Admixture in Latin America: Geographic Structure, Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 Individuals

Ruiz-Linares, Andrés; Adhikari, Kaustubh; Acuña-Alonzo, Víctor; Quinto‐Sanchez, Mirsha; Jaramillo, Claudia; Arias, William; Fuentes, Macarena; Pizarro, María; Everardo, Paola; Ávila, Francisco de; Gómez-Valdés, Jorge; León-Mimila, Paola; Hünemeier, Tábita; Ramallo, Virgínia; Cerqueira, Caio César Silva de; Burley, Mari-Wyn; Konca, Esra; Oliveira, Marcelo Zagonel de; Veronez, Maurício Roberto; Rubio‐Codina, Marta; Attanasio, Orazio; Gibbon, Sahra; Ray, Nicolas; Gallo, Carla; Poletti, Giovanni; Rosique, Javier; Schüler‐Faccini, Lavínia; Salzano, Francisco M.; Bortolini, Maria-Cátira; Canizales‐Quinteros, Samuel; Rothhammer, Francisco; Bedoya, Gabriel; Balding, David J.; González‐José, Rolando

doi:10.1371/journal.pgen.1004572

Cited by 367 publications

(433 citation statements)

References 45 publications

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“…In particular, we explore how genomic ancestry correlates with education, income, location, and mating patterns. These ethnically homogeneous but genetically admixed populations have more diverse physical features compared with genetically homogeneous populations (12).…”

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confidence: 99%

Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns

Zou

Park

Burchard

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Nonrandom mating in human populations has important implications for genetics and medicine as well as for economics and sociology. In this study, we performed an integrative analysis of a large cohort of Mexican and Puerto Rican couples using detailed socioeconomic attributes and genotypes. We found that in ethnically homogeneous Latino communities, partners are significantly more similar in their genomic ancestries than expected by chance. Consistent with this, we also found that partners are more closely related—equivalent to between third and fourth cousins in Mexicans and Puerto Ricans—than matched random male–female pairs. Our analysis showed that this genomic ancestry similarity cannot be explained by the standard socioeconomic measurables alone. Strikingly, the assortment of genomic ancestry in couples was consistently stronger than even the assortment of education. We found enriched correlation of partners’ genotypes at genes known to be involved in facial development. We replicated our results across multiple geographic locations. We discuss the implications of assortment and assortment-specific loci on disease dynamics and disease mapping methods in Latinos.

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confidence: 99%

Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns

Zou

Park

Burchard

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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“…Continental genomic ancestry in Latin America (and specifically, in Brazil) is correlated with a set of phenotypes, such as skin color and self-reported ethnicity, and social and cultural features, such as socioeconomic status (15)(16)(17). We observed a positive correlation across the three EPIGEN populations between SNP-specific Africans/Europeans F ST (a measurement of informativeness of ancestry) and SNP-specific F IT (a measurement of departure from Hardy-Weinberg equilibrium) …”

Section: Resultsmentioning

confidence: 99%

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

Kehdy

Gouveia

Machado

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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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 genomewide 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.Latin America | population genetics | Salvador SCAALA | Bambuí Cohort Study of Ageing | Pelotas Birth Cohort Study L atin Americans, who are classical models of the effects of admixture in human populations (1, 2), remain underrepresented in studies of human genomic diversity, notwithstanding recent studies (3, 4). Indeed, no large genome-wide study on admixed South Americans has been conducted so far. Brazil is the largest and most populous Latin-American country. Its over 200 million inhabitants are the product of post-Columbian admixture between Amerindians, Europeans colonizers or immigrants, and African slaves (1). Interestingly, Brazil was the destiny of nearly 40% of the African diaspora, receiving seven times more slaves than the United States (nearly 4 million vs. 600,000).Here, we present results of the EPIGEN Brazil Initiative (https:// epigen.grude.ufmg.br), the most comprehensive up-to-date genomic analysis of a Latin-American population. We genotyped nearly 2.2 million SNPs in 6,487 admixed individuals from three population-based cohorts from different regions with distinct demographic and socioeconomic backgrounds and sequenced the whole genome of 30 individuals from these populations at an To whom correspondence should be addressed. Email: edutars@ic...

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“…Genomic data involving 730,525 marker SNPs was obtained from these samples (see further details in Ruiz-Linares et al, 2014). The SNPs were pruned to remove Linkage Disequilibrium, and after removing correlated SNPs, 90,000 SNPs were left for analysis.…”

Section: Estimation Of Genetic Ancestrymentioning

confidence: 99%

Facial asymmetry and genetic ancestry inLatinAmerican admixed populations

Quinto‐Sanchez

Adhikari

Acuña-Alonzo

et al. 2015

American J Phys Anthropol

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Fluctuating and directional asymmetry are aspects of morphological variation widely used to infer environmental and genetic factors affecting facial phenotypes. However, the genetic basis and environmental determinants of both asymmetry types is far from being completely known. The analysis of facial asymmetries in admixed individuais can be of help to characterize the impact of a genome's heterozygosity on the deveiopmental basis of both fl.uctuating and directional asymmetries. Here we characterize the association between genetic ancestry and individual asymmetry on a sample of Latin-American admixed populations. To do so, three-dimensional (3D) facial shape attributes were explored on a sample of 4,104 volunteers aged between 18 and 85 years. Individual ancestry and heterozygosity was estimated using more than 730,000 genome-wide markers. Multivariate techniques applied to geometric morphometric data were used to evaluate the magnitude and significance of directional and ftuctuating asymmetry (FA), as well as correiations and multipie regressions aimed to estimate the relationship between facial FA scores and heterozygosity and a set of covariates. Resuits indicate that directional and FA are both signi:ficant, the former being the strongest expression of asymmetry in this sample. In addition, our analyses suggest that there are some specific patterns of facial asymmetries characterizing the different ancestry groups. Finally, we find that more heterozygous individuais exhibit lower leveis of asymmetry. Our results highlight the importance of including ancestry-admixture estimators, especially when the analyses are aimed to compare leveis of asymmetries on groups differing on socioeconomic leveis, as a proxy to estimate developmental noise. Am J Phys Anthropol 000:000--000, 2015.

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Admixture in Latin America: Geographic Structure, Phenotypic Diversity and Self-Perception of Ancestry Based on 7,342 Individuals

Cited by 367 publications

References 45 publications

Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns

Genetic and socioeconomic study of mate choice in Latinos reveals novel assortment patterns

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

Facial asymmetry and genetic ancestry inLatinAmerican admixed populations

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