Spatiotemporal fluctuations of population structure in the Americas revealed by a meta‐analysis of the first decade of archaeogenomes
Spatiotemporal fluctuations of population structure in the Americas revealed by a meta‐analysis of the first decade of archaeogenomes
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考古基因组第一个十年的荟萃分析揭示了美洲人口结构的时空波动
DOI：
10.1002/ajpa.24673
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
DeGiorgio, Michael
中科院分区：
文献类型：
--
作者：
Campelo dos Santos, Andre Luiz;Lavalle Sullasi, Henry Socrates;Gokcumen, Omer;Lindo, John;DeGiorgio, Michael
自2010年以来，来自数百名古代美洲原住民的全基因组数据有助于了解美洲的史前史。然而，这些样本从未被作为一个单一的数据集进行研究，它们之间以及与当今人口之间的独特关系可能从未被发现。在这里，我们重新评估了2010年至2019年期间发表的223个古代美洲原住民的基因组多样性和人口结构。材料和方法来自古代美洲的基因组数据与Simons基因组多样性项目的278个现今基因组的全球参考面板合并，然后通过ADMIXTURE，D‐statistics，PCA，t-SNE，和UMAP。结果我们发现在古代和现代美洲的人口结构基本相似。然而，当代美洲原住民的人口结构，追溯到至少10，000年前，明显不如他们的古代同行多样化，这可能是欧洲接触的结果。此外，过去北美洲的人口结构水平高于南美洲，但古代巴西除外，巴西的人口结构水平相对较高。此外，我们在古代数据集中发现了一个遗传祖先的组成部分，它与当今的大洋洲种群密切相关，但与先前报道的澳大拉西亚信号不一致。最后，我们报告的古代Beringian血统的扩张，以前只报告了一个sample.DiscussionOverall，我们的研究结果支持一个复杂的方案解决美洲，容纳创始人的影响和出现的祖先混合事件在区域一级。
ObjectivesSince 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.Materials and MethodsThe 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.ResultsWe 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.DiscussionOverall, 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.
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影响因子：
64.8
作者：
Mallick, Swapan;Li, Heng;Lipson, Mark;Mathieson, Iain;Gymrek, Melissa;Racimo, Fernando;Zhao, Mengyao;Chennagiri, Niru;Nordenfelt, Susanne;Tandon, Arti;Skoglund, Pontus;Lazaridis, Iosif;Sankararaman, Sriram;Fu, Qiaomei;Rohland, Nadin;Renaud, Gabriel;Erlich, Yaniv;Willems, Thomas;Gallo, Carla;Spence, Jeffrey P.;Song, Yun S.;Poletti, Giovanni;Balloux, Francois;van Driem, George;de Knijff, Peter;Romero, Irene Gallego;Jha, Aashish R.;Behar, Doron M.;Bravi, Claudio M.;Capelli, Cristian;Hervig, Tor;Moreno-Estrada, Andres;Posukh, Olga L.;Balanovska, Elena;Balanovsky, Oleg;Karachanak-Yankova, Sena;Sahakyan, Hovhannes;Toncheva, Draga;Yepiskoposyan, Levon;Tyler-Smith, Chris;Xue, Yali;Abdullah, M. Syafiq;Ruiz-Linares, Andres;Beall, Cynthia M.;Di Rienzo, Anna;Jeong, Choongwon;Starikovskaya, Elena B.;Metspalu, Ene;Parik, Juri;Villems, Richard;Henn, Brenna M.;Hodoglugil, Ugur;Mahley, Robert;Sajantila, Antti;Stamatoyannopoulos, George;Wee, Joseph T. S.;Khusainova, Rita;Khusnutdinova, Elza;Litvinov, Sergey;Ayodo, George;Comas, David;Hammer, Michael F.;Kivisild, Toomas;Klitz, William;Winkler, Cheryl A.;Labuda, Damian;Bamshad, Michael;Jorde, Lynn B.;Tishkoff, Sarah A.;Watkins, W. Scott;Metspalu, Mait;Dryomov, Stanislav;Sukernik, Rem;Singh, Lalji;Thangaraj, Kumarasamy;Paeaebo, Svante;Kelso, Janet;Patterson, Nick;Reich, David
通讯作者：
Reich, David
影响因子：
64.8
作者：
通讯作者：
--
DOI：
10.1093/pnasnexus/pgac047
发表时间：
2022-05
期刊：
PNAS NEXUS
影响因子：
--
作者：
Lindo, John;De La Rosa, Rosseirys;Santos, Andre L. C. D.;Sans, Monica;DeGiorgio, Michael;Figueiro, Gonzalo
通讯作者：
Figueiro, Gonzalo
以古代 DNA 为基础，研究人类基因的新历史和地理。
DOI：
10.1016/j.tig.2014.07.007
发表时间：
2014
期刊：
Trends in genetics : TIG
影响因子：
--
作者：
Pickrell,JosephK;Reich,David
通讯作者：
Reich,David
DOI：
10.1073/pnas.0903341106
发表时间：
2009-09-22
影响因子：
11.1
作者：
DeGiorgio, Michael;Jakobsson, Mattias;Rosenberg, Noah A.
通讯作者：
Rosenberg, Noah A.