Article

Reconstructing the Population Genetic History of the Caribbean

Andrés Moreno‐EstradaDepartment of Genetics, Stanford University School of Medicine, Stanford, California, United States of AmericaSimon GravelDepartment of Genetics, Stanford University School of Medicine, Stanford, California, United States of AmericaFouad ZakhariaDepartment of Genetics, Stanford University School of Medicine, Stanford, California, United States of AmericaJacob L. McCauleyCenter for Genetic Epidemiology and Statistical Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of AmericaJake ByrnesAncestry.com DNA, LLC, San Francisco, California, United States of AmericaChristopher R. GignouxDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, California, United States of AmericaPatricia A. Ortiz-TelloDepartment of Genetics, Stanford University School of Medicine, Stanford, California, United States of AmericaRicardo MartínezCenter for Genetic Epidemiology and Statistical Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of AmericaDale J. HedgesCenter for Genetic Epidemiology and Statistical Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of AmericaRichard MorrisCenter for Genetic Epidemiology and Statistical Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of AmericaCeleste EngDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, California, United States of AmericaKarla SandovalDepartment of Genetics, Stanford University School of Medicine, Stanford, California, United States of AmericaSuehelay Acevedo‐AcevedoDepartment of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto RicoPaul J. NormanDepartment of Structural Biology, Stanford University School of Medicine, Stanford, California, United States of AmericaZ. LayrisseCenter of Experimental Medicine “Miguel Layrisse”, IVIC, Caracas, VenezuelaPeter ParhamDepartment of Structural Biology, Stanford University School of Medicine, Stanford, California, United States of AmericaJuan Carlos Martínez‐CruzadoDepartment of Biology, University of Puerto Rico at Mayaguez, Mayaguez, Puerto RicoEsteban G. BurchardDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, California, United States of AmericaMichael L. CuccaroCenter for Genetic Epidemiology and Statistical Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of AmericaEden R. MartinCenter for Genetic Epidemiology and Statistical Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of AmericaCarlos D. BustamanteDepartment of Genetics, Stanford University School of Medicine, Stanford, California, United States of America

2013en

ABI

Abstract

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 postcolonial 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.

Identifiers

DOI: 10.1371/journal.pgen.1003925

Citations and references

Cited by 30 references

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