Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations.

While South Americans are underrepresented in human genomic diversity studies, Brazil has been a classical model for population genetics studies on admixture. We present the results of the EPIGEN Brazil Initiative, the most comprehensive up-to-date genomic analysis of any Latin-American population. A population-based genome-wide analysis of 6,487 individuals was performed in the context of worldwide genomic diversity to elucidate how ancestry, kinship, and inbreeding interact in three populations with different histories from the Northeast (African ancestry: 50%), Southeast, and South (both with European ancestry >70%) of Brazil. We showed that ancestry-positive assortative mating permeated Brazilian history. We traced European ancestry in the Southeast/South to a wider European/Middle Eastern region with respect to the Northeast, where ancestry seems restricted to Iberia. By developing an approximate Bayesian computation framework, we infer more recent European immigration to the Southeast/South than to the Northeast. Also, the observed low Native-American ancestry (6-8%) was mostly introduced in different regions of Brazil soon after the European Conquest. We broadened our understanding of the African diaspora, the major destination of which was Brazil, by revealing that Brazilians display two within-Africa ancestry components: one associated with non-Bantu/western Africans (more evident in the Northeast and African Americans) and one associated with Bantu/eastern Africans (more present in the Southeast/South). Furthermore, the whole-genome analysis of 30 individuals (42-fold deep coverage) shows that continental admixture rather than local post-Columbian history is the main and complex determinant of the individual amount of deleterious genotypes.

X-chromosomal genetic diversity and linkage disequilibrium patterns in Amerindians and non-Amerindian populations.

OBJECTIVES: We report X-chromosomal linkage disequilibrium (LD) patterns in Amerindian (Kogi, Wayuu, and Zenu) and admixed Latin American (Central Valley of Costa Rica and Southern Brazilian Gaucho) populations. METHODS: Short tandem repeats (STRs) widespread along the X-chromosome were investigated in 132 and 124 chromosomes sampled from the Amerindian tribes and the admixed Latin American populations, respectively. Diversity indexes (gene diversity and average numbers of alleles per locus) were estimated for each population and the level of LD was inferred with an exact test. RESULTS: The Amerindian populations presented lower genetic diversity and a higher proportion of loci in LD than the admixed ones. Two haplotype blocks were identified in the X-chromosome, both restricted to the Amerindians. The first involved DXS8051 and DXS7108 in Xp22.22 and Xp22.3, while the second found only among the Kogi, included eight loci in a region between Xp11.4 and Xq21.1. CONCLUSIONS: In accordance to previous work done with other populations, human isolates, such as Amerindian tribes, seem to be an optimal choice for the implementation of association studies due to the wide extent of LD which can be found in their gene pool. On the other hand, the low proportion of loci in LD found in both admixed populations studied here could be explained by events related to their history and similarities between the allele frequencies in the parental stocks.

Demographic and evolutionary trajectories of the Guarani and Kaingang natives of Brazil.

A total of 278 individuals from two Brazilian Indian tribes (Guarani and Kaingang) living in five different localities had their mitochondrial DNA sequenced for the first hypervariable segment (HVS-I), and a fraction of them was also studied for seven biallelic Y-chromosome polymorphisms. Nineteen HVS-I lineages were detected, which showed distinct distributions in the two tribes. The G(ST) value obtained with the mtDNA data is about 5 times higher for the Guarani as compared to the Kaingang, suggesting a higher level of differentiation between the three Guarani partialities than between the two Kaingang villages. Non-Amerindian admixture varied with sex and in the Guarani was only observed through the paternal line. Using these data and those of other Tupian and Jêan tribes, it was possible to make inferences about past migratory movements and the genetic differentiation of these populations.