自2010年以来,来自数百名古代美洲原住民的全基因组数据为理解美洲史前史做出了贡献。然而,这些样本从未作为单个数据集进行过研究,它们之间以及与当今人口之间的独特关系可能从未曝光。这里,我们重新评估了2010年至2019年间发表的223名古代美洲原住民的基因组多样性和种群结构。
■来自古代美洲的基因组数据与来自西蒙斯基因组多样性计划的278个现今基因组的全球参考小组合并,然后通过ADMIXTURE进行分析,D-统计,PCA,t-SNE,和UMAP。
■我们在古代和今天的美洲发现了很大程度上相似的人口结构。然而,当代美洲原住民的人口结构,在这里可以追溯到至少一万年前,明显不像古代同行那样多样化,欧洲接触的可能结果。此外,过去,北美的人口结构水平高于南美,除了古代巴西,具有相对较高的结构。此外,我们在古代数据集中发现了遗传祖先的一个组成部分,该组成部分与当今的海洋种群密切相关,但与先前报道的澳大利亚信号不一致。最后,我们报告了古代柏林根祖先的扩张,以前只报告了一个样本。
■总的来说,我们的发现支持了美洲定居的复杂情景,在区域层面容纳创始人效应的发生和祖先混合事件的出现。
UNASSIGNED: Since 2010, genome-wide data from hundreds of ancient Native Americans have contributed to the understanding of Americas\' prehistory. However, these samples have never been studied as a single dataset, and distinct relationships among themselves and with present-day populations may have never come to light. Here, we reassess genomic diversity and population structure of 223 ancient Native Americans published between 2010 and 2019.
UNASSIGNED: The genomic data from ancient Americas was merged with a worldwide reference panel of 278 present-day genomes from the Simons Genome Diversity Project and then analyzed through ADMIXTURE, D-statistics, PCA, t-SNE, and UMAP.
UNASSIGNED: We find largely similar population structures in ancient and present-day Americas. However, the population structure of contemporary Native Americans, traced here to at least 10,000 years before present, is noticeably less diverse than their ancient counterparts, a possible outcome of the European contact. Additionally, in the past there were greater levels of population structure in North than in South America, except for ancient Brazil, which harbors comparatively high degrees of structure. Moreover, we find a component of genetic ancestry in the ancient dataset that is closely related to that of present-day Oceanic populations but does not correspond to the previously reported Australasian signal. Lastly, we report an expansion of the Ancient Beringian ancestry, previously reported for only one sample.
UNASSIGNED: Overall, our findings support a complex scenario for the settlement of the Americas, accommodating the occurrence of founder effects and the emergence of ancestral mixing events at the regional level.