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Improved recovery o...
Improved recovery of ancient DNA from subfossil wood - application to the world's oldest Late Glacial pine forest
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- Lendvay, Bertalan (author)
- Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland.
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- Hartmann, Martin (author)
- Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland.
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- Brodbeck, Sabine (author)
- Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland.
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- Nievergelt, Daniel (author)
- Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland.
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- Reinig, Frederick (author)
- Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland.
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- Zoller, Stefan (author)
- ETH, Genet Divers Ctr, Univ Str 16, CH-8092 Zurich, Switzerland.
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- Parducci, Laura, 1965- (author)
- Uppsala universitet,Växtekologi och evolution
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- Gugerli, Felix (author)
- Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland.
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- Buentgen, Ulf (author)
- Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland.;Univ Cambridge, Dept Geog, Downing Pl, Cambridge CB2 3EN, England.;Masaryk Univ, Global Change Res Ctr, Brno 61300, Czech Republic.
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- Sperisen, Christoph (author)
- Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland.
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Swiss Fed Inst Forest Snow & Landscape Res WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland ETH, Genet Divers Ctr, Univ Str 16, CH-8092 Zurich, Switzerland. (creator_code:org_t)
- 2017-12-15
- 2018
- English.
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In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 217:4, s. 1737-1748
- Related links:
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https://nph.onlineli...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Subject headings
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- 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.
Subject headings
- NATURVETENSKAP -- Biologi -- Botanik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Botany (hsv//eng)
Keyword
- ancient DNA
- DNA metabarcoding
- experimental contamination
- laser cleaning
- post-mortem DNA damage
- subfossil wood
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Lendvay, Bertala ...
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Hartmann, Martin
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Brodbeck, Sabine
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Nievergelt, Dani ...
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Reinig, Frederic ...
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Zoller, Stefan
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Parducci, Laura, ...
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Gugerli, Felix
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Buentgen, Ulf
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Sperisen, Christ ...
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- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Botany
- Articles in the publication
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New Phytologist
- By the university
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Uppsala University