A Comparison of HLA Data of the North American Black with African Black and North American Caucasoid Populations

For purposes of genetic comparison, the available HLA data on United States and African Black, together with United States Caucasoid populations, are summarized. Antigen frequencies and pairwise linkage disequilibria are presented for the HLA-A, -B and -C loci in Black populations typed for the 1975 Histocompatibility Testing Workshop. The Black population samples comprise 356 North American Blacks and 411 African Blacks of whom 222 were Bantu. These are compared with a sample of 503 American Caucasoids. All significant linkage disequilibria between the A and B loci found in North American Blacks were also present in the North American Caucasoids. Between the B and C loci, Bw35 and Cw4 were in strong linkage disequilibrium in all groups. Significantly stron association between the A and C loci (Aw28 with Cw3) were observed only in the African Blacks. There were unique disequilibria both in the American Caucasoids and African Blacks. Although the frequencies of many antigens in U.S. Blacks lie between those in Africans and U.S. Caucasoids, there are exceptions such as Aw33, Bw35, Cw4.     

Study of the HLA system in the Haitian population

The HLA-A and HLA-B phenotypes of 329 unrelated Haitian adults were determined and gene and haplotype frequencies were estimated. A summary of the data is presented together with a brief comparison with American Black, American White, and African Black populations. HLA gene and haplotype frequencies of Haitians are quite similar to those for American Blacks. The frequency of Aw34 appears to be smaller in Haitians than in American and African Blacks. No statistically significant differences were found in the frequencies of B-locus antigens.     

Y chromosome microsatellite variation in three populations of Jerba Island (Tunisia)

Six Y-chromosome linked microsatellites were typed in a sample of 135 unrelated males representing three different ethnic groups: Arabs, Berbers and Blacks of Jerba Island (Tunisia). Analysis of variation at the six Y chromosome STRs showed significant differences in allele distributions between the Black group and the two other Islander groups. The Black group revealed the highest level of genetic diversity as compared to Arabs and Berbers, while the latter group was the most homogenous. Allele frequencies obtained for the three islander groups analysed were compared to data available for some European, Mediterranean and African populations. Principal-coordinate analyses showed genetic differentiation between the three geographically closed groups of Jerba. The absence of the YAP insertion marker and the position of Arabs and Jerban Blacks near the European cluster would suggest their relative 'admixture' with European populations.     

Factor IX mutations in South Africans and African Americans are compatible with primarily endogenous influences upon recent germline mutations

Similar patterns of germline mutations in the factor IX gene (F9) have been observed in certain geographically and racially diverse populations. Germline mutation data have not been available from any region of Africa or from the Black race. Analysis of mutation data for Blacks is of interest, since this race has a high frequency of polymorphism compared to other races. This high frequency has been interpreted as evidence for the "out of Africa" hypothesis for the origin of humans, but it is possible that Blacks have a higher mutation rate due to genetic differences or environmental exposures. We report 26 independent mutations that were detected in patients of mixed races with hemophilia B from South Africa. The pattern of mutation in patients from this African country was similar to that of U.S. Caucasians. In addition, 22 independent mutation were detected in African American patients. The patterns of independent germline mutation in 22 African Americans (and in a combination 34 North American and African Blacks) is similar to that of U.S. Caucasians. Neither genetic differences between the Black and Caucasian races nor environmental and cultural differences between South Africa and the U.S. alter the germline pattern of mutation observed in F9. Hum Mutat 16:372, 2000.     

Population structure and admixture in Cerro Largo, Uruguay, based on blood markers and mitochondrial DNA polymorphisms.

Recent studies of the Uruguayan population revealed different amounts of Amerindian and African genetic contributions. Our previous analysis of Afro-Uruguayans from the capital city of the Department of Cerro Largo showed a high proportion of African genes, and the effects of directional mating involving Amerindian women. In this paper, we extended the analysis to a sample of more than 100 individuals representing a random sample of the population of the whole Department. Based on 18 autosomal markers and one X-linked marker, we estimated 82% European, 8% Amerindian, and 10% African contributions to their ancestry, while from seven mitochondrial DNA site-specific polymorphic markers and sequences of hypervariable segment I, we determined 49% European, 30% Amerindian, and 21% African maternal contributions. Directional matings between Amerindian women and European men were detected, but differences involving Africans were not significant. Data about the specific origins of maternal lineages were also provided, and placed in a historical context.     

Modified-Symbol Digit Modalities Test for African Americans, Caribbean Black Americans, and non-Latino Whites: nationally representative normative data from the National Survey of American Life.

