Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments

Maria A. Nieves-Colón, Andrew T. Ozga, William J. Pestle, Andrea Cucina, Vera Tiesler, Travis W. Stanton, Anne C. Stone

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

Objectives: The tropics harbor a large part of the world's biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semi-tropical sites in Tanzania, Mexico, and Puerto Rico (N = 12). Materials and Methods: All samples were extracted twice, built into double-stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500. The first extraction protocol, Method D, was previously designed for recovery of ultrashort DNA fragments from skeletal remains. The second, Method H, modifies the first by adding an initial EDTA wash and an extended digestion and decalcification step. Results: No significant difference was found in overall ancient DNA yields or post-mortem damage patterns recovered from samples extracted with either method, irrespective of tissue type. However, Method H samples had higher endogenous content and more mapped reads after quality-filtering, but also higher clonality. In contrast, samples extracted with Method D had shorter average DNA fragments. Discussion: Both methods successfully recovered endogenous ancient DNA. But, since surviving DNA in ancient or historic remains from tropical contexts is extremely fragmented, our results suggest that Method D is the optimal choice for working with samples from warm and humid environments. Additional optimization of extraction conditions and further testing of Method H with different types of samples may allow for improvement of this protocol in the future.

Original languageEnglish (US)
Pages (from-to)824-836
Number of pages13
JournalAmerican Journal of Physical Anthropology
Volume166
Issue number4
DOIs
StatePublished - Aug 2018
Externally publishedYes

Bibliographical note

Funding Information:
National Science Foundation, Grant Numbers: BCS-1622479, BCS-0612727; the Rust Family Foundation; the Leakey Foundation; Arizona State University Strategic Initiative Funds; Fundación Roberto Hernández; Fundación Pedro y Elena Hernández; the Selz Foundation; Jerry Murdoch

Funding Information:
The authors thank the research team at the Gombe National Park, Dr. Mike Wilson, Dr. Anne Pusey, and Dr. Ian Gilby for facilitating research with the Gombe chimpanzees. They especially thank Dr. Jane Goodall for ensuring the preservation of skeletal material and making them available for further study, and Dr. Rebecca Nockerts for preparing the samples. In addition, they also thank Dr. L. Antonio Curet and Dr. Tim Webster for helpful discussion, and the support staff and volunteers at the Ceremonial Center of Tibes Archaeological Park, and the Yaxuna archaeological site for invaluable logistics support. Lastly, they thank the three reviewers whose thoughtful comments and suggestions led to improvement of this article. Research with Puerto Rico samples was supported by National Science Foundation Grant BCS-061272 to W.J.P., National Science Foundation Doctoral Dissertation Improvement Award BCS-1622479 and Rust Family Foundation grant in Archaeology to M.N.C. Funding for work with Gombe samples was provided by the Leakey Foundation, ASU Strategic Initiative Funds, Office of the President of Arizona State University to A.C.S, and the Institute of Human Origins' DNA and Human Origins at ASU project. They thank the Consejo de Arqueolog?a of the Instituto Nacional de Antropolog?a e Historia for granting the permits to conduct the research at Yaxuna, which was generously supported by the Fundaci?n Roberto Hern?ndez, Fundaci?n Pedro y Elena Hern?ndez, the Selz Foundation, and Jerry Murdoch. M.N.C wishes to further thank the Arizona State University School of Human Evolution and Social Change Dissertation Completion Fellowship program for providing financial assistance during the time this work was completed.

Funding Information:
The authors thank the research team at the Gombe National Park, Dr. Mike Wilson, Dr. Anne Pusey, and Dr. Ian Gilby for facilitating research with the Gombe chimpanzees. They especially thank Dr. Jane Goodall for ensuring the preservation of skeletal material and making them available for further study, and Dr. Rebecca Nockerts for preparing the samples. In addition, they also thank Dr. L. Antonio Curet and Dr. Tim Webster for helpful discussion, and the support staff and volunteers at the Ceremonial Center of Tibes Archaeological Park, and the Yaxuna archaeological site for invaluable logistics support. Lastly, they thank the three reviewers whose thoughtful comments and suggestions led to improvement of this article. Research with Puerto Rico samples was supported by National Science Foundation Grant BCS-061272 to W.J.P., National Science Foundation Doctoral Dissertation Improvement Award BCS-1622479 and Rust Family Foundation grant in Archaeology to M.N. C. Funding for work with Gombe samples was provided by the Leakey Foundation, ASU Strategic Initiative Funds, Office of the President of Arizona State University to A.C.S, and the Institute of Human Origins’ DNA and Human Origins at ASU project. They thank the Consejo de Arqueología of the Instituto Nacional de Antropolo-gía e Historia for granting the permits to conduct the research at Yaxuna, which was generously supported by the Fundación Roberto Hernández, Fundación Pedro y Elena Hernández, the Selz Foundation, and Jerry Murdoch. M.N.C wishes to further thank the Arizona State University School of Human Evolution and Social Change Dissertation Completion Fellowship program for providing financial assistance during the time this work was completed.

Publisher Copyright:
© 2018 Wiley Periodicals, Inc.

Keywords

  • DNA extraction
  • ancient DNA
  • next-generation sequencing
  • skeletal remains
  • tropics

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