Data and Meta

'data/SNPs' contains SNP data provided in plink and gds format along with a README of how each file was produced. 'data/spatial' contains the shapefiles used for the maps. Please uncompress each one before use. 'meta/maizteocintle_SNP50k_meta_extended.txt' is a text file containing sampling locality, lat, long, and other metadata of each of the samples. Columns correspond to the data collected as part of the Global Maize Proyect and are further detailed at http://www.biodiversidad.gob.mx/genes/pdf/proyecto/Anexo13_Base %20de%20datos/Contenido%20y%20observaciones%20de%20la%20BdeD.pd

Scripts for analyses and plots

Content: 'admixtureplot.R' to plot admixture analyses, 'maices_estimatingpopgenstats_wrapall.R' R code for estimating He, Ho, and Fst, 'maices_PCAs_plots.html' and 'maices_PCAs_plots.Rmd' show a Rmarkdown document used to plot the PCA, NJ trees and maps. 'runadmixture.sh' code used to run admixture. These scripts need the data and metada available at the DataandMetadata.zip section of this repositor

Genomic Insights into the Ancestry and Demographic History of South America

<div><p>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.</p></div

Global ancestry analysis of South American populations.

<p>(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. <i>K</i> = 4 and <i>K</i> = 13 models are shown above, <i>K</i> = 2 through <i>K</i> = 15 models are available in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005602#pgen.1005602.s004" target="_blank">S4</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005602#pgen.1005602.s005" target="_blank">S5</a> Figs.</p

Native American ancestry specific analysis.

<p>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.</p

Global ancestry proportions estimated through ADMIXTURE K = 4.

<p>Global ancestry proportions estimated through ADMIXTURE K = 4.</p

European ancestry specific analysis.

<p>(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 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005602#sec008" target="_blank">Methods</a>).</p

Models of Migration into the Caribbean after the advent of admixture.

1<p>Three migration models were tested for each admixed population: a simple model of single pulses of migrants from each source population, beginning with Europeans and Native Americans at T₁ followed by African migrants at T₂ (EUR,NAT+AFR); the simple model followed by an additional pulse of European migrants (EUR,NAT+AFR+EUR); the simple model followed by an additional pulse of African migrants (EUR,NAT+AFR+AFR). Log likelihoods given either model were compared and we present the model with the best Bayesian Information Criterion (log likelihood values in bold).</p>2<p>The maximum likelihood estimate of time since admixture initially began. We assume prior migration between the populations was zero. Time since migration began is indicated in generations.</p

Demographic reconstruction since the onset of admixture in the Caribbean.

<p>We used the length distribution of ancestry tracts within each population from A) insular and B) mainland Caribbean countries of origin. Scatter data points represent the observed distribution of ancestry tracts, and solid-colored lines represent the distribution from the model, with shaded areas indicating 68.3% confidence intervals. We used Markov models implemented in <i>Tracts</i> to test different demographic models for best fitting the observed data. Insular populations are best modeled when allowing for a second pulse of African ancestry, and mainland populations when a second pulse of European ancestry is allowed. Admixture time estimates (in number of generations ago), migration events, volume of migrants, and ancestry proportions over time are given for each population under the best-fitting model. The estimated age for the onset of admixture among insular populations is consistently older (i.e., 16–17) compared to that among mainland populations (i.e., 14).</p

Sub-continental origin of Native American components in the Caribbean.

<p>A) Ancestry-specific PCA analysis restricted to Native American segments from admixed Caribbean individuals (colored circles) and a reference panel of indigenous populations (gray symbols) from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003925#pgen.1003925-Reich1" target="_blank">[11]</a>, grouped by sampling location. Darker symbols denote countries of origin with populations clustering closer to our Caribbean samples. Indigenous Colombian populations were classified into East and West of the Andes to ease the interpretation of their differential clustering in ASPCA. Population labels are shown for samples defining PC axes and representative clusters within locations. B) ADMIXTURE model for <i>K</i> = 16 ancestral clusters considering additional Latino samples, a representative subset of African and European source populations, and 52 Native American populations from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003925#pgen.1003925-Reich1" target="_blank">[11]</a>, plus three additional Native Venezuelan tribes genotyped for this project. Vertical thin bars represent individuals and white spaces separate populations. Native American populations from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003925#pgen.1003925-Reich1" target="_blank">[11]</a> are grouped according to linguistic families reported therein. Labels are shown for the populations representing the 12 Native American clusters identified at <i>K</i> = 16. Clusters involving multiple populations are identified by those with the highest membership values. C) Map showing the major indigenous components shared across the Caribbean basin as revealed by ADMIXTURE at <i>K</i> = 16 from B). Namely, Mesoamerican (blue), Chibchan (yellow), and South American (green). Colored bars represent individuals and their approximate sampling locations. Bars pooling genetically similar individuals from more than one population are plotted from left to right following north to south coordinates as listed by population labels. Guarani, Wichi, and Chane from north Argentina are pooled with Arara but only the location of the latter is shown to allow us to provide a zoomed view of the Caribbean region (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003925#pgen.1003925-Reich1" target="_blank">[11]</a> for the full map of sampling locations). The thick arrow represents schematically the most accepted origin of the Arawak expansion from South America into the Great Antilles around 2,500 years ago according to linguistic and archaeological evidence <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003925#pgen.1003925-Diamond1" target="_blank">[30]</a>. Asterisks next to population labels denote Arawakan populations included in our reference panel. The thin arrow indicates gene flow between South America and Mesoamerica, possibly following a coastal or maritime route, accounting for the Mayan mixture and supporting pre-Columbian back migrations across the Caribbean.</p