RESUMO
Rural communities comprise around 20% of Caribbean and South American populations, but are under-represented in autosomal marker databases. That deficiency is problematic for forensic genetics, as it relies on accurate descriptions of genetic variation and population structure. Brazilian populations were shaped by an intense, complex and heterogeneous process of admixture encompassing mainly Amerindians, Sub-Saharan Africans and Europeans. Quilombos are Brazilian populations with significant African descent that have remained genetically isolated to some extent from surrounding populations. In the reported study, we analyzed three rural Quilombo populations: Kalunga; Riacho de Sacutiaba e Sacutiaba; and Mocambo, along with a dataset from the HGDP-CEPH panel. Aiming to contribute to representative genetic databases of forensic interest, we analyse the three rural Quilombos populations and investigate how their genetic makeup relates to their history by analyzing an established forensic test, comprising 46 ancestry-informative (AIM) Indels. The panel was chosen for its high power in differentiating the main contributing populations of Brazil. Parental populations were selected from HGDP-CEPH data available at the forInDel allele frequency browser based on historic patterns applicable to the study populations and the amount of variability observed within and between continents. Our results show the main admixture components in the Quilombos are African and European. Those estimates are in accordance with previous analyses for both uniparental and autosomal markers. PCA, structure analysis and ancestry estimates indicate a correlation between the extent of isolation and the degree of admixture in the Quilombos: Kalunga is the most isolated population and accordingly has a higher African admixture component (67.3%). Sacutiaba is the smallest and most impacted by migration, with the highest European component (46.8%). Mocambo neighbors a Native American population and therefore has the highest Amerindian contribution (12.2%). Our results are consistent with the history and demography of Quilombos. The heterogeneity observed in these populations stresses the genetic diversity that Latin American and Caribbean rural populations can have and reiterates the need to describe them in greater detail.
Assuntos
Etnicidade/genética , Genética Populacional , População Rural , Brasil , Cromossomos Humanos Y , Impressões Digitais de DNA , DNA Mitocondrial/genética , Frequência do Gene , Humanos , Mutação INDEL , Repetições de Microssatélites , Polimorfismo de Nucleotídeo Único , Análise de Componente PrincipalRESUMO
BACKGROUND: Balancing the subject composition of case and control groups to create homogenous ancestries between each group is essential for medical association studies. METHODS: We explored the applicability of single-tube 34-plex ancestry informative markers (AIM) single nucleotide polymorphisms (SNPs) to estimate the African Component of Ancestry (ACA) to design a future case-control association study of a Brazilian urban sample. RESULTS: One hundred eighty individuals (107 case group; 73 control group) self-described as white, brown-intermediate or black were selected. The proportions of the relative contribution of a variable number of ancestral population components were similar between case and control groups. Moreover, the case and control groups demonstrated similar distributions for ACA <0.25 and >0.50 categories. Notably a high number of outlier values (23 samples) were observed among individuals with ACA <0.25. These individuals presented a high probability of Native American and East Asian ancestral components; however, no individuals originally giving these self-described ancestries were observed in this study. CONCLUSIONS: The strategy proposed for the assessment of ancestry and adjustment of case and control groups for an association study is an important step for the proper construction of the study, particularly when subjects are taken from a complex urban population. This can be achieved using a straight forward multiplexed AIM-SNPs assay of highly discriminatory ancestry markers.
Assuntos
População Negra/genética , Estudos de Casos e Controles , Hipercolesterolemia/genética , Indígenas Sul-Americanos/etnologia , Polimorfismo de Nucleotídeo Único , População Urbana , Povo Asiático/etnologia , Povo Asiático/genética , População Negra/etnologia , Brasil/etnologia , Feminino , Humanos , Indígenas Sul-Americanos/genética , Masculino , Grupos Populacionais/etnologia , Grupos Populacionais/genética , População Branca/etnologia , População Branca/genéticaRESUMO
Background: Balancing the subject composition of case and control groups to create homogenous ancestries between each group is essential for medical association studies. Methods: We explored the applicability of single-tube 34-plex ancestry informative markers (AIM) single nucleotide polymorphisms (SNPs) to estimate the African Component of Ancestry (ACA) to design a future case-control association study of a Brazilian urban sample. Results: One hundred eighty individuals (107 case group; 73 control group) self-described as white, brown-intermediate or black were selected. The proportions of the relative contribution of a variable number of ancestral population components were similar between case and control groups. Moreover, the case and control groups demonstrated similar distributions for ACA 0.50 categories. Notably a high number of outlier values (23 samples) were observed among individuals with ACA <0.25. These individuals presented a high probability of Native American and East Asian ancestral components; however, no individuals originally giving these self-described ancestries were observed in this study. Conclusions: The strategy proposed for the assessment of ancestry and adjustment of case and control groups for an association study is an important step for the proper construction of the study, particularly when subjects are taken from a complex urban population. This can be achieved using a straight forward multiplexed AIM-SNPs assay of highly discriminatory ancestry markers.
