Genetic Diversity in the Lesser Antilles and Its Implications for the Settlement of the Caribbean Basin

Abstract

Historical discourses about the Caribbean often chronicle West African and European influence to the general neglect of indigenous people’s contributions to the contemporary region. Consequently, demographic histories of Caribbean people prior to and after European contact are not well understood. Although archeological evidence suggests that the Lesser Antilles were populated in a series of northward and eastern migratory waves, many questions remain regarding the relationship of the Caribbean migrants to other indigenous people of South and Central America and changes to the demography of indigenous communities post-European contact. To explore these issues, we analyzed mitochondrial DNA and Y-chromosome diversity in 12 unrelated individuals from the First Peoples Community in Arima, Trinidad, and 43 unrelated Garifuna individuals residing in St. Vincent. In this community-sanctioned research, we detected maternal indigenous ancestry in 42% of the participants, with the remainder having haplotypes indicative of African and South Asian maternal ancestry. Analysis of Y-chromosome variation revealed paternal indigenous American ancestry indicated by the presence of haplogroup Q-M3 in 28% of the male participants from both communities, with the remainder possessing either African or European haplogroups. This finding is the first report of indigenous American paternal ancestry among indigenous populations in this region of the Caribbean. Overall, this study illustrates the role of the region’s first peoples in shaping the genetic diversity seen in contemporary Caribbean populations.

Ancient DNA reconstructs the genetic legacies of pre-contact Puerto Rico communities

“…This distribution contrasts with mtDNA haplogroup patterns reported for PC-Guadeloupe and for most present-day islanders, including Cubans and Dominicans (Martínez-Cruzado, et al 2005;Benn-Torres, et al 2007;Mendizabal, et al 2008;Vilar, et al 2014;Benn-Torres, et al 2015;Schurr, et al 2016). Differences in mtDNA diversity patterns between the Greater and Lesser Antilles have been reported previously and may reflect distinct island founder populations or the effects of genetic drift and relative isolation between ancient island communities (Vilar, et al 2014;Benn-Torres, et al 2015). We find support for the latter scenario through our best fit demographic model in which pre-contact island populations diverge from each other after initial settlement with limited subsequent gene flow.…”

“…For example, while PC-PR communities carried high frequencies of A2 and C1 mtDNA lineages, ancient communities from Cuba and Dominican Republic had high frequencies of C1 and D1 (Lalueza-Fox, et al 2001;Lalueza-Fox, et al 2003). This distribution contrasts with mtDNA haplogroup patterns reported for PC-Guadeloupe and for most present-day islanders, including Cubans and Dominicans (Martínez-Cruzado, et al 2005;Benn-Torres, et al 2007;Mendizabal, et al 2008;Vilar, et al 2014;Benn-Torres, et al 2015;Schurr, et al 2016). Differences in mtDNA diversity patterns between the Greater and Lesser Antilles have been reported previously and may reflect distinct island founder populations or the effects of genetic drift and relative isolation between ancient island communities (Vilar, et al 2014;Benn-Torres, et al 2015).…”

A genetic history of the pre-contact Caribbean

“…yr BP, such ancestry did eventually reach the island(Extended Data Tables 2 and 3). We also find support for the persistence of Indigenous ancestry in uniparental haplogroups, where major Indigenous-specific haplogroups identified in our ancient individuals are still found in the Caribbean today33,[35][36][37] , despite the introduction of European and African haplogroups over the last ~500 years.Detection of our newly discovered deep branch of haplogroup C1d (the only haplogroup in our dataset unique to the Caribbean) in a modern individual from Puerto Rico from the 1000 Genomes Project adds to the weight of this evidence.…”

“…At the same time, our results confirm the magnitude of population collapse following European colonization and the killing of Indigenous people. The severity of this collapse is evidenced, for example, in the frequencies of mitochondrial haplogroups such as B2 and D1 that were common in our data but are rare in present-day Caribbean populations33 .…”

Analysis of biogeographic ancestry reveals complex genetic histories for indigenous communities of St. Vincent and Trinidad

“…It was these complicated histories of St. Vincent and Trinidad that first led us to begin a population genetics study of the islands' Indigenous communities (Benn Torres et al, ). In this initial work, we detected maternal Indigenous ancestry in 42% of the participants, with the remainder exhibiting African and South Asian maternal ancestry.…”