Reconstructing the population genetic history of the Caribbean.
Reconstructing the population genetic history of the Caribbean.
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DOI：
10.1371/journal.pgen.1003925
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发表时间：
2013-11
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：
Moreno-Estrada A;Gravel S;Zakharia F;McCauley JL;Byrnes JK;Gignoux CR;Ortiz-Tello PA;Martínez RJ;Hedges DJ;Morris RW;Eng C;Sandoval K;Acevedo-Acevedo S;Norman PJ;Layrisse Z;Parham P;Martínez-Cruzado JC;Burchard EG;Cuccaro ML;Martin ER;Bustamante CD
加勒比盆地是近代史上一些最复杂的相互作用的家园，这些相互作用发生在以前分化的人类种群之间。在这里，我们通过对330个个体的全基因组变异模式进行研究，这些个体来自三个大安地列斯群岛（古巴、波多黎各、伊斯帕尼奥拉岛）、两个大陆（洪都拉斯、哥伦比亚）和三个南美土著（Yukpa、Bari和Warao）种群。我们将这些数据与一个独特的数据库相结合，该数据库包含来自欧洲、非洲和美洲原住民的3000多名个体的基因组变异。我们使用当地祖先推断和土地长度分布来测试该地区殖民前和殖民后历史的不同人口情景。我们开发了一种新的祖先特异性PCA （ASPCA）方法，从混合基因组中重建美洲原住民、欧洲人和非洲人单倍型的次大陆起源。我们发现，加勒比岛民最可能的土著祖先来源是亚马逊内陆部落、中美洲和尤卡坦半岛共有的南美土著成分，这表明在前哥伦比亚时代，加勒比海地区有广泛的基因流动。我们发现了两次非洲移民潮的证据。第一个脉冲——今天反映在更短、更古老的祖先谱系上——包含的基因成分更类似于跨大西洋奴隶贸易早期阶段的西非沿海地区。第二个脉冲——由更长、更年轻的区域反映出来——与今天的西非和中非人口更相似，这支持了后来跨大西洋驱逐的历史记录。令人惊讶的是，我们还发现了一个拉丁裔特定的欧洲组成部分，它与它的亲本伊比利亚源种群有很大的差异，可能是由于欧洲的创始种群规模较小。我们证明，混合基因组中的祖先成分可以追溯到不同的次大陆来源人群，其分辨率远高于之前的想象，即使有限的前哥伦布加勒比海单倍型存活下来。拉丁美洲人通常被认为是一个单一的异质群体，其复杂的变异在一些社会、人口和生物医学背景下没有得到充分的认识。通过利用基因组数据，我们在次大陆水平上描述了加勒比人口的祖先成分，并揭示了区分岛屿与大陆加勒比人口以及其他西班牙裔/拉丁裔群体的人口结构的精细模式。我们为岛屿人口中美洲原住民成分的南美内陆起源和加勒比海盆地广泛的前哥伦布基因流动提供了遗传证据。来自加勒比海的欧洲人组成部分显示出与伊比利亚人亲代种群的显著差异，这可能是新世界殖民化期间创始人效应的结果。基于人口模型，我们重建了自大陆混合开始以来加勒比地区复杂的人口历史。我们发现，岛屿人口最好的模型是吸收了两个非洲移民脉冲的混合物，与跨大西洋奴隶贸易的早期和最活跃阶段相吻合。这两种脉冲似乎起源于西非的不同地区，在今天的非洲-加勒比基因组上留下了两个可区分的特征，并为加勒比奴隶贸易的基因影响提供了线索。
The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse—which today is reflected by shorter, older ancestry tracts—consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse—reflected by longer, younger tracts—is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source populations with far greater resolution than previously thought, even when limited pre-Columbian Caribbean haplotypes have survived. Latinos are often regarded as a single heterogeneous group, whose complex variation is not fully appreciated in several social, demographic, and biomedical contexts. By making use of genomic data, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups. We provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. The Caribbean-derived European component shows significant differentiation from parental Iberian populations, presumably as a result of founder effects during the colonization of the New World. Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with the early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures on present-day Afro-Caribbean genomes and shedding light on the genetic impact of the slave trade in the Caribbean.
