Genomic Insights into the Ancestry and Demographic History of South America

Abstract

South America has a complex demographic history shaped by multiple migration and admixture events in pre- and post-colonial times. Settled over 14,000 years ago by Native Americans, South America has experienced migrations of European and African individuals, similar to other regions in the Americas. However, the timing and magnitude of these events resulted in markedly different patterns of admixture throughout Latin America. We use genome-wide SNP data for 437 admixed individuals from 5 countries (Colombia, Ecuador, Peru, Chile, and Argentina) to explore the population structure and demographic history of South American Latinos. We combined these data with population reference panels from Africa, Asia, Europe and the Americas to perform global ancestry analysis and infer the subcontinental origin of the European and Native American ancestry components of the admixed individuals. By applying ancestry-specific PCA analyses we find that most of the European ancestry in South American Latinos is from the Iberian Peninsula; however, many individuals trace their ancestry back to Italy, especially within Argentina. We find a strong gradient in the Native American ancestry component of South American Latinos associated with country of origin and the geography of local indigenous populations. For example, Native American genomic segments in Peruvians show greater affinities with Andean indigenous peoples like Quechua and Aymara, whereas Native American haplotypes from Colombians tend to cluster with Amazonian and coastal tribes from northern South America. Using ancestry tract length analysis we modeled post-colonial South American migration history as the youngest in Latin America during European colonization (9–14 generations ago), with an additional strong pulse of European migration occurring between 3 and 9 generations ago. These genetic footprints can impact our understanding of population-level differences in biomedical traits and, thus, inform future medical genetic studies in the region.

Latin Americans show wide-spread Converso ancestry and the imprint of local Native ancestry on physical appearance

“…Since admixture proportions in Latin Americans vary greatly, we analyzed each individual separately; simulations confirmed the accuracy of GLOBETROTTER in this setting (Supplementary Note 1). Inferred dates for events involving Iberian components had a median of 10 generations (IQR=7-13), consistent with other estimates for admixture in Latin America 6,10,11 . Noticeably, individuals with more recent inferred dates of admixture have greater Native ancestry (Fig.…”

Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia

“…S4). These results are consistent with the ancestry estimations in Chilean individuals based on migration events in pre-and post-colonial periods reported by other groups (Reich et al 2012;Homburger et al 2015).…”

Mutations in BRCA1, BRCA2 and other breast and ovarian cancer susceptibility genes in Central and South American populations

“…South America has a complex demographic history shaped by multiple migration and admixture events in pre-and post-colonial times [104], including settlement by Native Americans, European colonization and the African slave trade [104]. Moreover, the continental ancestry of the admixed populations in South America is not homogenous.…”

“…Moreover, the continental ancestry of the admixed populations in South America is not homogenous. For example, the Argentine population is a mixture of European (0.673), Native American (0.277), West African (0.036) and East Asian (0.014) González-Rivera et al [53] components, while the proportions in the Peruvian population are European (0.26), Native American (0.683), West African (0.032) and East Asian (0.025) [104]. Uruguay is unique among South American countries in that it has almost no communities of Native American or African descent [105].…”