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.

中文翻译：

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南美洲西部当前的基因组景观：安第斯山脉、亚马逊流域和太平洋海岸。


对南美洲原住民遗传多样性的研究有助于揭示该大陆的人口分布和分化，但主要生态地理领域的可用数据很少。其中包括太平洋海岸，一条潜在的早期迁徙路线；安第斯山脉，是最广阔、最复杂的社会的所在地，也是非洲大陆使用最广泛的土著语系之一（盖丘亚语）的所在地；亚马逊流域的人口结构和丰富的文化多样性尚未得到充分研究。在这里，我们探索了来自这三个领域的 176 名个体的基因结构，并使用 Affymetrix Human Origins 阵列进行了基因分型。我们推断美洲原住民血统成分中有多种血统来源；一种在海岸和安第斯山脉具有明显的优势，并且在邻近的亚马逊流域至少有两个不同的基底，包括以前未被发现的厄瓜多尔北部和哥伦比亚的祖先特征。亚马逊种群最近也参与了彼此之间以及跨生态地理领域的基因流动，这与小型、孤立群体的传统观点不符。同一语系使用者之间的远距离遗传联系表明，这里的土著语言不仅仅是通过文化接触传播的。最后，美洲原住民在不同时期与后哥伦布时代的欧洲和非洲人混合在一起，很少有长期隔离的情况。通过我们的结果，我们强调了将非洲大陆的未充分研究区域纳入高分辨率遗传学研究的重要性，并且我们说明了 SNP 芯片阵列在信息丰富的区域规模分析中的潜力。