The Current Genomic Landscape of Western South America: Andes, Amazonia, and Pacific Coast

Abstract

Studies of Native South American genetic diversity have helped to shed light on the peopling and differentiation of the continent, but available data are sparse for the major ecogeographic domains. These include the Pacific Coast, a potential early migration route; the Andes, home to the most expansive complex societies and to one of the most widely spoken indigenous language families of the continent (Quechua); and Amazonia, with its understudied population structure and rich cultural diversity. Here, we explore the genetic structure of 176 individuals from these three domains, genotyped with the Affymetrix Human Origins array. We infer multiple sources of ancestry within the Native American ancestry component; one with clear predominance on the Coast and in the Andes, and at least two distinct substrates in neighboring Amazonia, including a previously undetected ancestry characteristic of northern Ecuador and Colombia. Amazonian populations are also involved in recent gene-flow with each other and across ecogeographic domains, which does not accord with the traditional view of small, isolated groups. Long-distance genetic connections between speakers of the same language family suggest that indigenous languages here were spread not by cultural contact alone. Finally, Native American populations admixed with post-Columbian European and African sources at different times, with few cases of prolonged isolation. With our results we emphasize the importance of including understudied regions of the continent in high-resolution genetic studies, and we illustrate the potential of SNP chip arrays for informative regional-scale analysis.

A Paleogenomic Reconstruction of the Deep Population History of the Andes

“…The percentage of total variation explained by each PC is shown in parentheses on each axis.

Figure S4 PCA of Additional Samples Removed from Figure 2 , Related to Figure 2 Principal Components Analysis (PCA) of ancient samples projected onto modern individuals from the Andes and Amazon region ( Barbieri et al., 2019 ). Eigenvector 1 coordinates were reversed so that the PCA correlates with geographical structure.

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“… Principal Components Analysis (PCA) of ancient samples projected onto modern individuals from the Andes and Amazon region ( Barbieri et al., 2019 ). Eigenvector 1 coordinates were reversed so that the PCA correlates with geographical structure.…”

“…We combined the new data with previously published ancient DNA data from Lindo et al., 2018 , Moreno-Mayar et al., 2018a , Moreno-Mayar et al., 2018b ), Posth et al., 2018 , Raghavan et al., 2015 , Rasmussen et al., 2014 , Rasmussen et al., 2015 , Scheib et al., 2018 , and Schroeder et al. (2018) and compared it with the genetic diversity of different present-day peoples ( Barbieri et al., 2019 , Mallick et al., 2016 , Reich et al., 2012 ). We determined when the genetic structure observed today in the Central Andes first began to develop and assessed the degree to which gene flows over time have modulated this structure.…”

The genetic structure and adaptation of Andean highlanders and Amazonian dwellers is influenced by the interplay between geography and culture

“…Archaeological findings of recent decades have rejected the traditional view of the Amazonian environment as incompatible with complex pre-Columbian societies, and have revealed that the Amazonian basin has produced the earliest ceramics of South America, that endogenous agricultural complex societies have developed there, and that population sizes were larger than previously thought 22 . Population genetics studies by Barbieri et al 23 have reported episodes of gene flow in the Amazonia, which suggest that Amazonian populations were not necessarily isolated groups. Moreover, people living in the Peruvian Coast, the Andes, and the Amazon Yunga had cultural and commercial interactions during the last millennia, sharing practices such as sweet potato and manioc cultivation, ceramic iconography and styles (e.g.…”

Estudio ecomorfológico de la variación craneana en poblaciones prehistóricas de Perú

“…Esto brinda apoyo a algunos trabajos previos que describieron la existencia de una varianza baja entre poblaciones de los Andes, fundamentalmente debida a aislamiento geográfico, especialmente entre muestras de los andes/amazonia, y/o costa/sierra (Hrdlička 1911(Hrdlička , 1914Newman 1943;Tarazona-Santos et al 2001;Ross et al 2008). Dicho patrón puede ser resultado de dinámicas poblacionales con matrimonios preferenciales basadas en la exogamia y/o exoginia, tal como ha sido reportado recientemente para poblaciones de los Andes, Amazonia, y la costa Pacífica, basados en una combinación de datos genéticos y lingüísticos (Arias et al 2017(Arias et al , 2018Barbieri et al 2019). La presencia de sociedades de gran escala, tanto en los Andes como en la costa, puede haber promovido el flujo génico entre individuos, así como también combinado poblaciones que carecían de contacto previo o que era muy esporádico.…”