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.
Highlights
Our understanding of fine-scale patterns of population structure in humans has dramatically increased with the advent and deployment of fast, inexpensive, and accurate genome-wide technologies for assaying variation [1,2,3]
Our understanding of regional patterns of genomic variation is quite poor in many parts of the world in populations that are currently underrepresented in GWAS studies, including those in Latin America [4]
As expected from historical records [21,22] and previous results from other Latino populations in the Caribbean [6] and Mexico [5], South American Latino individuals show a mixture of European, Native American, and African ancestry
Summary
Our understanding of fine-scale patterns of population structure in humans has dramatically increased with the advent and deployment of fast, inexpensive, and accurate genome-wide technologies for assaying variation [1,2,3]. Our understanding of regional patterns of genomic variation is quite poor in many parts of the world in populations that are currently underrepresented in GWAS studies, including those in Latin America [4]. Understanding patterns of genomic variation is especially important for populations throughout the Americas, which have undergone multiple recent admixture events, making the reconstruction of their evolutionary past and the design of multi-ethnic medical genetic studies challenging. The South American landmass features unique geographic, archaeological, and historical records that are distinct from other regions of the Americas [8]. The contributions of these events to patterns of genomic variation remains to be laid out to a greater extent. The largest human settlements in South America, occurred throughout the Andean region and likely represent a major source of Native American variation in present day South
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