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Improved recovery of ancient DNA from subfossil wood - application to the world's oldest Late Glacial pine forest
Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..
Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..
Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..
Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..ORCID iD: 0000-0003-0402-9348
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2018 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 4, p. 1737-1748Article in journal (Refereed) Published
Abstract [en]

Ancient DNA from historical and subfossil wood has a great potential to provide new insights into the history of tree populations. However, its extraction and analysis have not become routine, mainly because contamination of the wood with modern plant material can complicate the verification of genetic information. Here, we used sapwood tissue from 22 subfossil pines that were growing c. 13000yr bp in Zurich, Switzerland. We developed and evaluated protocols to eliminate surface contamination, and we tested ancient DNA authenticity based on plastid DNA metabarcoding and the assessment of post-mortem DNA damage. A novel approach using laser irradiation coupled with bleaching and surface removal was most efficient in eliminating contaminating DNA. DNA metabarcoding confirmed which ancient DNA samples repeatedly amplified pine DNA and were free of exogenous plant taxa. Pine DNA sequences of these samples showed a high degree of cytosine to thymine mismatches, typical of post-mortem damage. Stringent decontamination of wood surfaces combined with DNA metabarcoding and assessment of post-mortem DNA damage allowed us to authenticate ancient DNA retrieved from the oldest Late Glacial pine forest. These techniques can be applied to any subfossil wood and are likely to improve the accessibility of relict wood for genome-scale ancient DNA studies.

Place, publisher, year, edition, pages
2018. Vol. 217, no 4, p. 1737-1748
Keywords [en]
ancient DNA, DNA metabarcoding, experimental contamination, laser cleaning, post-mortem DNA damage, subfossil wood
National Category
Botany
Identifiers
URN: urn:nbn:se:uu:diva-373254DOI: 10.1111/nph.14935ISI: 000424284400030PubMedID: 29243821OAI: oai:DiVA.org:uu-373254DiVA, id: diva2:1278069
Funder
Swedish Research Council, 2013-D0568401Available from: 2019-01-11 Created: 2019-01-11 Last updated: 2019-01-11Bibliographically approved

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Parducci, Laura

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