Assuntos
Genômica , Polimorfismo Genético , População Urbana , População Urbana/classificaçãoRESUMO
BACKGROUND: From Paleo-Indian times to recent historical episodes, the Mesoamerican isthmus played an important role in the distribution and patterns of variability all around the double American continent. However, the amount of genetic information currently available on Central American continental populations is very scarce. In order to shed light on the role of Mesoamerica in the peopling of the New World, the present study focuses on the analysis of the mtDNA variation in a population sample from El Salvador. METHODOLOGY/PRINCIPAL FINDINGS: We have carried out DNA sequencing of the entire control region of the mitochondrial DNA (mtDNA) genome in 90 individuals from El Salvador. We have also compiled more than 3,985 control region profiles from the public domain and the literature in order to carry out inter-population comparisons. The results reveal a predominant Native American component in this region: by far, the most prevalent mtDNA haplogroup in this country (at approximately 90%) is A2, in contrast with other North, Meso- and South American populations. Haplogroup A2 shows a star-like phylogeny and is very diverse with a substantial proportion of mtDNAs (45%; sequence range 16090-16365) still unobserved in other American populations. Two different Bayesian approaches used to estimate admixture proportions in El Salvador shows that the majority of the mtDNAs observed come from North America. A preliminary founder analysis indicates that the settlement of El Salvador occurred about 13,400+/-5,200 Y.B.P.. The founder age of A2 in El Salvador is close to the overall age of A2 in America, which suggests that the colonization of this region occurred within a few thousand years of the initial expansion into the Americas. CONCLUSIONS/SIGNIFICANCE: As a whole, the results are compatible with the hypothesis that today's A2 variability in El Salvador represents to a large extent the indigenous component of the region. Concordant with this hypothesis is also the observation of a very limited contribution from European and African women ( approximately 5%). This implies that the Atlantic slave trade had a very small demographic impact in El Salvador in contrast to its transformation of the gene pool in neighbouring populations from the Caribbean facade.
Assuntos
DNA Mitocondrial/genética , Efeito Fundador , Genética Populacional , Teorema de Bayes , El Salvador , Etnicidade , Feminino , Frequência do Gene , Variação Genética , Geografia , Humanos , Indígenas Norte-Americanos , Masculino , Filogenia , Reação em Cadeia da PolimeraseRESUMO
We present population genetic data of 15 STRs (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, PENTA D, PENTA E, TH01, TPOX and VWA) obtained from a sample of 617 unrelated individuals from Colombia. Deviations from Hardy-Weinberg equilibrium were assessed and allele frequencies and parameters of forensic interest for each STR were calculated. The combined power of exclusion (PE) and the combined power of discrimination (PD) for the 15 tested STR loci were 0, 99999895 and more than 0, 9999999, respectively. The combined MP value was 1 in 1, 07888 x 10(-17). Population comparisons between our sample and neighbouring populations from Latin America were carried out. Significant differences in above six markers were observed between our sample and two populations from Rio de Janeiro.
Assuntos
Genética Populacional , Repetições de Microssatélites , Alelos , Colômbia , DNA/genética , DNA/isolamento & purificação , Impressões Digitais de DNA , Frequência do Gene , Marcadores Genéticos , Humanos , Reação em Cadeia da PolimeraseRESUMO
In the recent history of Colombia, two factors have contributed to change the population structure, the Spanish conquest and the slave trading promoted principally by Portugal, England and Spain. As a consequence the native population of Colombia has been reduced and mixed with the European and African arriving groups. To assess the male ancestry of the Cauca population, we have examined the frequency of the major Y-chromosome lineages by typing 30 Y-SNPs in two populations from this region: 105 Afro-Colombian individuals and 110 Caucasian-Mestizo individuals. Among the 33 haplogroups defined with the SNPs analysed, 15 haplogroups were detected, 10 of them being shared by both populations. In order to investigate how the level of admixture is, and to compare the genetic background with other neighbour populations, other South American samples previously published were used for comparative analysis.
