Genetic analysis of archaeological wood remains: first results and prospects

Deguilloux, Marie‐France; Bertel, Louis; Celant, Alessandra; Pémonge, Marie‐Hélène; Sadori, Laura; Magri, Donatella; Petit, Rémy J.

doi:10.1016/j.jas.2005.12.012

Cited by 22 publications

(18 citation statements)

References 39 publications

(59 reference statements)

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“…So far, only a few attempts have been made to extract and analyse ancient DNA (aDNA) from subfossil wood. Some studies have demonstrated the possibility of amplifying and sequencing aDNA from buried and waterlogged wood (Dumolin-Lap egue et al, 1999;Tani et al, 2003;Deguilloux et al, 2006;Liepelt et al, 2006;G omez-Zeled on et al, 2017). Although a few promising results have emerged, a multitude of data-related and methodological limitations have been encountered.…”

Section: Introductionmentioning

confidence: 99%

Improved recovery of ancient DNA from subfossil wood – application to the world's oldest Late Glacial pine forest

et al. 2017

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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. 13 000 yr 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.

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Section: Introductionmentioning

confidence: 99%

Improved recovery of ancient DNA from subfossil wood – application to the world's oldest Late Glacial pine forest

et al. 2017

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“…4 Anthracological analysis, which is supported by microscopy techniques, [5][6][7] can be subsequently correlated to radiocarbon dating for archaeological purposes. 8 Other techniques have been recently applied to the identification of wood remains, namely, synchrotron X-ray microtomography, 9 gas chromatography/mass spectrometry [10][11][12] and solid-state nuclear magnetic resonance 13,14 techniques, among others. 15 Genetic analysis including DNA barcoding methodologies, [16][17][18] based on DNA sequencing after non-destructive extraction can also be applied, in favorable cases, for studying ancient vegetal matter.…”

Section: Introductionmentioning

confidence: 99%

“…15 Genetic analysis including DNA barcoding methodologies, [16][17][18] based on DNA sequencing after non-destructive extraction can also be applied, in favorable cases, for studying ancient vegetal matter. 10,19 Chemotaxonomy, the method of biological classification based on the chemical composition of living organisms, can be based on a variety of compounds, from proteins, carbohydrates fatty acids, aldehydes, primary and secondary alcohols, ketones, long-chain alkanes, alkyl esters, triterpenoids, tocopherols, or aromatic compounds. 20 The chemical composition of wood, in particular, polyphenolic compounds, 21 was early used for chemotaxonomic purposes.…”

Section: Introductionmentioning

confidence: 99%

Identification of vegetal species in wooden objects using in situ microextraction-assisted voltammetry of microparticles

Doménech‐Carbó

Ferragud-Adam

et al. 2017

Anal. Methods

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“…A detailed reference map of chloroplast DNA variation in the European white oak has been established (Deguilloux et al 2003a). Different sequence regions amplified by polymerase chain reaction (PCR) have been used for the identification of the Quercus genus (Deguilloux et al 2002;Deguilloux et al 2003b;Deguilloux et al 2006), the Pinaceae family (Vendramin et al 1996), and the Dipterocarpaceae family (Kajita et al 1998), but a general protocol for DNA purification from wood samples and subsequent PCR amplification does not exist (Rachmayanti et al 2006). Here, we attempt to fill this gap and to solve the problem raised by Provan et al 10 years ago, namely designing truly 'universal' PCR primers that uncover widespread polymorphisms in the plant kingdom (Provan et al 2001).…”

Section: Introductionmentioning

confidence: 99%

Wood identification with PCR targeting noncoding chloroplast DNA

2011

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Wood identification is extremely important in the modern forest industry. It also has significant applications in forensics, as well as in archeology and ecological research. In this study, five universal primer pairs amplifying chloroplast noncoding sequences of 300-1,200 bp were designed. Sequencing these amplicons in combination can lead to reliable identification of logs and wood products to cultivar, ecotype, or even the falling population. These primer pairs work on both gymnosperms and angiosperm trees. They also are potentially applicable to accurately identify shrubs and herbaceous species. In addition, a wood DNA purification method is proposed in which N-phenacylthiazolium bromide (PTB) is used to increase the quality and quantity of extracted DNA. This method was first validated using air-dried timber disks from three different tree species that were felled 4 years ago. The sapwood and outer heartwood provided the best locations for DNA extraction. The method was also successfully applied to extract DNA from the recalcitrant processed white oak wood, randomly selected staves of wine barrels. The single nucleotide polymorphism detected on the oak DNA sequences showed correlation to their geographical origins.

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Genetic analysis of archaeological wood remains: first results and prospects

Cited by 22 publications

References 39 publications

Improved recovery of ancient DNA from subfossil wood – application to the world's oldest Late Glacial pine forest

Improved recovery of ancient DNA from subfossil wood – application to the world's oldest Late Glacial pine forest

Identification of vegetal species in wooden objects using in situ microextraction-assisted voltammetry of microparticles

Wood identification with PCR targeting noncoding chloroplast DNA

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