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A genetic history of the pre-contact Caribbean

Daniel M. Fernandes, Kendra A. Sirak, Harald Ringbauer, Jakob Sedig, Nadin Rohland, Olivia Cheronet, Matthew Mah, Swapan Mallick, Iñigo Olalde, Brendan J. Culleton, Nicole Adamski, Rebecca Bernardos, Guillermo Bravo, Nasreen Broomandkhoshbacht, Kimberly Callan, Francesca Candilio, Lea Demetz, Kellie Sara Duffett Carlson, Laurie Eccles, Suzanne Freilich, Ann Marie Lawson, Kirsten Mandl, Fabio Marzaioli, Jonas Oppenheimer, Kadir T. Özdogan, Constanze Schattke, Ryan Schmidt, Kristin Stewardson, Filippo Terrasi, Fatma Zalzala, Carlos Arredondo Antúnez, Ercilio Vento Canosa, Roger Colten, Andrea Cucina, Francesco Genchi, Claudia Kraan, Francesco La Pastina, Michaela Lucci, Marcio Veloz Maggiolo, Beatriz Marcheco-Teruel, Clenis Tavarez Maria, Cristian Martinez, Ingeborg París, Michael Pateman, Tanya Simms, Carlos Garcia Sivoli, Miguel Vilar, Douglas J. Kennett, William F. Keegan, Alfredo Coppa, Mark Lipson, Ron Pinhasi, David Reich
doi: https://doi.org/10.1101/2020.06.01.126730
Daniel M. Fernandes
1Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
2CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
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  • For correspondence: reich@genetics.med.harvard.edu
Kendra A. Sirak
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
4Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Harald Ringbauer
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
4Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Jakob Sedig
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
4Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Nadin Rohland
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
5Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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Olivia Cheronet
1Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
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Matthew Mah
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
4Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
5Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
6Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Swapan Mallick
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
4Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
5Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
6Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Iñigo Olalde
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
7Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain
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Brendan J. Culleton
8Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
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Nicole Adamski
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
6Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Rebecca Bernardos
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
6Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Guillermo Bravo
1Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
9Department of Legal Medicine, Toxicology and Physical Anthropology, University of Granada, Granada, Spain
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Nasreen Broomandkhoshbacht
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
6Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
30Department of Anthropology, University of California, Santa Cruz, CA 95064, USA
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Kimberly Callan
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
6Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Francesca Candilio
10Superintendency of Archaeology, Fine Arts and Landscape for the city of Cagliari and the provinces of Oristano and South Sardinia, Cagliari, Italy
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Lea Demetz
1Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
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Kellie Sara Duffett Carlson
1Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
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Laurie Eccles
11Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA
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Suzanne Freilich
1Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
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Ann Marie Lawson
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
6Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Kirsten Mandl
1Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
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Fabio Marzaioli
12Department of Mathematics and Physics, Campania University “Luigi Vanvitelli”, 81100 Caserta, Italy
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Jonas Oppenheimer
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
6Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
31Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA
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Kadir T. Özdogan
1Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
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Constanze Schattke
1Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
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Ryan Schmidt
13CIBIO - InBIO, University of Porto, Campus de Vairão, 4485-661 Vairão, Portugal
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Kristin Stewardson
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
6Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Filippo Terrasi
12Department of Mathematics and Physics, Campania University “Luigi Vanvitelli”, 81100 Caserta, Italy
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Fatma Zalzala
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
6Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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Carlos Arredondo Antúnez
14Museo Antropológico Montané, University of Havana, Havana, Cuba
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Ercilio Vento Canosa
15Matanzas University of Medical Sciences, Carretera de Quintanilla Km 101, 40100 Matanzas, Cuba
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Roger Colten
16Peabody Museum of Natural History, Yale University, New Haven, CT 06511, USA
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Andrea Cucina
17Facultad de Ciencias Antropológicas, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
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Francesco Genchi
18Department of Environmental Biology, Sapienza University of Rome, Square Aldo Moro, 5, Rome 00185, Italy
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Claudia Kraan
19National Archaeological-Anthropological Memory Management (NAAM), 13 Johan van Walbeeckplein, Willemstad, Curaçao
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Francesco La Pastina
18Department of Environmental Biology, Sapienza University of Rome, Square Aldo Moro, 5, Rome 00185, Italy
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Michaela Lucci
20DANTE Laboratory of Diet and Ancient Technology, Sapienza University of Rome, Rome, Italy
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Marcio Veloz Maggiolo
21Universidad Autonoma de Santo Domingo, Sanchez, San Francisco de Macorís 31000, Dominican Republic
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Beatriz Marcheco-Teruel
22National Center of Medical Genetics, Medical University of Havana, Havana, Cuba
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Clenis Tavarez Maria
23Museo del Hombre Dominicano, Plaza de la Cultura Juan Pablo Duarte, Av. Pedro Henríquez Ureña, Santo Domingo 10204, Dominican Republic
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Cristian Martinez
23Museo del Hombre Dominicano, Plaza de la Cultura Juan Pablo Duarte, Av. Pedro Henríquez Ureña, Santo Domingo 10204, Dominican Republic
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Ingeborg París
24Instituto de Investigaciones Bioantropológicas y Arqueológicas, Universidad de Los Andes, Mérida, Venezuela
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Michael Pateman
25Turks and Caicos National Museum Foundation, Front St, Cockburn Town TKCA 1ZZ, Turks and Caicos Islands
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Tanya Simms
26Department of Biology, University of The Bahamas, P.O. Box N-4912, Nassau, The Bahamas
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Carlos Garcia Sivoli
24Instituto de Investigaciones Bioantropológicas y Arqueológicas, Universidad de Los Andes, Mérida, Venezuela
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Miguel Vilar
27National Geographic Society, Washington, DC 20036, USA
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Douglas J. Kennett
28Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
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William F. Keegan
29Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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Alfredo Coppa
1Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
18Department of Environmental Biology, Sapienza University of Rome, Square Aldo Moro, 5, Rome 00185, Italy
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  • For correspondence: reich@genetics.med.harvard.edu
Mark Lipson
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
4Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Ron Pinhasi
1Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
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  • For correspondence: reich@genetics.med.harvard.edu
David Reich
3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
4Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
5Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
6Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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  • For correspondence: reich@genetics.med.harvard.edu
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Abstract

