Genetic diversity inPuertoRico and its implications for the peopling of theIsland and theWestIndies

Abstract

Puerto Rico and the surrounding islands rest on the eastern fringe of the Caribbean's Greater Antilles, located less than 100 miles northwest of the Lesser Antilles. Puerto Ricans are genetic descendants of pre-Columbian peoples, as well as peoples of European and African descent through 500 years of migration to the island. To infer these patterns of pre-Columbian and historic peopling of the Caribbean, we characterized genetic diversity in 326 individuals from the southeastern region of Puerto Rico and the island municipality of Vieques. We sequenced the mitochondrial DNA (mtDNA) control region of all of the samples and the complete mitogenomes of 12 of them to infer their putative place of origin. In addition, we genotyped 121 male samples for 25 Y-chromosome single nucleotide polymorphism and 17 STR loci. Approximately 60% of the participants had indigenous mtDNA haplotypes (mostly from haplogroups A2 and C1), while 25% had African and 15% European haplotypes. Three A2 sublineages were unique to the Greater Antilles, one of which was similar to Mesoamerican types, while C1b haplogroups showed links to South America, suggesting that people reached the island from the two distinct continental source areas. However, none of the male participants had indigenous Y-chromosomes, with 85% of them instead being European/Mediterranean and 15% sub-Saharan African in origin. West Eurasian Y-chromosome short tandem repeat haplotypes were quite diverse and showed similarities to those observed in southern Europe, North Africa and the Middle East. These results attest to the distinct, yet equally complex, pasts for the male and female ancestors of modern day Puerto Ricans.

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

“…This topology is consistent with patterns noted in previous research that suggest multiple independent introductions of A2 lineages into Puerto Rico and the Caribbean, with subsequent expansion of some derived haplotypes across island populations (Martínez-Cruzado 2010; Vilar, et al 2014).…”

“…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).…”

“…These patterns differ among populations and reflect the sex-biased nature of colonial and post-colonial demographic processes (Bryc, et al 2010;). For instance, Puerto Ricans have high proportions of European and African ancestry in autosomal and Y-chromosome loci, but large proportions of Native American ancestry in the mitochondrial genome (Martínez-Cruzado, et al 2005;Via, et al 2011;Vilar, et al 2014). This Native American ancestry 4 component, presumed to originate from ancient island populations, has been used as a proxy to reconstruct pre-contact genetic variation (Martínez-Cruzado 2010; ).…”

Genetic Diversity on the Sex Chromosomes

“…2014; van Oven et al. 2014; Vilar et al. 2014) or between the X chromosome and autosomes (see Hammer et al.…”

Genetic analysis of paleo-colombians from Nemocón, Cundinamarca provides insights on the early peopling of northwestern South America

“…Network A2: Figure 3 (Vilar, et al 2014), and in ancient Argentina (Mendisco, et al 2014). This evidence shows that Hap.…”