Genomic Insights into the Ancestry and Demographic History of South America.
Genomic Insights into the Ancestry and Demographic History of South America.
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DOI：
10.1371/journal.pgen.1005602
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发表时间：
2015-12
期刊：
影响因子：
4.5
通讯作者：
Bustamante CD
中科院分区：
文献类型：
--
作者：
Homburger JR;Moreno-Estrada A;Gignoux CR;Nelson D;Sanchez E;Ortiz-Tello P;Pons-Estel BA;Acevedo-Vasquez E;Miranda P;Langefeld CD;Gravel S;Alarcón-Riquelme ME;Bustamante CD
南美洲有一个复杂的人口历史，在前殖民时代和后殖民时代的多次移民和混合事件形成的。南美洲在14，000多年前由美洲原住民定居，与美洲其他地区类似，经历了欧洲和非洲人的移民。然而，这些事件的时间和规模导致了整个拉丁美洲明显不同的混合模式。我们使用来自5个国家（哥伦比亚，厄瓜多尔，秘鲁，智利和阿根廷）的437个混合个体的全基因组SNP数据来探索南美拉丁美洲人的人口结构和人口统计学历史。我们将这些数据与来自非洲，亚洲，欧洲和美洲的人口参考面板相结合，以进行全球血统分析，并推断混合个体的欧洲和美洲原住民血统成分的次大陆起源。通过应用特定祖先的PCA分析，我们发现，大多数南美拉丁美洲人的欧洲血统是从伊比利亚半岛，但是，许多人的祖先追溯到意大利，特别是在阿根廷。我们发现一个很强的梯度，在美洲原住民血统组成部分的南美洲拉丁美洲人与原产国和当地土著人口的地理。例如，秘鲁人的美洲原住民基因组片段与克丘亚人和艾马拉人等安第斯土著民族有更大的亲缘关系，而秘鲁人的美洲原住民单倍型往往与南美洲北方的亚马逊河和沿海部落聚在一起。使用祖先道长度分析，我们模拟了后殖民南美移民的历史，在拉丁美洲最年轻的欧洲殖民（9-14代前），与欧洲移民的额外的强烈脉冲发生在3至9代前。这些遗传足迹可以影响我们对生物医学特征的人群水平差异的理解，从而为该地区未来的医学遗传研究提供信息。南美洲拥有超过4亿人口，拥有丰富的人口历史，包括美洲原住民定居，欧洲殖民和非洲奴隶贸易。我们使用基因组数据来推断哪些来自欧洲和美洲的人群促成了这些混合事件。我们提供的证据，混合南美拉丁美洲人的美洲原住民血统的多个起源。美洲原住民祖先的组成部分与地理密切相关，表明欧洲殖民者和当地美洲原住民人口之间的混合发生在整个南美洲。我们还表明，南美洲拉丁美洲人的欧洲血统主要来自伊比利亚半岛，然而，相当数量的阿根廷人有欧洲血统来自其他南欧地区。南美洲人群中欧洲混血儿的遗传信号比在墨西哥和加勒比地区观察到的信号更年轻。我们发现的第二个欧洲移民到南美洲的许多地区的原始殖民化之后的脉冲的证据。这些结果表明，在南美洲的拉丁美洲人口的异质性，并有助于阐明复杂的遗传和混合事件，塑造了该地区的人口结构。
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. South America is home to over 400 million people who share a rich demographic history, including settlement by Native Americans, European colonization, and the African slave trade. We use genomic data to infer which populations from Europe and the Americas contributed to these admixture events. We provide evidence for multiple origins of the Native American ancestry of admixed South American Latinos. The Native American ancestral component correlates strongly with geography, indicating that admixture occurred between European colonists and local Native American populations throughout South America. We also show that the European ancestry of South American Latinos comes mainly from the Iberian peninsula, however, a significant number of Argentinians have European ancestry from other Southern European regions. The genetic signal of European admixture in South American populations is younger than the signal observed in Mexico and the Caribbean. We find evidence for a second pulse of European migration to many regions of South America subsequent to the original colonization. These results demonstrate the heterogeneous nature of the Latino population in South America and help elucidate the complex genetic and admixture events that shaped the population structure of the region.