从全基因组和全外显子组数据重建美洲原住民迁移
Reconstructing Native American Migrations from Whole-genome and Whole-exome Data
摘要：
有很大的科学和大众的兴趣，了解在美洲人口的遗传史。我们希望了解大陆的不同地区何时有人居住，定居者来自哪里，以及目前的居民与早期人口的遗传关系。最近的研究使用基因分型阵列和单亲标记揭开了非洲大陆遗传史的一部分。1000个基因组计划提供了一个独特的机会，通过提供来自哥伦比亚（CLM），墨西哥裔美国人（MXL）和波多黎各（PUR）人群的100多个测序的低覆盖率基因组和外显子组来提高我们对人群遗传历史的理解。在这里，我们探讨了非洲，欧洲和美洲原住民祖先对这些人群的基因组贡献。估计美洲原住民血统在MXL中占48%，在CLM中占25%，在PUR中占13%。PUR的美洲原住民祖先与奥里诺科河流域周围的人口关系最密切，证实了加勒比地区泰诺人的南美洲祖先。我们提出了新的方法来估计的等位基因频率在美洲原住民部分的人口，并模拟其分布使用的人口模型为三个祖先的美洲原住民人口。这些祖先很可能是连续分裂的：最有可能的情况是，基于16000年前美洲的人口（kya），支持MXL祖先分裂12.2kya，随后分裂为CLM和PUR 11.7kya。该模型还包括墨西哥的62，000人，哥伦比亚的8，700人和波多黎各的1，900人。建模身份的血统和祖先道的长度，我们发现，接触后的人口显着不同的有效规模和迁移模式，波多黎各显示最小的有效规模和早期从欧洲迁移。
英文摘要：
There is great scientific and popular interest in understanding the genetic history of populations in the Americas. We wish to understand when different regions of the continent were inhabited, where settlers came from, and how current inhabitants relate genetically to earlier populations. Recent studies unraveled parts of the genetic history of the continent using genotyping arrays and uniparental markers. The 1000 Genomes Project provides a unique opportunity for improving our understanding of population genetic history by providing over a hundred sequenced low coverage genomes and exomes from Colombian (CLM), Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore the genomic contributions of African, European, and Native American ancestry to these populations. Estimated Native American ancestry is 48% in MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Taíno people of the Caribbean. We present new methods to estimate the allele frequencies in the Native American fraction of the populations, and model their distribution using a demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas 16 thousand years ago (kya), supports that the MXL Ancestors split 12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The model also features effective populations of 62,000 in Mexico, 8,700 in Colombia, and 1,900 in Puerto Rico. Modeling Identity-by-descent and ancestry tract length, we show that post-contact populations differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe.
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