Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba

TLDR

Before European arrival, Cuba was inhabited by Tainos and Ciboneys of South American origin, later largely replaced by Europeans and African slaves, and the extent of genetic intermixing remains unclear. The study aimed to elucidate the demographic processes shaping modern Cuban genetic ancestry. Researchers genotyped the mitochondrial hypervariable region I and five coding SNPs in 245 individuals, and 40 Y‑chromosome SNPs in 132 males to assess maternal and paternal lineages. Maternal lineages show 33 % Native American, 45 % African, and 22 % Eurasian ancestry, while paternal lineages are 80 % Eurasian and 20 % African with no Native American contribution, indicating a pronounced sex‑biased admixture.

Abstract

Abstract Background Before the arrival of Europeans to Cuba, the island was inhabited by two Native American groups, the Tainos and the Ciboneys. Most of the present archaeological, linguistic and ancient DNA evidence indicates a South American origin for these populations. In colonial times, Cuban Native American people were replaced by European settlers and slaves from Africa. It is still unknown however, to what extent their genetic pool intermingled with and was 'diluted' by the arrival of newcomers. In order to investigate the demographic processes that gave rise to the current Cuban population, we analyzed the hypervariable region I (HVS-I) and five single nucleotide polymorphisms (SNPs) in the mitochondrial DNA (mtDNA) coding region in 245 individuals, and 40 Y-chromosome SNPs in 132 male individuals. Results The Native American contribution to present-day Cubans accounted for 33% of the maternal lineages, whereas Africa and Eurasia contributed 45% and 22% of the lineages, respectively. This Native American substrate in Cuba cannot be traced back to a single origin within the American continent, as previously suggested by ancient DNA analyses. Strikingly, no Native American lineages were found for the Y-chromosome, for which the Eurasian and African contributions were around 80% and 20%, respectively. Conclusion While the ancestral Native American substrate is still appreciable in the maternal lineages, the extensive process of population admixture in Cuba has left no trace of the paternal Native American lineages, mirroring the strong sexual bias in the admixture processes taking place during colonial times.