Exploring Cuba’s population structure and demographic history using genome-wide data

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.

Genetic Consequences of the Transatlantic Slave Trade in the Americas

“…9 Categorizing Nigeria in this way also corresponds to the historical geographic occupancy of groups with genetic, ethnic, and linguistic differences: the Yoruba in the Bight of Benin and Esan and Igbo in the Bight of Biafra. 4 We considered current Atlantic African populations to be suitable proxies for past populations in Africa given limited migration and current population structure following a latitudinal gradient 13 , 39 , 40 ( Figures S1–S6 ). We combined regions of Europe participating in the transatlantic slave trade by broad historical descriptors 7 and population structure ( Figures S7–S9; Table S3 ), which are largely described by geographic proximity.…”

Tracing the genetic legacy in the French Caribbean islands: A study of mitochondrial and Y‐chromosome lineages in the Guadeloupe archipelago

“…These markers have been successfully studied in various Caribbean groups and revealed considerable variability in the degree and sources of admixture. In the Hispanic Caribbean islands, such as Puerto Rico (Martínez‐Cruzado et al, , ), the Dominican Republic (Tajima et al, ), or Cuba (Fortes‐Lima et al, ; Marcheco‐Teruel et al, ; Mendizabal et al, ), the indigenous component remained relatively high, with up to 60% of maternal Amerindian lineages for the current population of Puerto Rico. However, Mendizabal et al () showed that if 33% of maternal lineages in Cuba could be associated with an Amerindian origin, no Amerindian paternal lineage could be detected, demonstrating a robust sexual bias in the admixture process.…”

Complex genetic admixture histories reconstructed with Approximate Bayesian Computations

“…Sex-biased admixture processes are known to have influenced admixed populations, and in particular populations descending from the TAST (MORENO-ESTRADA et al . 2013; FORTES-LIMA et al . 2018).…”

“…For instance, intense migrations from Haitian slave-descendants in the 19 th century have already been shown to possibly have contributed to the admixture patterns of other populations in the Caribbean and continental America (MORENO-ESTRADA et al . 2013; FORTES-LIMA et al . 2018).…”