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, 11 (12), e1005602

Genomic Insights Into the Ancestry and Demographic History of South America


Genomic Insights Into the Ancestry and Demographic History of South America

Julian R Homburger et al. PLoS Genet.


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.

Conflict of interest statement

I have read the journal's policy and the authors of this manuscript have the following competing interests: CDB is on the Scientific Advisory Boards of, Personalis, Liberty Biosecurity, 23andMe’s ‘‘Roots into the Future’’ project and Etalon DX. He is also a founder and Chair of the SAB of IdentifyGenomics. None of these entities played a role in the design, interpretation, or presentation of these results.


Fig 1
Fig 1. Global ancestry analysis of South American populations.
(a) Principal Components Analysis of admixed individuals and continental reference panels. Each individual is represented as a point colored by country, region, or continent of origin. (b) Map of sampled populations. Countries of origin for admixed South Americans are highlighted and colored as in (a). (c) ADMIXTURE plot of admixed individuals and continental reference panels. Each individual is represented as a thin vertical bar. The colors represent the proportion of ancestry assigned to each cluster for each individual. K = 4 and K = 13 models are shown above, K = 2 through K = 15 models are available in S4 and S5 Figs.
Fig 2
Fig 2. European ancestry specific analysis.
(a) European Ancestry Specific PCA of haploid genomes from Colombia and Ecuador with greater than 25% estimated European ancestry combined with 2,882 haploid genomes from the POPRES data set. Admixed Latino individuals are shown in shades of grey, while European individuals are colored according to region and represented as a two-character country code. (b) European Ancestry Specific PCA of haploid genomes from Peru, Chile, and Argentina with greater than 25% estimated European ancestry combined with the same reference European data set as in (a). The inset map shows the color-coded regions within Europe of the POPRES reference panel. To maximize SNP overlap between data sets, ASPCA analyses were performed separately for each subset of South American Latino populations (see Methods).
Fig 3
Fig 3. Native American ancestry specific analysis.
Native American Ancestry Specific PCA of all Latino haploid genomes with greater than 25% estimated Native American ancestry. Each masked haploid genome from admixed individuals is represented by a single point colored by population of origin. Native American haploid genomes are plotted as the first three letters of the population name and colored according to the regional groupings. The approximate sampling location for each of the Native American parental populations is shown on the map of Latin America.
Fig 4
Fig 4. Tract length analysis and admixture times.
(a) Bar graph comparing estimated migration times for the best-fitting model in each of the South American countries (blue) with previously published migration times for the Caribbean islands [6] and Mexico [40] (grey). The estimated second European migration time (in generations ago) is shown in dark blue for the models. (b-f) Best-fitting Tracts model for Colombia (b) Ecuador (c), Peru (d), Chile (e), and Argentina (f). These models have an initial admixture event between Native American and European populations followed by a pulse of African migration, subsequently followed by an additional European migration event. The ancestry tract decay (top) compares the expected and observed tract length distributions based upon the best-fit model, with the shaded area indicating the 68.7% confidence interval. The points indicate the observed values. The migration model (bottom of each graph) shows the change in admixture proportion over time. From left to right along the time scale in generations ago (GA), the circles on top indicate the occurrence of admixture events, with the size of the circle corresponding to the magnitude of incoming migrants from each of the ancestral populations.

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