Abstract
Cuba is the most populated country in the Caribbean and has a rich and heterogeneous genetic heritage. Here, we take advantage of dense genomic data from 860 Cuban individuals to reconstruct the genetic structure and ancestral origins of this population. We found distinct admixture patterns between and within the Cuban provinces. Eastern provinces have higher African and Native American ancestry contributions (average 26% and 10%, respectively) than the rest of the Cuban provinces (average 17% and 5%, respectively). Furthermore, in the Eastern Cuban region, we identified more intense sex-specific admixture patterns, strongly biased towards European male and African/Native American female ancestries. Our subcontinental ancestry analyses in Cuba highlight the Iberian population as the best proxy European source population, South American and Mesoamerican populations as the closest Native American ancestral component, and populations from West Central and Central Africa as the best proxy sources of the African ancestral component. Finally, we found complex admixture processes involving two migration pulses from both Native American and African sources. Most of the inferred Native American admixture events happened early during the Cuban colonial period, whereas the African admixture took place during the slave trade and more recently as a probable result of large-scale migrations from Haiti.
Highlights
Cuba is the most populated country in the Caribbean and has a rich and heterogeneous genetic heritage
The multidimensional scaling (MDS) plot based on the allele-sharing dissimilarity (ASD) matrix shows highly variable genetic patterns across populations having experienced the transatlantic slave trade (TAST) (Fig. 1a), including Hispanic/Latino populations in the Americas
The Cuban individuals lie on the EuropeanAfrican trajectory, to African-descendants from USA and Barbados, most Cuban individuals are much closer to the European cluster than the African cluster (Fig. 1b)
Summary
Cuba is the most populated country in the Caribbean and has a rich and heterogeneous genetic heritage. In the Eastern Cuban region, we identified more intense sexspecific admixture patterns, strongly biased towards European male and African/Native American female ancestries. Most of the inferred Native American admixture events happened early during the Cuban colonial period, whereas the African admixture took place during the slave trade and more recently as a probable result of large-scale migrations from Haiti. Around 350 BCE, the arrival of Arawak-speaking people from Venezuela, associated with the horticulturalist Saladoid culture, changed the anthropological landscape in the Caribbean, and became the major group[3]. While broad embarkation regions can be identified based on historical evidence[9,12], the geographical origins of enslaved Africans forcibly displaced during the TAST remain unclear. Archaeologists and historians have reconstructed the migratory processes underlying Cuban demographic history, a number of long-standing questions remain unsolved, mostly due to the patchy archaeological and historical records[6], and the incomplete and biased information regarding the illegal slave trade[12]
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