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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南美西部地区当前的基因组景观：安第斯山脉，亚马逊地区和太平洋海岸。

对南美原住民遗传多样性的研究有助于阐明该大陆的人种和分化，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（一条可能的早期迁徙路线）；安第斯山脉是最广阔的复杂社会的所在地，也是非洲大陆使用最广泛的土著语言家族之一（盖丘亚语）；和亚马孙地区，其人口结构被广泛研究，文化多样性丰富。在这里，我们探索了来自这三个域的176个个体的遗传结构，并使用Affymetrix人类起源阵列进行了基因分型。我们在美国原住民血统组成部分中推断出多种血统起源；其中一种在海岸和安第斯山脉具有明显优势，在邻近的亚马逊河至少有两种不同的底物，包括厄瓜多尔北部和哥伦比亚先前未发现的血统特征。亚马逊种群还相互之间以及跨生态地理区域参与了最近的基因流动，这与传统的小而孤立群体的观点不符。同一语言家庭的讲者之间的远距离遗传联系表明，这里的土著语言并不是仅通过文化交流而传播的。最后，美洲原住民在不同时期与后哥伦布时期的欧洲和非洲人口混合在一起，很少出现长期孤立的情况。通过我们的研究结果，我们强调了在高分辨率遗传研究中纳入未被研究的区域的重要性，并说明了SNP芯片阵​​列在信息性区域规模分析中的潜力。