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Randomized Controlled Trial
, 8 (9), e75145
eCollection

Revisiting the Genetic Ancestry of Brazilians Using Autosomal AIM-Indels

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Randomized Controlled Trial

Revisiting the Genetic Ancestry of Brazilians Using Autosomal AIM-Indels

Fernanda Saloum de Neves Manta et al. PLoS One.

Abstract

There are many different studies that contribute to the global picture of the ethnic heterogeneity in Brazilian populations. These studies use different types of genetic markers and are focused on the comparison of populations at different levels. In some of them, each geographical region is treated as a single homogeneous population, whereas other studies create different subdivisions: political (e.g., pooling populations by State), demographic (e.g., urban and rural), or ethnic (e.g., culture, self-declaration, or skin colour). In this study, we performed an enhanced reassessment of the genetic ancestry of ~ 1,300 Brazilians characterised for 46 autosomal Ancestry Informative Markers (AIMs). In addition, 798 individuals from twelve Brazilian populations representing the five geographical macro-regions of Brazil were newly genotyped, including a Native American community and a rural Amazonian community. Following an increasing North to South gradient, European ancestry was the most prevalent in all urban populations (with values up to 74%). The populations in the North consisted of a significant proportion of Native American ancestry that was about two times higher than the African contribution. Conversely, in the Northeast, Center-West and Southeast, African ancestry was the second most prevalent. At an intrapopulation level, all urban populations were highly admixed, and most of the variation in ancestry proportions was observed between individuals within each population rather than among population. Nevertheless, individuals with a high proportion of Native American ancestry are only found in the samples from Terena and Santa Isabel. Our results allowed us to further refine the genetic landscape of Brazilians while establishing the basis for the effective application of an autosomal AIM panel in forensic casework and clinical association studies within the highly admixed Brazilian populations.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Map of Brazil showing the geographical location of the populations considered in the present study.
Figure 2
Figure 2. MDS plot of the FST pairwise genetic distances between the studied populations.
(SI: Santa Isabel do Rio Negro; MA: Manaus; BE: Belém; PE: Pernambuco; AL: Alagoas; MS: Mato Grosso do Sul; TE: Terena; MG: Minas Gerais; ES: Espírito Santo; RJ: Rio de Janeiro; SP: São Paulo; PR: Paraná; SC: Santa Catarina; RS: Rio Grande do Sul.) FST genetic distances were assessed by Arlequin software and the MDS plot was represented using the software STATISTICA.
Figure 3
Figure 3. Average ancestral membership proportions obtained for the Brazilian testing populations using 46 AIM-Indels.
Estimates were obtained using STRUCTURE, for the following options: k=3; 100,000 burnin steps followed by 100,000 MCMC iterations; Admixture model (“Use population Information to test for migrants”); and allele frequencies were correlated and updated using only individuals with POPFLAG=1.
Figure 4
Figure 4. Individual ancestry estimates obtained for the HGDP-CEPH reference samples and individuals tested from Brazilian populations using 46 AIM-Indels (AFR: Africa; EUR: Europe; NAM: Native American; SI: Santa Isabel do Rio Negro; MA: Manaus; BE: Belém; PE: Pernambuco; AL: Alagoas; MS: Mato Grosso do Sul; TE: Terena; MG: Minas Gerais; ES: Espírito Santo; RJ: Rio de Janeiro; SP: São Paulo; PR: Paraná; SC: Santa Catarina; RS: Rio Grande do Sul).
Ancestry estimates were obtained using STRUCTURE, for the following options: k=3; 100,000 burnin steps followed by 100,000 MCMC iterations; Admixture model (“Use population Information to test for migrants”); and allele frequencies were correlated and updated using only individuals with POPFLAG=1.
Figure 5
Figure 5. Comparison of the European, African and Native American ancestry estimates obtained in the present work and in previous studies for the five regions of Brazil.
In the present work, the overall values indicated for each region are a weighted average of ancestry estimates of the population samples studied in that region considering their respective representation among inhabitants. A: Callegari-Jacques et al. [10]; B: Godinho et al. [11]; C: Lins et al. [20]; D: Pena et al. [40]; E: this study.

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References

    1. Parra EJ, Marcini A, Akey J, Martinson J, Batzer MA et al. (1998) Estimating African American admixture proportions by use of population-specific alleles. Am J Hum Genet 63: 1839-1851. doi:10.1086/302148. PubMed: 9837836. - DOI - PMC - PubMed
    1. Kosoy R, Nassir R, Tian C, White PA, Butler LM et al. (2009) Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Hum Mutat 30: 69-78. doi:10.1002/humu.20822. PubMed: 18683858. - DOI - PMC - PubMed
    1. Pereira R, Phillips C, Pinto N, Santos C, Santos SEB et al. (2012) Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing. PLOS ONE 7: e29684. doi:10.1371/journal.pone.0029684. PubMed: 22272242. - DOI - PMC - PubMed
    1. Pritchard JK, Donnelly P (2001) Case-control studies of association in structured or admixed populations. Theor Popul Biol 60: 227-237. doi:10.1006/tpbi.2001.1543. PubMed: 11855957. - DOI - PubMed
    1. Zembrzuski VM, Callegari-Jacques SM, Hutz MH (2006) Application of an African Ancestry Index as a genomic control approach in a Brazilian population. Ann Hum Genet 70: 822-828. doi:10.1111/j.1469-1809.2006.00270.x. PubMed: 17044857. - DOI - PubMed

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Financial support was granted by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ) and DNA Program – State University and Justice Court of Rio de Janeiro (UERJ/TJRJ/MPRJ), Brazil. IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education and is partially supported by the Portuguese Foundation for Science and Technology (FCT). RP is supported by a postdoctoral fellowship from FCT (SFRH/BPD/81986/2011). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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