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Cited by 105Environmental DNA in Biodiversity StudiesPolar Research and EcologyForensic and Genetic Research

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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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Murchie, Tyler J., Kuch, Melanie, Duggan, Ana T., Ledger, Marissa L., Roche, Kévin, Klunk, Jennifer, Karpinski, Emil, Hackenberger, Dirk, Sadoway, Tara, MacPhee, Ross, Froese, Duane, Poinar, Hendrik·2021·Quaternary Research
DOI 10.1017/qua.2020.59

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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.

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  • Early eDNA analyses relied on molecular cloning of PCR-amplified meta-barcodes, but massively parallel sequencing facilitated access to entire molecular diversity of individual animals and plants.

    “Early analyses relied on molecular cloning of PCR-amplified meta-barcodes, but massively parallel sequencing facilitated access to the entire molecular diversity of individual animals and plants 325 .”

    From Ancient DNA analysis (2021) · cites this paper as [325]

    The PCR metabarcoding section describes amplification of genetic barcodes, and the Introduction says high-throughput sequencing can identify diverse organisms from one sample. The paper does not say early analyses relied on molecular cloning. Its Introduction also says environmental DNA generally precludes genomic reconstruction of single individuals, so it does not support access to the entire molecular diversity of individual animals and plants. Page numbers are unavailable in our copy. (LLM, conf=0.85)

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Metadata

Authors
Murchie, T. J., Kuch, M., Duggan, A. T., Ledger, M. L., Roche, K., Klunk, J., Karpinski, E., Hackenberger, D., Sadoway, T., MacPhee, R., Froese, D., & Poinar, H.
Affiliations
  • McMaster University (CA)
  • University of Cambridge (GB)
  • Centre National de la Recherche Scientifique (FR)
  • University Health Network (CA)
  • American Museum of Natural History (US)
  • University of Alberta (CA)
Corresponding author
  • Murchie, Tyler J.
  • Poinar, Hendrik
ORCID
Venue
Quaternary Research
Publisher
Cambridge University Press (CUP)
Published
2020-09-01
Volume
99
Pages
305-328
ISSN
  • 0033-5894 (ISSN-L)
  • 1096-0287
DOI
10.1017/qua.2020.59
OpenAlex
W3081719801
Cited by
105
References
8
Citations by year
2026: 21 · 2025: 14 · 2024: 14 · 2023: 24 · 2022: 16 · 2021: 12 · 2020: 4
FWCI
7.05
Type
journal article
Language
en
Open access
Licence
www.cambridge.org/core/terms (unspecified)
Locations
  • Quaternary Research (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • HAL (submittedVersion)
Funders
  • Arctic Institute of North America
  • McMaster University
  • Polar Knowledge Canada
  • Garfield Weston Foundation
  • Agence Nationale de la Recherche (ANR-18-EBI4-0008)
  • Canadian Institutes of Health Research
  • Natural Sciences and Engineering Research Council of Canada
  • Social Sciences and Humanities Research Council of Canada
Topics
  • Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
  • Physical Sciences › Environmental Science › Ecology › Polar Research and Ecology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
Keywords
sedimentary ancient DNA, ancient environmental DNA, DNA extraction optimization, target enrichment, permafrost, Pleistocene-Holocene transition, Yukon, mammoth, Equus, DNA inhibitors

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