Reconstructing Native American Migrations from Whole-Genome and Whole-Exome Data

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 especially Native American ancestry to these populations. Estimated Native American ancestry is in MXL, in CLM, and 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 thousand years ago (kya), supports that the MXL Ancestors split kya, with a subsequent split of the ancestors to CLM and PUR kya. The model also features effective populations of in Mexico, in Colombia, and in Puerto Rico. Modeling Identity-by-descent (IBD) and ancestry tract length, we show that post-contact populations also differ markedly in their effective sizes and migration patterns, with Puerto Rico showing the smallest effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations.

学界与大众均对解析美洲人群的遗传历史抱有极高的研究热情与关注度。本研究旨在厘清美洲大陆不同区域的人类定居时间、移民的起源地，以及当代人群与早期人群的遗传亲缘关系。既往研究已通过基因分型芯片（genotyping arrays）与单亲遗传标记（uniparental markers），初步解析了美洲大陆的部分群体遗传历史。千人基因组计划（1000 Genomes Project）为深化我们对群体遗传历史的认知提供了独特契机：其公开了来自哥伦比亚裔（CLM）、墨西哥裔美国人（MXL）与波多黎各裔（PUR）人群的百余个低覆盖度测序基因组与外显子组（exomes）数据。本研究聚焦非洲、欧洲，尤其美洲原住民祖先成分对上述三个人群的基因组贡献。经估算，MXL、CLM与PUR人群均携带美洲原住民祖先成分；其中PUR人群的美洲原住民祖先成分与奥里诺科河流域周边人群亲缘关系最近，这一结果证实了加勒比地区泰诺人（Taíno）的南美祖先起源。我们提出了全新方法以估算人群中美洲原住民组分的等位基因频率（allele frequencies），并基于三个美洲原住民祖先群体构建群体历史模型（demographic model）以刻画其分布特征。上述祖先群体的分化时间间隔极短：基于美洲大陆千年前（kya）的定居事件推演，最合理的场景为MXL祖先群体先于千年前完成分化，随后CLM与PUR的祖先群体再行分化。该模型同时给出了墨西哥、哥伦比亚与波多黎各人群的有效群体规模。通过对同源同一性（Identity-by-descent, IBD）与祖先片段长度进行建模，我们发现殖民后人群的有效群体规模与迁徙模式同样存在显著差异：波多黎各人群展现出最小的有效群体规模，且更早出现来自欧洲的基因流。最后，我们通过比对IBD分型与祖先成分分配结果，找到了三个人群的欧洲奠基者之间存在亲缘关系的相关证据。