Normative neuropsychological data for U.S. racial/ethnic minorities are limited. Extant norms are based on small, regional groups that may not be nationally representative. The objectives of this study were to (1) provide norms for a modified Symbol Digit Modalities Test (M-SDMT) based on a nationally representative sample of African Americans, Caribbean Blacks, and non-Latino Whites (NLW) living in areas with large populations of Blacks; and (2) determine significant correlates of M-SDMT performance. The M-SDMT was administered to a subset of respondents from the National Survey of American Life in standard face-to-face interviews. M-SDMT performance was influenced by race/ethnicity, age, education, and gender. African Americans and NLW groups had similar M-SDMT performances, which differed from Caribbean Blacks. The Black ethnic differences in M-SDMT were not explained by the sociodemographic factors considered in this study. Unlike previous work, this study supports the consideration of Black ethnicity when evaluating Black neuropsychological test performance.     

Maternal component in the familial aggregation of hypertension

To assess maternal versus paternal contributions to the familial aggregation of hypertension, we examined family history data from 344 hypertensive probands (69 African American, 153 US Caucasian, 122 Greek Caucasian) ascertained without respect to parental hypertension status. The proportion of hypertensive mothers (81.7, 65.0 and 84.8% for African Americans, US Caucasians and Greek Caucasians, respectively) of these probands was significantly greater than the proportion of hypertensive fathers (50.0, 44.9 and 48.3%, respectively) in all three ethnic groups. The lifetime risk of hypertension was significantly greater for mothers compared with fathers of these hypertensive probands (p<0.001). Examination of the proband's siblings indicated that maternal history of hypertension was associated with greater lifetime risk for hypertension than paternal history (p<0.01). In conclusion, we observe a consistent maternal component in the inheritance of hypertension. Although we cannot separate a maternal genetic from epigenetic or environmental effect, our findings suggest that genetic research should include studies of the mitochondrial as well as nuclear genome. Furthermore, when assessing a patient's risk for hypertension, particular attention should be paid to the maternal family history.     

The use of common mitochondrial variants to detect and characterise population structure in the Australian population: implications for genome-wide association studies

There is an increasing recognition of the potential role of variants in mitochondrial DNA and nuclear-encoded mitochondrial proteins in modifying disease risk. This has led to a rise in the number of mitochondrial association studies being undertaken. The unique inheritance pattern of mitochondria makes mitochondrial DNA variation susceptible to having geographical structure. Such a structure may have a dramatic impact on mitochondrial association studies, particularly in heterogeneous populations. By combining self-reported ancestry data and mitochondrial genotype data for a sample of 3839 individuals from 1037 Australian families, population substructure is tested by looking for evidence of differences in mitochondrial haplogroup and single nucleotide polymorphism (SNP) frequencies between different ancestral groups in Australia. In addition, the substructure within ancestral groups is tested by comparing the similarity of mates to randomly drawn pairs of individuals from the same ancestral group. It is shown that there are significant differences in the frequency of variants both between European and non-European groups, and within Europe. This agrees with previous studies of European mitochondrial variation. No evidence was found for structure within ancestral groups. These results have implications for future association studies in the Australian population, and other populations of heterogeneous ancestry.     

Genetic composition of Brazilian population samples based on a set of twenty‐eight ancestry informative SNPs

Ancestry informative SNPs can be useful to estimate individual and population biogeographical ancestry. Brazilian population is characterized by a genetic background of three parental populations (European, African, and Brazilian Native Amerindians) with a wide degree and diverse patterns of admixture. In this work we analyzed the information content of 28 ancestry‐informative SNPs into multiplexed panels using three parental population sources (African, Amerindian, and European) to infer the genetic admixture in an urban sample of the five Brazilian geopolitical regions. The SNPs assigned apart the parental populations from each other and thus can be applied for ancestry estimation in a three hybrid admixed population. Data was used to infer genetic ancestry in Brazilians with an admixture model. Pairwise estimates of F_st among the five Brazilian geopolitical regions suggested little genetic differentiation only between the South and the remaining regions. Estimates of ancestry results are consistent with the heterogeneous genetic profile of Brazilian population, with a major contribution of European ancestry (0.771) followed by African (0.143) and Amerindian contributions (0.085). The described multiplexed SNP panels can be useful tool for bioanthropological studies but it can be mainly valuable to control for spurious results in genetic association studies in admixed populations. Am. J. Hum. Biol., 2010. © 2009 Wiley‐Liss, Inc.     

