Afro-Derived Amazonian Populations: Inferring Continental Ancestry and Population Substructure

Abstract

A panel of Ancestry Informative Markers (AIMs) was used to identify population substructure and estimate individual and overall interethnic admixture in 294 individuals from seven African-derived communities of the Brazilian Amazon. A panel of 48 biallelic markers, representing the insertion (IN) or the deletion (DEL) of small DNA fragments, was employed for this purpose. Overall interethnic admixture estimates showed high miscegenation with other ethnic groups in all populations (between 46% and 64%). The proportion of ancestral genes varied significantly among individuals of the sample: the contribution of African genes varied between 12% and 75%; of European genes between 10% and 73%; and of Amerindians genes between 8% and 66%. The obtained data reveal a high contribution of Amerindian genes in these communities, unlike in other African-derived communities of the Northeast and the South of Brazil. In addition, the majority of the Amerindian contribution may result from the preferential inclusion of indigenous women in the African descent groups. High heterogeneity of the proportion of interethnic admixture among analyzed individuals was found when the proportion of ancestral genes of each individual of the sample was estimated. This heterogeneity is reflected in the fact that four populations can be considered as substructured and that the global African descent sample is possibly formed by two subpopulations. 46% and 64%). The proportion of ancestral genes varied significantly among individuals of the sample: the contribution of African genes varied between 12% and 75%; of European genes between 10% and 73%; and of Amerindians genes between 8% and 66%. The obtained data reveal a high contribution of Amerindian genes in these communities, unlike in other African-derived communities of the Northeast and the South of Brazil. In addition, the majority of the Amerindian contribution may result from the preferential inclusion of indigenous women in the African descent groups. High heterogeneity of the proportion of interethnic admixture among analyzed individuals was found when the proportion of ancestral genes of each individual of the sample was estimated. This heterogeneity is reflected in the fact that four populations can be considered as substructured and that the global African descent sample is possibly formed by two subpopulations. Keywords AMAZON, AIM, AFRICAN DESCENT, INDEL, POPULATION SUBSTRUCTUREThe Brazilian population is the product of the miscegenation of three main ethnic groups: Amerindians, Europeans, and Africans. It is estimated that approximately four million Africans were brought by force to Brazil as slaves between 1550 and 1870 (Klein 1986). The distinct geographical regions of Brazil received different numbers of African slaves, being greater in the Northeast and lower in the North (Santos and Guerreiro 1995). The arrival of African slaves to the Amazon began in the mid-17th century (1750). It is estimated that at least 53,000 Africans arrived in the Brazilian Amazon during the ...

Ancestry, diversity, and genetics of health-related traits in African-derived communities (quilombos) from Brazil

“…Regarding autosomal ancestry, as expected, most of the evaluated communities have predominant African ancestry, ranging from 38.2% in Pacoval (Northern Brazil) to 97.33% in Sertão do Valongo (Southern Brazil) (Da Silva et al 1999;De Oliveira et al 2001;de Souza and Culpi 2005;Maciel et al 2011) (Fig. 1, Tables 1 and S2).…”

“…Variability in ancestry proportions is probably associated with the founder effect (as many quilombos are known to have been founded by few individuals) as well as with differences in the level of admixture over the generations. Thus, greater proportions of African ancestry are observed in Cajueiro;16-Pontal;17-Mimbó;18-Sítio Velho;19-Mocambo;20-Tamauari;21-Barra;22-São Gonçalo;23-Gaucinha;24-Marinhos;25-Abobral;26-André Lopes;27-Galvão;28-Ivapo-runduva;29-Maria Rosa;30-Nhunguara;31-Pedro Cubas;32-Pilões;33-São Pedro;34-Sapatu;35-Kalunga;36-Paredão;37-Sertão do Valongo (Schneider et al 1987;Bortolini et al 1995Bortolini et al , 1997Bortolini et al , 1998Bortolini et al , 1999Arpini-Sampaio et al 1999;Guerreiro et al 1999;Ribeiro-Dos-Santos et al 2002;Cayres Vallinoto et al 2003;Abe-Sandes et al 2004;de Souza and Culpi 2005;Barbosa et al 2006;Silva et al 2006;Carvalho et al 2008;Scliar et al 2009;Ribeiro et al 2009Ribeiro et al , 2011Amorim et al 2011;Maciel et al 2011;Palha et al 2011;Kimura et al 2013Kimura et al , 2017…”

Genetics and genomics in Brazil: a promising future

“…It has been shown that European ancestry is evenly preponderant across the country; the African contribution has reached the highest proportion in the Northeast (∼30.3%), followed in decreasing order by the Southeast (∼18.9%), South (∼12.7%), and North (∼10.9%) regions, while the Amerindian contribution is the highest in the North (∼19.4%) region, and relatively evenly spread across the other regions (Santos et al 2010; Pena et al 2011). An unexpected high Amerindian contribution is also found in semi-isolated communities founded by African-slaves refugees, the “quilombos” (Lopes Maciel et al 2011; Kimura et al 2013; Gontijo et al 2014). Our colonization history also accounts for the high incidence of some diseases.…”

Inferring paternal history of rural African‐derived Brazilian populations from Y chromosomes

“…In general, nuclear DNA polymorphisms showed a trihybrid pattern of admixture among Africans, Europeans, and Native Americans, in different proportions Cayres-Vallinoto, Vallinoto, Valente, & Guerreiro, 2003;Cotrim, Auricchio, Vicente, Otto, & Mingroni-Netto, 2004;Da Silva et al, 1999;Kimura et al, 2013;Lopes Maciel et al, 2011;Scliar, Vaintraub, Vaintraub, & Fonseca, 2009). In general, nuclear DNA polymorphisms showed a trihybrid pattern of admixture among Africans, Europeans, and Native Americans, in different proportions Cayres-Vallinoto, Vallinoto, Valente, & Guerreiro, 2003;Cotrim, Auricchio, Vicente, Otto, & Mingroni-Netto, 2004;Da Silva et al, 1999;Kimura et al, 2013;Lopes Maciel et al, 2011;Scliar, Vaintraub, Vaintraub, & Fonseca, 2009).…”

“…Quilombo remnants from different parts of Brazil have been investigated in genetic surveys, with the goal of estimating the contribution of distinct ancestral components to current populations. In general, nuclear DNA polymorphisms showed a trihybrid pattern of admixture among Africans, Europeans, and Native Americans, in different proportions Cayres-Vallinoto, Vallinoto, Valente, & Guerreiro, 2003;Cotrim, Auricchio, Vicente, Otto, & Mingroni-Netto, 2004;Da Silva et al, 1999;Kimura et al, 2013;Lopes Maciel et al, 2011;Scliar, Vaintraub, Vaintraub, & Fonseca, 2009). Uniparental markers (Y chromosome and mitochondrial DNA) revealed the demographic phenomenon of directional mating of European males with Native American and African females, and African males with Native American females (Abe-Sandes, Silva, & Zago, 2004;Bortolini et al, 1999;Carvalho et al, 2010;Ribeiro-dos-Santos et al, 2002;Ribeiro et al, 2009Ribeiro et al, , 2011.…”