Humans settled the Caribbean ~6,000 years ago, with intensified agriculture and ceramic use marking a shift from the Archaic Age to the Ceramic Age ~2,500 years ago. To shed new light on the history of Caribbean people, we report genome-wide data from 184 individuals predating European contact from The Bahamas, Cuba, Hispaniola, Puerto Rico, Curaçao, and northwestern Venezuela. A largely homogeneous ceramic-using population most likely originating in northeastern South America and related to present-day Arawak-speaking groups moved throughout the Caribbean at least 1,800 years ago, spreading ancestry that is still detected in parts of the region today. These people eventually almost entirely replaced Archaic-related lineages in Hispaniola but not in northwestern Cuba, where unadmixed Archaic-related ancestry persisted into the last millennium. We document high mobility and inter-island connectivity throughout the Ceramic Age as reflected in relatives buried ~75 kilometers apart in Hispaniola and low genetic differentiation across many Caribbean islands, albeit with subtle population structure distinguishing the Bahamian islands we studied from the rest of the Caribbean and from each other, and long-term population continuity in southeastern coastal Hispaniola differentiating this region from the rest of the island. Ceramic-associated people avoided close kin unions despite limited mate pools reflecting low effective population sizes (2Ne=1000-2000) even at sites on the large Caribbean islands. While census population sizes can be an order of magnitude larger than effective population sizes, pan-Caribbean population size estimates of hundreds of thousands are likely too large. Transitions in pottery styles show no evidence of being driven by waves of migration of new people from mainland South America; instead, they more likely reflect the spread of ideas and people within an interconnected Caribbean world.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵32 These authors jointly supervised this work: William F. Keegan, Alfredo Coppa, Mark Lipson, Ron Pinhasi, David Reich

  • https://reich.hms.harvard.edu/datasets

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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A genetic history of the pre-contact Caribbean
Daniel M. Fernandes, Kendra A. Sirak, Harald Ringbauer, Jakob Sedig, Nadin Rohland, Olivia Cheronet, Matthew Mah, Swapan Mallick, Iñigo Olalde, Brendan J. Culleton, Nicole Adamski, Rebecca Bernardos, Guillermo Bravo, Nasreen Broomandkhoshbacht, Kimberly Callan, Francesca Candilio, Lea Demetz, Kellie Sara Duffett Carlson, Laurie Eccles, Suzanne Freilich, Ann Marie Lawson, Kirsten Mandl, Fabio Marzaioli, Jonas Oppenheimer, Kadir T. Özdogan, Constanze Schattke, Ryan Schmidt, Kristin Stewardson, Filippo Terrasi, Fatma Zalzala, Carlos Arredondo Antúnez, Ercilio Vento Canosa, Roger Colten, Andrea Cucina, Francesco Genchi, Claudia Kraan, Francesco La Pastina, Michaela Lucci, Marcio Veloz Maggiolo, Beatriz Marcheco-Teruel, Clenis Tavarez Maria, Cristian Martinez, Ingeborg París, Michael Pateman, Tanya Simms, Carlos Garcia Sivoli, Miguel Vilar, Douglas J. Kennett, William F. Keegan, Alfredo Coppa, Mark Lipson, Ron Pinhasi, David Reich
bioRxiv 2020.06.01.126730; doi: https://doi.org/10.1101/2020.06.01.126730
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A genetic history of the pre-contact Caribbean
Daniel M. Fernandes, Kendra A. Sirak, Harald Ringbauer, Jakob Sedig, Nadin Rohland, Olivia Cheronet, Matthew Mah, Swapan Mallick, Iñigo Olalde, Brendan J. Culleton, Nicole Adamski, Rebecca Bernardos, Guillermo Bravo, Nasreen Broomandkhoshbacht, Kimberly Callan, Francesca Candilio, Lea Demetz, Kellie Sara Duffett Carlson, Laurie Eccles, Suzanne Freilich, Ann Marie Lawson, Kirsten Mandl, Fabio Marzaioli, Jonas Oppenheimer, Kadir T. Özdogan, Constanze Schattke, Ryan Schmidt, Kristin Stewardson, Filippo Terrasi, Fatma Zalzala, Carlos Arredondo Antúnez, Ercilio Vento Canosa, Roger Colten, Andrea Cucina, Francesco Genchi, Claudia Kraan, Francesco La Pastina, Michaela Lucci, Marcio Veloz Maggiolo, Beatriz Marcheco-Teruel, Clenis Tavarez Maria, Cristian Martinez, Ingeborg París, Michael Pateman, Tanya Simms, Carlos Garcia Sivoli, Miguel Vilar, Douglas J. Kennett, William F. Keegan, Alfredo Coppa, Mark Lipson, Ron Pinhasi, David Reich
bioRxiv 2020.06.01.126730; doi: https://doi.org/10.1101/2020.06.01.126730

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