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A genetic history of the pre-contact Caribbean.

ABSTRACT: Humans settled the Caribbean about 6,000 years ago, and ceramic use and intensified agriculture mark a shift from the Archaic to the Ceramic Age at around 2,500 years ago^1-3. Here we report genome-wide data from 174 ancient individuals from The Bahamas, Haiti and the Dominican Republic (collectively, Hispaniola), Puerto Rico, Curaçao and Venezuela, which we co-analysed with 89 previously published ancient individuals. Stone-tool-using Caribbean people, who first entered the Caribbean during the Archaic Age, derive from a deeply divergent population that is closest to Central and northern South American individuals; contrary to previous work⁴, we find no support for ancestry contributed by a population related to North American individuals. Archaic-related lineages were >98% replaced by a genetically homogeneous ceramic-using population related to speakers of languages in the Arawak family from northeast South America; these people moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools that reflect small effective population sizes, which we estimate to be a minimum of 500-1,500 and a maximum of 1,530-8,150 individuals on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the individuals who we analysed lived. Census sizes are unlikely to be more than tenfold larger than effective population sizes, so previous pan-Caribbean estimates of hundreds of thousands of people are too large^5,6. Confirming a small and interconnected Ceramic Age population⁷, we detect 19 pairs of cross-island cousins, close relatives buried around 75 km apart in Hispaniola and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically differentiated groups from the mainland, but instead reflected interactions within an interconnected Caribbean world^1,8.

SUBMITTER: Fernandes DM

PROVIDER: S-EPMC7864882 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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A genetic history of the pre-contact Caribbean.

Fernandes Daniel M DM Sirak Kendra A KA Ringbauer Harald H Sedig Jakob J Rohland Nadin N Cheronet Olivia O Mah Matthew M Mallick Swapan S Olalde Iñigo I Culleton Brendan J BJ Adamski Nicole N Bernardos Rebecca R Bravo Guillermo G Broomandkhoshbacht Nasreen N Callan Kimberly K Candilio Francesca F Demetz Lea L Carlson Kellie Sara Duffett KSD Eccles Laurie L Freilich Suzanne S George Richard J RJ Lawson Ann Marie AM Mandl Kirsten K Marzaioli Fabio F McCool Weston C WC Oppenheimer Jonas J Özdogan Kadir T KT Schattke Constanze C Schmidt Ryan R Stewardson Kristin K Terrasi Filippo F Zalzala Fatma F Antúnez Carlos Arredondo CA Canosa Ercilio Vento EV Colten Roger R Cucina Andrea A Genchi Francesco F Kraan Claudia C La Pastina Francesco F Lucci Michaela M Maggiolo Marcio Veloz MV Marcheco-Teruel Beatriz B Maria Clenis Tavarez CT Martínez Christian C París Ingeborg I Pateman Michael M Simms Tanya M TM Sivoli Carlos Garcia CG Vilar Miguel M Kennett Douglas J DJ Keegan William F WF Coppa Alfredo A Lipson Mark M Pinhasi Ron R Reich David D

Nature 20201223 7844

Humans settled the Caribbean about 6,000 years ago, and ceramic use and intensified agriculture mark a shift from the Archaic to the Ceramic Age at around 2,500 years ago<sup>1-3</sup>. Here we report genome-wide data from 174 ancient individuals from The Bahamas, Haiti and the Dominican Republic (collectively, Hispaniola), Puerto Rico, Curaçao and Venezuela, which we co-analysed with 89 previously published ancient individuals. Stone-tool-using Caribbean people, who first entered the Caribbean ...[more]

PMID: 33361817

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Project 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.

Project description:BACKGROUND:The Caribbean pillar coral Dendrogyra cylindrus was recently listed as a threatened species under the United States Endangered Species Act. One of the major threats to this species is its low, virtually undetectable recruitment rate. To our knowledge, sexually-produced recruits have never been found in over 30 years of surveys of Caribbean reefs. Until recently, the reproductive behavior of D. cylindrus was uncharacterized, limiting efforts to study its early life history, identify population bottlenecks, and conduct outplanting projects with sexually-produced offspring. In Curaçao, we observed the spawning behavior of this species over three years and five lunar cycles. We collected gametes from spawning individuals on three occasions and attempted to rear larvae and primary polyp settlers. RESULTS:Here we describe successful fertilization methods for D. cylindrus and we document rapid embryonic development. We describe the successful propagation of embryos to the swimming larvae stage, the first settlement of larvae in the laboratory, and the survival of primary polyp settlers for over seven months. We show that spawning times are highly predictable from year to year relative to the lunar cycle and local sunset times. We use colony-level data to confirm that males begin spawning before females. We also provide the first reports of split-spawning across months in this species. CONCLUSIONS:Together, our findings of consistent spawning times, split-spawning, rapid embryonic development, and remarkable robustness of larvae and settlers now enable expanded research on the early life history and settlement ecology of D. cylindrus. This will help biologists to identify the population bottlenecks in nature that underlie low recruitment rates. Further, the settlement of D. cylindrus larvae in the laboratory now makes out-planting for restoration more feasible. Asynchronous spawning times and rapid embryonic development may have important consequences for population biology, connectivity, and management, by affecting fertilization dynamics and larval dispersal distances. We argue that a precautionary approach to conservation is warranted, given this species' peculiar life history traits and still-unresolved population structure. Overall, the natural history and husbandry contributions presented here should facilitate accelerated research and conservation of this threatened coral.

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A genetic history of the pre-contact Caribbean.

Publications

A genetic history of the pre-contact Caribbean.

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