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Data from: DNA from soil mirrors plant taxonomic and growth form diversity

Data from: DNA from soil mirrors plant taxonomic and growth form diversity
Data from: DNA from soil mirrors plant taxonomic and growth form diversity
Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually less than 100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses included amplification using plant-specific versatile primers, sequencing and estimation of taxonomic diversity. We tested in three steps whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes. First, soil DNA from eight boreal plant communities located in two different vegetation types (meadow and heath) was amplified. Plant diversity detected from boreal soil was highly consistent with plant functional and structural diversity estimated from conventional above-ground surveys. Second, we assessed DNA persistence using samples from formerly cultivated soils in temperate environments. We found that number of crop DNA sequences retrieved strongly varied with years since last cultivation, and crop sequences were absent from nearby, uncultivated plots. Third, we assessed the universal applicability of DNA metabarcoding using soil samples from tropical environments: a large proportion of species and families from the study site was efficiently recovered. The results open unprecedented opportunities for large-scale DNA-based biodiversity studies across a range of taxonomic groups using standardized metabarcoding approaches.,Yoccoz_et_al_Table_S1Supplementary Table with description of the results obtained for the Boreal site.Yoccoz_et_al_Table_S2Supplementary Table showing the results obtained for the Tropical site.Boreal_sequence_datafasta file.Tropical_sequence_dataFasta file.Temperate_sequence_dataFasta file.Temperate_sequence_data_filteredTab file.,
DRYAD
Yoccoz, Nigel G.
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Brathen, Kari-Anne
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Gielly, Ludovic
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Haile, James
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Edwards, Mary E.
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Goslar, Tomasz
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Von Stedingk, H.
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Brysting, Anne K.
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Coissac, Eric
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Pompanon, Francois
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Sønstebø, J. H.
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Miquel, Christian
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Valentini, Alice
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De Bello, Francesco
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Chave, Jérôme
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Thuiller, Wilfried
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Wincker, Patrick
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Cruaud, Corinne
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Gavory, Frederick
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Rasmussen, Morten
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Gilbert, M. Thomas P.
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Orlando, Ludovic
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Brochmann, Christian
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Willerslev, Eske
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Taberlet, Pierre
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Yoccoz, Nigel G.
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Brathen, Kari-Anne
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Gielly, Ludovic
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Haile, James
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Edwards, Mary E.
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Goslar, Tomasz
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Von Stedingk, H.
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Brysting, Anne K.
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Coissac, Eric
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Pompanon, Francois
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Sønstebø, J. H.
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Miquel, Christian
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Valentini, Alice
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De Bello, Francesco
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Chave, Jérôme
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Thuiller, Wilfried
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Wincker, Patrick
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Cruaud, Corinne
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Gavory, Frederick
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Rasmussen, Morten
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Gilbert, M. Thomas P.
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Orlando, Ludovic
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Brochmann, Christian
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Willerslev, Eske
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Taberlet, Pierre
f5769360-3873-49b1-b4ce-56e14b1d3aa0

Yoccoz, Nigel G., Gielly, Ludovic, Goslar, Tomasz, Brysting, Anne K., Coissac, Eric, Sønstebø, J. H., Chave, Jérôme, Thuiller, Wilfried, Wincker, Patrick, Cruaud, Corinne, Rasmussen, Morten, Gilbert, M. Thomas P., Orlando, Ludovic, Brochmann, Christian, Willerslev, Eske and Taberlet, Pierre (2012) Data from: DNA from soil mirrors plant taxonomic and growth form diversity. DRYAD doi:10.5061/dryad.m346b576 [Dataset]

Record type: Dataset

Abstract

Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually less than 100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses included amplification using plant-specific versatile primers, sequencing and estimation of taxonomic diversity. We tested in three steps whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes. First, soil DNA from eight boreal plant communities located in two different vegetation types (meadow and heath) was amplified. Plant diversity detected from boreal soil was highly consistent with plant functional and structural diversity estimated from conventional above-ground surveys. Second, we assessed DNA persistence using samples from formerly cultivated soils in temperate environments. We found that number of crop DNA sequences retrieved strongly varied with years since last cultivation, and crop sequences were absent from nearby, uncultivated plots. Third, we assessed the universal applicability of DNA metabarcoding using soil samples from tropical environments: a large proportion of species and families from the study site was efficiently recovered. The results open unprecedented opportunities for large-scale DNA-based biodiversity studies across a range of taxonomic groups using standardized metabarcoding approaches.,Yoccoz_et_al_Table_S1Supplementary Table with description of the results obtained for the Boreal site.Yoccoz_et_al_Table_S2Supplementary Table showing the results obtained for the Tropical site.Boreal_sequence_datafasta file.Tropical_sequence_dataFasta file.Temperate_sequence_dataFasta file.Temperate_sequence_data_filteredTab file.,

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More information

Published date: 1 January 2012

Identifiers

Local EPrints ID: 449323
URI: http://eprints.soton.ac.uk/id/eprint/449323
PURE UUID: 6d9d5c0d-214c-4f48-bb3a-59819bfbe13e
ORCID for Mary E. Edwards: ORCID iD orcid.org/0000-0002-3490-6682

Catalogue record

Date deposited: 24 May 2021 16:32
Last modified: 03 Jun 2021 01:38

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Contributors

Creator: Nigel G. Yoccoz
Contributor: Kari-Anne Brathen
Creator: Ludovic Gielly
Contributor: James Haile
Contributor: Mary E. Edwards ORCID iD
Creator: Tomasz Goslar
Contributor: H. Von Stedingk
Creator: Anne K. Brysting
Creator: Eric Coissac
Contributor: Francois Pompanon
Creator: J. H. Sønstebø
Contributor: Christian Miquel
Contributor: Alice Valentini
Contributor: Francesco De Bello
Creator: Jérôme Chave
Creator: Wilfried Thuiller
Creator: Patrick Wincker
Creator: Corinne Cruaud
Contributor: Frederick Gavory
Creator: Morten Rasmussen
Creator: M. Thomas P. Gilbert
Creator: Ludovic Orlando
Creator: Christian Brochmann
Creator: Eske Willerslev
Creator: Pierre Taberlet

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