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Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set

Published online by Cambridge University Press:  01 September 2020

Tyler J. Murchie*
Affiliation:
McMaster Ancient DNA Centre, McMaster University, Canada Department of Anthropology, McMaster University, Canada
Melanie Kuch
Affiliation:
McMaster Ancient DNA Centre, McMaster University, Canada Department of Anthropology, McMaster University, Canada
Ana T. Duggan
Affiliation:
McMaster Ancient DNA Centre, McMaster University, Canada Department of Anthropology, McMaster University, Canada
Marissa L. Ledger
Affiliation:
Department of Archaeology, University of Cambridge, United Kingdom
Kévin Roche
Affiliation:
CNRS UMR 5607 Ausonius, University of Bordeaux Montaigne, France CNRS UMR 6249 Chrono-Environment, University of Bourgogne Franche-Comté, France
Jennifer Klunk
Affiliation:
McMaster Ancient DNA Centre, McMaster University, Canada Department of Biology, McMaster University, Canada
Emil Karpinski
Affiliation:
McMaster Ancient DNA Centre, McMaster University, Canada Department of Biology, McMaster University, Canada
Dirk Hackenberger
Affiliation:
McMaster Ancient DNA Centre, McMaster University, Canada Department of Biochemistry, McMaster University, Canada
Tara Sadoway
Affiliation:
McMaster Ancient DNA Centre, McMaster University, Canada University Health Network, Toronto
Ross MacPhee
Affiliation:
Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History
Duane Froese
Affiliation:
Department of Earth and Atmospheric Sciences, University of Alberta
Hendrik Poinar*
Affiliation:
McMaster Ancient DNA Centre, McMaster University, Canada Department of Anthropology, McMaster University, Canada Department of Biochemistry, McMaster University, Canada
*
*Corresponding authors: Tyler J. Murchie and Hendrik Poinar, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ONL8S 4L8, Canada. E-mail address: murchiet@mcmaster.ca and poinarh@mcmaster.ca
*Corresponding authors: Tyler J. Murchie and Hendrik Poinar, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, ONL8S 4L8, Canada. E-mail address: murchiet@mcmaster.ca and poinarh@mcmaster.ca

Abstract

Sedimentary ancient DNA (sedaDNA) has been established as a viable biomolecular proxy for tracking taxon presence through time in a local environment, even in the total absence of surviving tissues. SedaDNA is thought to survive through mineral binding, facilitating long-term biomolecular preservation, but also challenging DNA isolation. Two common limitations in sedaDNA extraction are the carryover of other substances that inhibit enzymatic reactions, and the loss of authentic sedaDNA when attempting to reduce inhibitor co-elution. Here, we present a sedaDNA extraction procedure paired with targeted enrichment intended to maximize DNA recovery. Our procedure exhibits a 7.7–19.3x increase in on-target plant and animal sedaDNA compared to a commercial soil extraction kit, and a 1.2–59.9x increase compared to a metabarcoding approach. To illustrate the effectiveness of our cold spin extraction and PalaeoChip capture enrichment approach, we present results for the diachronic presence of plants and animals from Yukon permafrost samples dating to the Pleistocene-Holocene transition, and discuss new potential evidence for the late survival (~9700 years ago) of mammoth (Mammuthus sp.) and horse (Equus sp.) in the Klondike region of Yukon, Canada. This enrichment approach translates to a more taxonomically diverse dataset and improved on-target sequencing.

Type
Research Article
Copyright
Copyright © University of Washington. Published by Cambridge University Press, 2020

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Supplementary material: PDF

Murchie et al. supplementary material

Murchie et al. supplementary material

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Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set
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