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

Abstract

34Indigenous peoples have occupied the island of Puerto Rico since at least 3000 B.C. Due to the 35 demographic shifts that occurred after European contact, the origin(s) of these ancient populations, and 36 their genetic relationship to present-day islanders, are unclear. We use ancient DNA to characterize the 37 population history and genetic legacies of pre-contact Indigenous communities from Puerto Rico. Bone, 38 tooth and dental calculus samples were collected from 124 individuals from three pre-contact 39 archaeological sites: Tibes, Punta Candelero and Paso del Indio. Despite poor DNA preservation, we used 40 target enrichment and high-throughput sequencing to obtain complete mitochondrial genomes (mtDNA) 41 from 45 individuals and autosomal genotypes from two individuals. We found a high proportion of 42 Native American mtDNA haplogroups A2 and C1 in the pre-contact Puerto Rico sample (40% and 44%, 43 respectively). This distribution, as well as the haplotypes represented, support a primarily Amazonian 44 South American origin for these populations, and mirrors the Native American mtDNA diversity patterns 45 found in present-day islanders. Three mtDNA haplotypes from pre-contact Puerto Rico persist among 46 Puerto Ricans and other Caribbean islanders, indicating that present-day populations are reservoirs of pre-48 individuals from Puerto Rico and the Bahamas, suggesting a shared component of Indigenous Caribbean 49 ancestry with close affinity to South American populations. Our findings contribute to a more complete 50 reconstruction of pre-contact Caribbean population history and explore the role of Indigenous peoples in 51 shaping the biocultural diversity of present-day Puerto Ricans and other Caribbean islanders. 53Puerto Rico is the smallest of the Greater Antilles (Figure 1), the northernmost island grouping of the 55 Caribbean archipelago. The archaeological record of the island's prehistoric communities suggests a 56 dynamic population history with multiple peopling events, frequent migration, and expanding population 57 settlements (Rouse 1992; Rodríguez Ramos 2010). However, different lines of evidence produce 58 conflicting results about the origins and number of these migrations and the role of genetic admixture in

A genetic history of the pre-contact Caribbean

“…3c). Similar to previous work 13,14 , we are unable to identify a statistically significant signal of closer relatedness to Arawak-than to Cariban-or Tupian-speaking populations using f4-statistics ( Fig. 3b; Supplementary Information section 10; Supplementary Data 9), although we obtained a successful 1-way model with the Arawak-speaking Piapoco in qpAdm (p=0.519 or p=0.249, depending on the dataset used for Piapoco; Tables S13 and S14).…”

“…We merged the 184 ancient individuals that passed screening into a base dataset that included 61 previously published ancient American individuals 13 All comparative analyses involving present-day Indigenous American populations were performed on the Illumina dataset, whereas for qpAdm and qpWave's set of outgroup populations ("Right") we used the Human Origins dataset for increased coverage. All genome-wide analyses were performed on autosomal data.…”

“…We used the option 'newshrink: YES' to remap the points for the samples used to generate the PCA onto the positions where they would be expected to fall if they had been projected, thereby allowing the projected and non-projected samples to be appropriately co-visualized. We projected three previously published ancient individuals 13,14 and 184 new ancient individuals onto the first two principal components computed using 61 individuals from 23 present-day populations (Fig. 2a).…”

“…Ancient DNA data from the Caribbean to date comes from mitochondrial DNA [9][10][11][12][13] as well as genomewide data from a 1,000 year-old individual from The Bahamas 14 and two ancient individuals from Puerto Rico 13 . We screened 208 individuals for evidence of authentic ancient DNA (Supplementary Data 1) and generated genome-wide data passing standard criteria for authenticity for 184 unique ancient individuals who lived between ~3150-300 calibrated years (cal.…”

Faces Divulge the Origins of Caribbean Prehistoric Inhabitants

“…First, too few studies have been completed, although we would note that our Bahamas samples are part of an ongoing study of genetic relationships in the circum-Caribbean. Second, community-level identifiers are not yet available, it is difficult to evaluate the impacts of admixture over time 21,40 , and a high degree of genetic variability has been reported for the northwest Amazon homeland of the Carib migrants 41,42 . Third, previous studies have looked only at the two generally accepted Archaic Age and Arawak/ www.nature.com/scientificreports www.nature.com/scientificreports/ Taíno expansions, with some reference to the centuries later Carib migration into the Lesser Antilles 27 .…”