Genetic Diversity in the Lesser Antilles and Its Implications for the Settlement of the Caribbean Basin

RESEARCH ARTICLE Genetic Diversity in the Lesser Antilles and Its Implications for the Settlement of the Caribbean Basin Jada Benn Torres1*, Miguel G. Vilar2,3, Gabriel A. Torres1, Jill B. Gaieski2, Ricardo Bharath Hernandez4, Zoila E. Browne5, Marlon Stevenson5, Wendell Walters5,6, Theodore G. Schurr2, The Genographic Consortium¶ 1 Department of Anthropology, University of Notre Dame, Notre Dame, Indiana, United States of America, 2 Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America, 3 Missions Programs, National Geographic Society, Washington, D.C., United States of America, 4 Santa Rosa First Peoples Community, Arima, Trinidad and Tobago, 5 The Garifuna Heritage Foundation Inc., Kingston, St. Vincent and the Grenadines, 6 Sandy Bay Village, St. Vincent and the Grenadines ¶ Membership of the Genographic Consortium is provided in the Acknowledgments. * OPEN ACCESS Citation: Benn Torres J, Vilar MG, Torres GA, Gaieski JB, Bharath Hernandez R, Browne ZE, et al. (2015) Genetic Diversity in the Lesser Antilles and Its Implications for the Settlement of the Caribbean Basin. PLoS ONE 10(10): e0139192. doi:10.1371/ journal.pone.0139192 Editor: Francesc Calafell, Universitat Pompeu Fabra, SPAIN Received: July 13, 2014 Accepted: September 10, 2015 Published: October 8, 2015 Copyright: © 2015 Benn Torres et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: Data are available from the NCBI GenBank with accession numbers KT77741-98. A complete list of accession numbers can be found in the Supporting Information files. Funding: This work was supported by the National Geographic Society, IBM, Waitt Family Foundation, the University of Pennsylvania, and the Institute for Scholarship and Learning at the University of Notre Dame. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Abstract Historical discourses about the Caribbean often chronicle West African and European influence to the general neglect of indigenous people’s contributions to the contemporary region. Consequently, demographic histories of Caribbean people prior to and after European contact are not well understood. Although archeological evidence suggests that the Lesser Antilles were populated in a series of northward and eastern migratory waves, many questions remain regarding the relationship of the Caribbean migrants to other indigenous people of South and Central America and changes to the demography of indigenous communities post-European contact. To explore these issues, we analyzed mitochondrial DNA and Y-chromosome diversity in 12 unrelated individuals from the First Peoples Community in Arima, Trinidad, and 43 unrelated Garifuna individuals residing in St. Vincent. In this community-sanctioned research, we detected maternal indigenous ancestry in 42% of the participants, with the remainder having haplotypes indicative of African and South Asian maternal ancestry. Analysis of Y-chromosome variation revealed paternal indigenous American ancestry indicated by the presence of haplogroup Q-M3 in 28% of the male participants from both communities, with the remainder possessing either African or European haplogroups. This finding is the first report of indigenous American paternal ancestry among indigenous populations in this region of the Caribbean. Overall, this study illustrates the role of the region’s first peoples in shaping the genetic diversity seen in contemporary Caribbean populations. Introduction The Caribbean is a vast region encompassing nearly 3 million km2 in total area. Bordered by the Atlantic Ocean to in the east, it spans from the southern coast of the Bahamas to the PLOS ONE | DOI:10.1371/journal.pone.0139192 October 8, 2015 1 / 27 Genetic Diversity in the Lesser Antilles Competing Interests: The authors have the following interests. This study was partly funded by IBM. However, there are no patents, products in development or marketed products to declare, which is consistent with the Genographic Project protocol, which does not permit sponsors to commercially benefit from their support of the project. Furthermore, none of the funders had any role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. This situation does not alter the authors' adherence to all of the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors. northern coast of South America and the eastern coast of Mexico and Central America (Fig 1). Comprised of well over 700 islands, this region is currently home to an estimated 17 million people [1]. The initial presence of human populations within the region has been dated to 7,200 years before present (ybp) based on evidence from the Banwari Trace site in Trinidad [2]. Aside from this site, the first human settlement in the Caribbean dates to a migration event around 8,000–5,000 ybp marked by sites on Cuba, Hispañola and Puerto Rico [3–5]. Within the northern Lesser Antilles and Barbados, human occupation dates back as far as 5,000–3,000 ybp [3]. Both archeological and linguistic research suggest that, for the remaining islands of the Antilles, a series of migrations ending just prior to 1500 AD resulted in human presence throughout the region [6]. Possible sources of these population expansions to the southern Lesser Antilles include northern South America or, alternatively, the Greater Antilles through southward migrations [6–15]. As a result of these different expansions, at least eight different ethnic groups were present in the Caribbean at the time of European contact. These include the Guanahatebay in Cuba, the Macorix of Hispañola, the Ciguayo of Hispañola, the Lucayo (also referred to as Lucayan Taíno) in the Bahamas, the Ciboney of Haiti, Jamaica, and Cuba, the Classic Taíno in the Dominican Republic, Puerto Rico, the Virgin Islands, and the Leeward Islands, and the Kalipuna and the Karina Caribs in Windward islands of the Lesser Antilles [7,16]. The exact cultural, biological and linguistic affinities of these historical populations have yet to be fully determined. Indigenous Caribbean peoples were greatly affected by the assimilation, disease, and genocide brought about by European colonization and the Trans-Atlantic slave trade [17]. These Fig 1. A map of the Lesser Antilles showing the locations of St. Vincent and the Grenadines and Trinidad and Tobago. doi:10.1371/journal.pone.0139192.g001 PLOS ONE | DOI:10.1371/journal.pone.0139192 October 8, 2015 2 / 27 Genetic Diversity in the Lesser Antilles communities were also systematically dispersed to other islands or parts of the Americas during the colonial period, a (...truncated)