Reconstructing the Population Genetic History of the Caribbean. A. Moreno Estrada1, S. Gravel1, F. Zakharia1, J. L. McCauley2, J. K. Byrnes1, C. R. Gignoux3, P. Ortiz Tello1, K. Sandoval1, P. J. Norman4, P. Parham4, J. C. Martinez Cruzado5, E. Gonzalez Burchard3, M. L. Cuccaro2, E. R. Martin2, C. D. Bustamante1 1) Genetics, Stanford University, Stanford, CA; 2) Genetics, University of Miami, Miami, FL; 3) Genetics, University of California at San Francisco, San Francisco, CA; 4) Structural Biology, Stanford University, Stanford, CA; 5) Biology, University of Puerto Rico, Mayaguez, PR.

   The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, by generating genome-wide SNP array data from 330 individuals, we characterize ancestral components of Caribbean populations on a sub-continental level and unveil fine-scale patterns of population structure distinguishing insular from mainland Caribbean populations as well as from other Hispanic/Latino groups. We combined these data with our unique database on genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and a novel extended space Markov model of ancestry tract to test different demographic scenarios for the pre- and post-colonial history of the region. We provide genetic evidence for an inland South American origin of the Native American component in island populations and for extensive pre-Columbian gene flow across the Caribbean basin. The Caribbean-derived European component shows significant differentiation from parental Iberian populations, presumably as a result of founder effects during the colonization of the New World. Based on demographic models, we reconstruct the complex population history of the Caribbean since the onset of continental admixture. We find that insular populations are best modeled as mixtures absorbing two pulses of African migrants, coinciding with early and maximum activity stages of the transatlantic slave trade. These two pulses appear to have originated in different regions within West Africa, imprinting two distinguishable signatures in present day Afro-Caribbean genomes and shedding light on the genetic impact of the dynamics occurring during the slave trade in the Caribbean. These results demonstrate that dense population genomic data coupled with novel methods of analysis afford the possibility of recapitulating human population history from admixed genomes with far greater resolution than previously thought.

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