Reconstructing the population genetic history of the Caribbean.
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 A...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2013-11-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC3828151?pdf=render |
| _version_ | 1818156338684887040 |
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| author | Andrés Moreno-Estrada Simon Gravel Fouad Zakharia Jacob L McCauley Jake K Byrnes Christopher R Gignoux Patricia A Ortiz-Tello Ricardo J Martínez Dale J Hedges Richard W Morris Celeste Eng Karla Sandoval Suehelay Acevedo-Acevedo Paul J Norman Zulay Layrisse Peter Parham Juan Carlos Martínez-Cruzado Esteban González Burchard Michael L Cuccaro Eden R Martin Carlos D Bustamante |
| author_facet | Andrés Moreno-Estrada Simon Gravel Fouad Zakharia Jacob L McCauley Jake K Byrnes Christopher R Gignoux Patricia A Ortiz-Tello Ricardo J Martínez Dale J Hedges Richard W Morris Celeste Eng Karla Sandoval Suehelay Acevedo-Acevedo Paul J Norman Zulay Layrisse Peter Parham Juan Carlos Martínez-Cruzado Esteban González Burchard Michael L Cuccaro Eden R Martin Carlos D Bustamante |
| author_sort | Andrés Moreno-Estrada |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-11T14:56:43Z |
| format | Article |
| id | doaj.art-6ce760bab47e46af9f4b7c20c351dac8 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-11T14:56:43Z |
| publishDate | 2013-11-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-6ce760bab47e46af9f4b7c20c351dac82022-12-22T01:01:18ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042013-11-01911e100392510.1371/journal.pgen.1003925Reconstructing the population genetic history of the Caribbean.Andrés Moreno-EstradaSimon GravelFouad ZakhariaJacob L McCauleyJake K ByrnesChristopher R GignouxPatricia A Ortiz-TelloRicardo J MartínezDale J HedgesRichard W MorrisCeleste EngKarla SandovalSuehelay Acevedo-AcevedoPaul J NormanZulay LayrissePeter ParhamJuan Carlos Martínez-CruzadoEsteban González BurchardMichael L CuccaroEden R MartinCarlos D BustamanteThe 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.http://europepmc.org/articles/PMC3828151?pdf=render |
| spellingShingle | Andrés Moreno-Estrada Simon Gravel Fouad Zakharia Jacob L McCauley Jake K Byrnes Christopher R Gignoux Patricia A Ortiz-Tello Ricardo J Martínez Dale J Hedges Richard W Morris Celeste Eng Karla Sandoval Suehelay Acevedo-Acevedo Paul J Norman Zulay Layrisse Peter Parham Juan Carlos Martínez-Cruzado Esteban González Burchard Michael L Cuccaro Eden R Martin Carlos D Bustamante Reconstructing the population genetic history of the Caribbean. PLoS Genetics |
| title | Reconstructing the population genetic history of the Caribbean. |
| title_full | Reconstructing the population genetic history of the Caribbean. |
| title_fullStr | Reconstructing the population genetic history of the Caribbean. |
| title_full_unstemmed | Reconstructing the population genetic history of the Caribbean. |
| title_short | Reconstructing the population genetic history of the Caribbean. |
| title_sort | reconstructing the population genetic history of the caribbean |
| url | http://europepmc.org/articles/PMC3828151?pdf=render |
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