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来自1,092个人基因组的遗传变异的综合图。
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
64.8
作者：
Frazer, Kelly A.;Ballinger, Dennis G.;Cox, David R.;Hinds, David A.;Stuve, Laura L.;Gibbs, Richard A.;Belmont, John W.;Boudreau, Andrew;Hardenbol, Paul;Leal, Suzanne M.;Pasternak, Shiran;Wheeler, David A.;Willis, Thomas D.;Yu, Fuli;Yang, Huanming;Zeng, Changqing;Gao, Yang;Hu, Haoran;Hu, Weitao;Li, Chaohua;Lin, Wei;Liu, Siqi;Pan, Hao;Tang, Xiaoli;Wang, Jian;Wang, Wei;Yu, Jun;Zhang, Bo;Zhang, Qingrun;Zhao, Hongbin;Zhao, Hui;Zhou, Jun;Gabriel, Stacey B.;Barry, Rachel;Blumenstiel, Brendan;Camargo, Amy;Defelice, Matthew;Faggart, Maura;Goyette, Mary;Gupta, Supriya;Moore, Jamie;Nguyen, Huy;Onofrio, Robert C.;Parkin, Melissa;Roy, Jessica;Stahl, Erich;Winchester, Ellen;Ziaugra, Liuda;Altshuler, David;Shen, Yan;Yao, Zhijian;Huang, Wei;Chu, Xun;He, Yungang;Jin, Li;Liu, Yangfan;Shen, Yayun;Sun, Weiwei;Wang, Haifeng;Wang, Yi;Wang, Ying;Xiong, Xiaoyan;Xu, Liang;Waye, Mary M. Y.;Tsui, Stephen K. W.;Wong, J. Tze-Fei;Galver, Luana M.;Fan, Jian-Bing;Gunderson, Kevin;Murray, Sarah S.;Oliphant, Arnold R.;Chee, Mark S.;Montpetit, Alexandre;Chagnon, Fanny;Ferretti, Vincent;Leboeuf, Martin;Olivier, Jean-Franccois;Phillips, Michael S.;Roumy, Stephanie;Sallee, Clementine;Verner, Andrei;Hudson, Thomas J.;Kwok, Pui-Yan;Cai, Dongmei;Koboldt, Daniel C.;Miller, Raymond D.;Pawlikowska, Ludmila;Taillon-Miller, Patricia;Xiao, Ming;Tsui, Lap-Chee;Mak, William;Song, You Qiang;Tam, Paul K. H.;Nakamura, Yusuke;Kawaguchi, Takahisa;Kitamoto, Takuya;Morizono, Takashi;Nagashima, Atsushi;Ohnishi, Yozo;Sekine, Akihiro;Tanaka, Toshihiro;Tsunoda, Tatsuhiko;Deloukas, Panos;Bird, Christine P.;Delgado, Marcos;Dermitzakis, Emmanouil T.;Gwilliam, Rhian;Hunt, Sarah;Morrison, Jonathan;Powell, Don;Stranger, Barbara E.;Whittaker, Pamela;Bentley, David R.;Daly, Mark J.;de Bakker, Paul I. W.;Barrett, Jeff;Chretien, Yves R.;Maller, Julian;McCarroll, Steve;Patterson, Nick;Pe'er, Itsik;Price, Alkes;Purcell, Shaun;Richter, Daniel J.;Sabeti, Pardis;Saxena, Richa;Schaffner, Stephen F.;Sham, Pak C.;Varilly, Patrick;Altshuler, David;Stein, Lincoln D.;Krishnan, Lalitha;Smith, Albert Vernon;Tello-Ruiz, Marcela K.;Thorisson, Gudmundur A.;Chakravarti, Aravinda;Chen, Peter E.;Cutler, David J.;Kashuk, Carl S.;Lin, Shin;Abecasis, Goncalo R.;Guan, Weihua;Li, Yun;Munro, Heather M.;Qin, Zhaohui Steve;Thomas, Daryl J.;McVean, Gilean;Auton, Adam;Bottolo, Leonardo;Cardin, Niall;Eyheramendy, Susana;Freeman, Colin;Marchini, Jonathan;Myers, Simon;Spencer, Chris;Stephens, Matthew;Donnelly, Peter;Cardon, Lon R.;Clarke, Geraldine;Evans, David M.;Morris, Andrew P.;Weir, Bruce S.;Tsunoda, Tatsuhiko;Johnson, Todd A.;Mullikin, James C.;Sherry, Stephen T.;Feolo, Michael;Skol, Andrew
通讯作者：
Skol, Andrew
影响因子：
9.8
作者：
Mao, Xianyun;Bigham, Abigail W.;Parra, Esteban J.
通讯作者：
Parra, Esteban J.
影响因子：
7
作者：
Auton, Adam;Bryc, Katarzyna;Bustamante, Carlos D.
通讯作者：
Bustamante, Carlos D.
影响因子：
0.1
作者：
Demarchi, Dario A.;Ministro, Angelina Garcia
通讯作者：
Ministro, Angelina Garcia