Determination of population origin: a comparison of autosomal SNPs,Y-chromosomal and mtDNA haplogroups using a Malagasy population as example

Y-chromosomal and mitochondrial DNA (mtDNA) polymorphisms have been used for population studies for a long time. However, there is another possibility to define the origin of a population: autosomal single-nucleotide polymorphisms (SNPs) whose allele frequencies differ considerably in different populations. In an attempt to compare the usefulness of these approaches we studied a population from Madagascar using all the three mentioned approaches. Former investigations of Malagasy maternal (mtDNA) and paternal (Y chromosome) lineages have led to the assumption that the Malagasy are an admixed population with an African and Asian-Indonesian heritage. Our additional study demonstrated that more than two-third of the Malagasy investigated showed clearly a West African genotype regarding only the autosomal SNPs despite the fact that 64% had an Asian mtDNA and more than 70% demonstrated an Asian-Indonesian heritage in either mtDNA or Y-chromosomal haplogroup or both. Nonetheless, the admixture of the Malagasy could be confirmed. A clear African or Asian-Indonesian heritage according to all the three DNA approaches investigated was only found in 14% and 1% of male samples, respectively. Not even the European or Northern African influences, detected in 9% of males (Y-chromosomal analysis) and 11% of samples (autosomal SNPs) were consistent. No Malagasy in our samples showed a European or Northern African origin in both categories. So, the analysis of autosomal SNPs could confirm the admixed character of the Malagasy population, even if it pointed to a greater African influence as detectable by Y-chromosomal or mtDNA analysis.     

HLA-DRB1 and -DQB1 alleles in the Brazilian population of the northeastern region of the state of São Paulo

The HLA-DRB1 and -DQB1 alleles in 161 healthy unrelated individuals, including Caucasians, Blacks and Mulattos (mixed Caucasian and Black), from the Northeastern region of the state of S?o Paulo, Brazil were analysed. The 36 different DRB1 alleles detected included not only common Caucasian alleles, but also DRB1*0411, 0807 and 1402, typical of Amerindians, and DRB1*0302, 1503, and 0804, typical of African American Blacks.     

African-derived South American populations: A history of symmetrical and asymmetrical matings according to sex revealed by bi- and uni-parental genetic markers

Estimates of African, European, and Amerindian contributions to the gene pool of 11 predominantly African-derived South American populations were obtained using five autosomal and one Y chromosome hypervariable loci, as well as mitochondrial DNA (sequences of the first hypervariable segment of the control region, plus two restriction sites and the presence or absence of the CoII/tRNA^Lys intergenic 9-bp deletion). The three latter characteristics are reported here for the first time for 42 individuals living in three Brazilian populations. Thirty-eight sequences were identified in these persons; 17 (45%) could be classified as being of African, 4 (11%) of Amerindian, and 2 (5%) of European origin. Evidence for asymmetrical matings in relation to sex and ethnic group was obtained for nine of the 11 populations. The most consistent finding was the introduction of European genes through males, but the results differ in the several communities, indicating the importance of local factors in such interactions. Am. J. Hum. Biol. 11:551–563, 1999. © 1999 Wiley-Liss, Inc.     

Diversity of mtDNA lineages in Portugal: not a genetic edge of European variation

The analysis of the hypervariable regions I and II of mitochondrial DNA in Portugal showed that this Iberian population presents a higher level of diversity than some neighbouring populations. The classification of the different sequences into haplogroups revealed the presence of all the most important European haplogroups, including those that expanded through Europe in the Palaeolithic, and those whose expansion has occurred during the Neolithic. Additionally a rather distinct African influence was detected in this Portuguese survey, as signalled by the distributions of haplogroups U6 and L, present at higher frequencies than those usually reported in Iberian populations. The geographical distributions of both haplogroups were quite different, with U6 being restricted to North Portugal whereas L was widespread all over the country. This seems to point to different population movements as the main contributors for the two haplogroup introductions. We hypothesise that the recent Black African slave trade could have been the mediator of most of the L sequence inputs, while the population movement associated with the Muslim rule of Iberia has predominantly introduced U6 lineages.     

Benign sickle cell disease in Saudi Arabia: survival estimate and population dynamics

A survey of 8,084 adult Saudi male employment applicants yielded 872 with the sickle cell trait (AS) and 51 with sickle cell disease. Based on the known distribution of hemoglobin S genes between oasis and non-oasis populations in Saudi Arabia, and on calculation of the expected number of abnormal homozygotes within the non-oasis and oasis subgroups as well as the entire employment applicant group, it appears that virtually 100% of Saudis with SS disease survive to adult life. Saudi Arabs and other Caucasian populations in the Middle East exhibit a benign type of SS disease as compared with Blacks in Africa and the Americas. In the Middle East, gene contributions from SS individuals will shift equilibrium frequencies to higher levels than encountered in Black populations under sustained selective pressures, and the polymorphism will tend to be stable with decline in selective pressure. There are some indications that the hemoglobin S gene may have been a recent import into the Middle East.     

