Ancient DNA Reconstructs the Genetic Legacies of Precontact Puerto Rico Communities

Maria A. Nieves-Colón, William J. Pestle, Austin W. Reynolds, Bastien Llamas, Constanza De La Fuente, Kathleen Fowler, Katherine M. Skerry, Edwin Crespo-Torres, Carlos D. Bustamante, Anne C. Stone, Connie Mulligan

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Indigenous peoples have occupied the island of Puerto Rico since at least 3000 BC. Due to the demographic shifts that occurred after European contact, the origin(s) of these ancient populations, and their genetic relationship to present-day islanders, are unclear. We use ancient DNA to characterize the population history and genetic legacies of precontact Indigenous communities from Puerto Rico. Bone, tooth, and dental calculus samples were collected from 124 individuals from three precontact archaeological sites: Tibes, Punta Candelero, and Paso del Indio. Despite poor DNA preservation, we used target enrichment and high-throughput sequencing to obtain complete mitochondrial genomes (mtDNA) from 45 individuals and autosomal genotypes from two individuals. We found a high proportion of Native American mtDNA haplogroups A2 and C1 in the precontact Puerto Rico sample (40% and 44%, respectively). This distribution, as well as the haplotypes represented, supports a primarily Amazonian South American origin for these populations and mirrors the Native American mtDNA diversity patterns found in present-day islanders. Three mtDNA haplotypes from precontact Puerto Rico persist among Puerto Ricans and other Caribbean islanders, indicating that present-day populations are reservoirs of precontact mtDNA diversity. Lastly, we find similarity in autosomal ancestry patterns between precontact individuals from Puerto Rico and the Bahamas, suggesting a shared component of Indigenous Caribbean ancestry with close affinity to South American populations. Our findings contribute to a more complete reconstruction of precontact Caribbean population history and explore the role of Indigenous peoples in shaping the biocultural diversity of present-day Puerto Ricans and other Caribbean islanders.

Original languageEnglish (US)
Pages (from-to)611-626
Number of pages16
JournalMolecular biology and evolution
Issue number3
StatePublished - Mar 1 2020
Externally publishedYes

Bibliographical note

Funding Information:
We thank L. Antonio Curet, Alexandra Adams, Meredith Carpenter, Rosa Fregel, Kelly Blevins, the Crabbe family, Irma Zayas and the staff of the Centro Ceremonial Indígena de Tibes for support and assistance. This work was supported by the National Science Foundation (BCS-1622479 to M.A.N.-C. and BCS-0612727 to W.J.P.), the Rust Family Foundation Grant for Archaeological Research (RFF-2016-08 to M.A.N.-C.), Sigma Xi (G2012161222 and G201510151642390 to M.A.N.-C.) and pilot grant programs from the ASU School of Human Evolution and Social Change, School of International Letters and Cultures and Graduate and Professional Student Association. Sequence data generated through this study are available in the NCBI Short Read Archive (SRA) under BioProject accession PRJNA557308.


  • Caribbean
  • ancient DNA
  • human genetics
  • mitochondrial DNA

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