Assuntos
Cromossomos Humanos Y , Genética Populacional , Polimorfismo de Nucleotídeo Único , População/genética , Alelos , População Negra/genética , Colômbia , Impressões Digitais de DNA , Frequência do Gene , Marcadores Genéticos , Genética , Geografia , Haplótipos , Humanos , Indígenas Sul-Americanos/genética , Masculino , Reação em Cadeia da Polimerase , Controle de Qualidade , População Branca/genéticaRESUMO
Allele frequencies and some forensic parameters for 12 autosomal microsatellites (CSF1PO, TPOX, THO1, VWA, D16S539, D7S820, D13S317, D5S818, F13A1, FESFPS, F13B, LPL) were estimated from three departments from Northwestern Colombia. The total number of samples analysed was 1045 individuals. Comparative analysis among the three studied departments and with other published Colombian populations were also performed and discussed.
Assuntos
Frequência do Gene , Genética Populacional , Repetições de Microssatélites , Colômbia , Impressões Digitais de DNA , Humanos , Reação em Cadeia da PolimeraseRESUMO
During the period of the Atlantic slave trade (15th-19th centuries), millions of people were forced to move from Africa to many American destinations, changing dramatically the human landscape of the Americas. Here, we analyze mitochondrial DNA from two different American populations with African ancestry, with hitherto unknown European and Native American components. On the basis of historical records, African-Americans from Chocó (Colombia) and the Garífunas (or "Black Carib") of Honduras are likely to have had very different demographic histories, with a significant founder effect in the formation of the latter. Both the common features and differences are reflected in their mtDNA composition. Both show a minor component (approximately 16%) from Native Central/South Americans and a larger component (approximately 84%) from sub-Saharan Africans. The latter component is very diverse in the African-Americans from Chocó, similar to that of sub-Saharan Africans, but much less so in the Garífunas, with several mtDNA types elevated to high frequency, suggesting the action of genetic drift.
Assuntos
Negro ou Afro-Americano/genética , Negro ou Afro-Americano/história , DNA Mitocondrial/genética , Emigração e Imigração/história , Variação Genética/genética , Problemas Sociais/história , África/etnologia , Negro ou Afro-Americano/etnologia , Colômbia/epidemiologia , Genética Populacional/métodos , História do Século XV , História do Século XVI , História do Século XVII , História do Século XVIII , História do Século XIX , Honduras/epidemiologia , Humanos , Indígenas Centro-Americanos/genética , Indígenas Centro-Americanos/história , Indígenas Sul-Americanos/genética , Indígenas Sul-Americanos/história , Problemas Sociais/etnologiaRESUMO
Eight Y-chromosome STRs were investigated in a male population sample from El Salvador. Complete Y-chromosomal STRs haplotypes were obtained in 121 individuals, among which 107 different haplotypes were observed. The two most common haplotypes were shared by approximately 4% of the sample, while 100 haplotypes were unique. The gene diversity was 0.9883 and the discrimination capacity was 0.8926. The combined Y-chromosome STR polymorphisms provide a powerful discrimination tool for routine forensic applications.
Assuntos
Cromossomos Humanos Y , Genética Populacional , Haplótipos , Sequências de Repetição em Tandem , Impressões Digitais de DNA/métodos , El Salvador , Variação Genética , Humanos , MasculinoRESUMO
Nine STRs loci have been typed in a sample from Córdoba (Argentina).
Assuntos
Genética Populacional , Sequências de Repetição em Tandem , Argentina , Impressões Digitais de DNA/métodos , Frequência do Gene , Genótipo , Humanos , Reação em Cadeia da PolimeraseRESUMO
Eight Y-chromosome STRs were investigated in a male population sample from Córdoba region (Argentina). Complete Y-chromosomal STRs haplotypes were obtained in 100 individuals, among which 91 different haplotypes were observed. The most common haplotype was shared by 4% of the sample, while 86 haplotypes were unique. The gene diversity was 0.9875 and the discrimination capacity was 0.8600. The combined polymorphism provides a powerful discrimination tool for routine forensic applications.
Assuntos
Cromossomos Humanos Y , Genética Populacional , Haplótipos , Sequências de Repetição em Tandem , Argentina , Impressões Digitais de DNA/métodos , Humanos , MasculinoRESUMO
Allele frequencies for eight short tandem repeats (STRs) (D5S818, D7S820, F13B, LPL, TH01, TPOX, VWA31 and CSF1PO) were estimated from a sample of 155 unrelated individuals living in different departments of the southwest of Colombia, Caquetá, Cauca, Huila, Nariño, Putumayo and Cauca Valley.