Federal District population shows minor differences of the HLA‐DQA1 allele frequencies compared with the other two. In terms of genetic composition, these Mestizo populations show evidence of admixture with predominantly Spanish‐European (50–60%) and Amerindian (37–49%) contributions; the African contribution (1–3%) is minor. Together with the observation that in Nuevo León, the admixture estimates based on D1S80 and HLA‐DQA1, are virtually the same as those reported earlier from blood group loci, suggests that DNA markers, such as D1S80 and HLA‐DQA1 are useful for examining genetic homogeneity/heterogeneity across Mestizo populations of Mexico. The inverse relationship of the proportion of gene diversity due to population differences (G_st) to within population gene diversity (H_s) is also consistent with theoretical predictions, supporting the use of these markers for population genetics studies. Am. J. Hum. Biol. 14:257–263, 2002. © 2002 Wiley‐Liss, Inc.     

HLA molecular study of patients in a public kidney transplant program in Guatemala

Guatemala is a country located in Central America, and while it is one of the most populated countries in the region, the genetic diversity of the population has been poorly analyzed. Currently, there are no analyses of the distribution of human leukocyte antigen (HLA) system alleles in mixed ancestry (i.e., ladino) populations in Guatemala. The HLA system exhibits the most extensive polymorphism in the human genome and has been extensively analyzed in a large number of studies related to disease association, transplantation, and population genetics (with particular importance in the understanding of diversity in the human population). Here, we present HLA typing data from 127 samples of unrelated individuals from the kidney transplant program of the San Juan de Dios General Hospital (Guatemala City) using a PCR-SSOP-based (PCR-sequence specific oligonucleotide probes) typing method. We found 16 haplotypes that accounted for 39.76 % of the total haplotype diversity, of which thirteen have been reported previously in Native American populations and three have been reported in European populations. The analyses showed no deviations from Hardy-Weinberg equilibrium, and admixture estimates calculated with k = 3 ancestral components showed that Native American was the most represented component, followed by the European component. The African component was less prominent in the Guatemala mixed ancestry sample in comparison to samples from other countries in Central America. The HLA-based admixture results for Central America showed a continuum in the distribution of Native American, European and African ancestries throughout the region, which is consistent with the complex demographic history of the region.     

Mitochondrial DNA Variability in Bosnians and Slovenians

Mitochondrial DNA variability in two Slavonic‐speaking populations of the northwestern Balkan peninsula, Bosnians (N = 144) and Slovenians (N = 104), was studied by hypervariable segments I and II (HVS I and II) sequencing and restriction fragment‐length polymorphism (RFLP) analysis of the mtDNA coding region. The majority of the mtDNA detected in Southern Slavonic populations falls into the common West Eurasian mitochondrial haplogroups (e.g., H, pre‐V, J, T, U, K, I, W, and X). About 2% of the Bosnian mtDNAs encompass East Eurasian and African lineages (e.g., M and L1b, respectively). The distribution of mtDNA subclusters in Bosnians, Slovenians and the neighbouring European populations reveals that the common genetic substratum characteristic for Central and Eastern European populations (such as Germans, Poles, Russians and Finns) penetrates also South European territories as far as the Western Balkans. However, the observed differentiation between Bosnian and Slovenian mtDNAs suggests that at least two different migration waves of the Slavs may have reached the Balkans in the early Middle Ages.     

Prevalence of the fragile X syndrome in African‐Americans

Since the development of a molecular diagnosis for the fragile X syndrome in the early 1990s, several population‐based studies in Caucasians of mostly northern European descent have established that the prevalence is probably between one in 6,000 to one in 4,000 males in the general population. Reports of increased or decreased prevalence of the fragile X syndrome exist for a few other world populations; however, many of these are small and not population‐based. We present here the final results of a 4‐year study in the metropolitan area of Atlanta, Georgia, establishing the prevalence of the fragile X syndrome and the frequency of CGG repeat variants in a large Caucasian and African‐American population. Results demonstrate that one‐quarter to one‐third of the children identified with the fragile X syndrome attending Atlanta public schools are not diagnosed before the age of 10 years. Also, a revised prevalence for the syndrome revealed a higher point estimate for African‐American males (1/2,545; 95% CI: 1/5,208–1/1,289) than reported previously, although confidence intervals include the prevalence estimated for Caucasians from this (1/3,717; 95% CI: 1/7,692–1/1,869) and other studies. Further population‐based studies in diverse populations are necessary to explore the possibility that the prevalence of the fragile X syndrome differs among world populations. © 2002 Wiley‐Liss, Inc.