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Ancient DNA reconstructs the genetic legacies of pre-contact 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
doi: https://doi.org/10.1101/765685
Maria A. Nieves-Colón
1School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
2National Laboratory of Genomics for Biodiversity (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
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  • For correspondence: mnievesc@asu.edu
William J. Pestle
3Department of Anthropology, University of Miami, Coral Gables, Florida, USA
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Austin W. Reynolds
4Department of Anthropology, University of California, Davis, California, USA
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Bastien Llamas
5Australian Centre for Ancient DNA, School of Biological Sciences and Environment Institute, The University of Adelaide, Adelaide, SA, Australia
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Constanza de la Fuente
6Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
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Kathleen Fowler
1School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
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Katherine M. Skerry
1School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
7School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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Edwin Crespo-Torres
8Forensic Anthropology and Bioarcheology Laboratory, University of Puerto Rico, Rio Piedras, Puerto Rico.
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Carlos D. Bustamante
9Department of Biomedical Data Science, Stanford University, Stanford, California, USA
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Anne C. Stone
1School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
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Abstract

Indigenous peoples have occupied the island of Puerto Rico since at least 3000 B.C. 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 pre-contact Indigenous communities from Puerto Rico. Bone, tooth and dental calculus samples were collected from 124 individuals from three pre-contact 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 pre-contact Puerto Rico sample (40% and 44%, respectively). This distribution, as well as the haplotypes represented, support 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 pre-contact Puerto Rico persist among Puerto Ricans and other Caribbean islanders, indicating that present-day populations are reservoirs of pre-contact mtDNA diversity. Lastly, we find similarity in autosomal ancestry patterns between pre-contact 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 pre-contact Caribbean population history and explore the role of Indigenous peoples in shaping the biocultural diversity of present-day Puerto Ricans and other Caribbean islanders.

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  • ↵† Deceased.

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Posted September 12, 2019.
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Ancient DNA reconstructs the genetic legacies of pre-contact 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
bioRxiv 765685; doi: https://doi.org/10.1101/765685
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Ancient DNA reconstructs the genetic legacies of pre-contact 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
bioRxiv 765685; doi: https://doi.org/10.1101/765685

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