Ancient DNA pp 149-161 | Cite as

Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA

  • Ruth V. Nichols
  • Emily Curd
  • Peter D. Heintzman
  • Beth ShapiroEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1963)


All organisms release their DNA into the environment through processes such as excretion and the senescence of tissues and limbs. This DNA, often referred to as environmental DNA (eDNA) or sedimentary ancient DNA (sedaDNA), can be recovered from both present-day and ancient soils, fecal samples, bodies of water and lake cores, and even air. While eDNA is a potentially useful record of past and present biodiversity, several challenges complicate data generation and interpretation of results. Most importantly, eDNA samples tend to be highly taxonomically mixed, and the target organism or group of organisms may be present at very low abundance within this mixture. To overcome this challenge, enrichment approaches are often used to target specific taxa of interest. Here, we describe a protocol to amplify metabarcodes or short, variable loci that identify lineages within broad taxonomic groups (e.g., plants, mammals), using the polymerase chain reaction (PCR) with established generic “barcode” primers. We also provide a catalog of animal and plant barcode primers that, because they target relatively short fragments of DNA, are potentially suitable for use with degraded DNA.

Key words

Ancient DNA Universal primers Environmental DNA sedaDNA Metabarcoding Amplicon sequencing 



P.D.H. acknowledges support from the Research Council of Norway (Grant 250963: “ECOGEN”).


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Ruth V. Nichols
    • 1
  • Emily Curd
    • 2
  • Peter D. Heintzman
    • 3
  • Beth Shapiro
    • 1
    Email author
  1. 1.Department of Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzUSA
  2. 2.Department of Ecology and Evolutionary BiologyUniversity of California Los AngelesLos AngelesUSA
  3. 3.Tromsø University MuseumUiT—The Arctic University of NorwayTromsøNorway

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