The Complex and Diversified Mitochondrial Gene Pool of Berber Populations

The mitochondrial DNA variation of 295 Berber-speakers from Morocco (Asni, Bouhria and Figuig) and the Egyptian oasis of Siwa was evaluated by sequencing a portion of the control region (including HVS-I and part of HVS-II) and surveying haplogroup-specific coding region markers. Our findings show that the Berber mitochondrial pool is characterized by an overall high frequency of Western Eurasian haplogroups, a somehow lower frequency of sub-Saharan L lineages, and a significant (but differential) presence of North African haplogroups U6 and M1, thus occupying an intermediate position between European and sub-Saharan populations in PCA analysis. A clear and significant genetic differentiation between the Berbers from Maghreb and Egyptian Berbers was also observed. The first are related to European populations as shown by haplogroup H1 and V frequencies, whereas the latter share more affinities with East African and Nile Valley populations as indicated by the high frequency of M1 and the presence of L0a1, L3i, L4*, and L4b2 lineages. Moreover, haplogroup U6 was not observed in Siwa. We conclude that the origins and maternal diversity of Berber populations are old and complex, and these communities bear genetic characteristics resulting from various events of gene flow with surrounding and migrating populations.     

Evaluating self-declared ancestry of U.S. Americans with autosomal, Y-chromosomal and mitochondrial DNA

The current U.S. population represents an amalgam of individuals originating mainly from four continental regions (Africa, Europe, Asia and America). To study the genetic ancestry and compare with self-declared ancestry we have analyzed paternally, maternally and bi-parentally inherited DNA markers sensitive for indicating continental genetic ancestry in all four major U.S. American groups. We found that self-declared U.S. Hispanics and U.S. African Americans tend to show variable degrees of continental genetic admixture among the three genetic systems, with evidence for a marked sex-biased admixture history. Moreover, for these two groups we observed significant regional variation across the country in genetic admixture. In contrast, self-declared U.S. European and U.S. Asian Americans were genetically more homogeneous at the continental ancestry level. Two autosomal ancestry-sensitive markers located in skin pigmentation candidate genes showed significant differences in self-declared U.S. African Americans or U.S. European Americans, relative to their assumed parental populations from Africa or Europe. This provides genetic support for the importance of skin color in the complex process of ancestry identification.     

DNA markers near the cystic fibrosis locus: further analysis of the British population.

Genetic analysis of the CF locus in the British Caucasian population has been extended using six DNA probes detecting nine polymorphic loci. Data are presented on (1) diagnostic usefulness of probes, and (2) allele frequencies for each probe in this population. For the probes pXV2C and KM19 (those closest to the CF locus) allele frequencies are further subdivided into male and female derived chromosomes 7. The allele frequencies for both probes on non-CF bearing chromosomes 7, but not on CF carrying chromosomes 7, are substantially different in males and females. Combined haplotypes for pXV2C and KM19 show that, as has been observed in other northern European populations, almost 90% of CF chromosomes in this population carry the pXV2C/KM19, 1/2 (2.1 kb/6.6 kb) haplo-type.     

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 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.     

Substantial native American female contribution to the population of Tacuarembó, Uruguay,reveals past episodes of sex‐biased gene flow

For many years it has been assumed that the population of Uruguay is almost exclusively European‐derived and that the biological contribution of the native population as well as of individuals of African descent is negligible. Several recent studies based on a variety of genetic markers, mostly morphological and serological markers, have produced quite a different picture of the constitution of the Uruguayan population. The Native American contribution varies from 1–20%, while the African contribution ranges from 7–15%, in different regions of the country. In the present study we examine the way the admixture process took place in Uruguay by analyzing the ancestry of maternal lineages in a sample from the northern city of Tacuarembó. To accomplish this goal we typed mitochondrial DNA (mtDNA) markers of Native American, African, and European origin and estimated the proportions of each parental group in the admixed population. We found that 62% of all mtDNA haplogroups were of Native American descent, a surprising figure considering the “European roots” of the country. Consequently, this result assimilates Uruguay to the rest of Latin American populations where sex‐biased gene flow between European men and Native American women has been the rule. We further analyzed the distribution of the four major founding mitochondrial lineages in Tacuarembó and compared it to other South American populations. We discuss our findings in the light of historical records and assess the need for additional genetic studies. Am. J. Hum. Biol. 16:289–297, 2004. © 2004 Wiley‐Liss, Inc.