Using palaeoenvironmental DNA to reconstruct past environments: progress and prospects

Rawlence, Nicolas J.; Lowe, David J.; Wood, Jamie R.; Young, Jennifer M.; Churchman, G. Jock; Huang, Doreen Yu-Tuan; Cooper, Alan

doi:10.1002/jqs.2740

Cited by 102 publications

(89 citation statements)

References 187 publications

(333 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This approach could benefit from taxonomy-free DNA techniques to reconstruct past community responses to stressors, and evaluate ecosystem and diversity change through time. For example, ancient DNA (aDNA), an emerging tool which is used in a similar way to eDNA (Bohmann et al 2014;Rawlence et al 2014;Kidwell 2015), could be employed to identify long-term shifts in community structure due to past climate change or environmental perturbations.…”

Section: Molecular-based Indicatorsmentioning

confidence: 99%

Recommendations for the Next Generation of Global Freshwater Biological Monitoring Tools

Jackson

Weyl

Altermatt

et al. 2016

Advances in Ecological Research

View full text Add to dashboard Cite

SummaryBiological monitoring has a long history in freshwaters, where much of the pioneering work in this field was developed over a hundred years ago -but few of the traditional monitoring tools provide the global perspective on biodiversity loss and its consequences for ecosystem functioning that are now needed. Rather than forcing existing monitoring paradigms to respond to questions they were never originally designed to address, we need to take a step back and assess the prospects for novel approaches that could be developed and adopted in the future. To resolve some of the issues with indicators currently used to inform policymakers, we highlight new biological monitoring tools that are being used, or could be developed in the near future, which (1) consider less-studied taxonomic groups; (2) are standardised across regions to allow global comparisons, and (3) measure change over multiple time points. The new tools we suggest make use of some of the key technological and logistical advances seen in recent years -including remote sensing, molecular tools, and local-to-global citizen science networks. We recommend that these new indicators should be considered in future assessments of freshwater ecosystem health and contribute to the evidence base for global to regional (and national) assessments of biodiversity and ecosystem services: for example, within the emerging framework of the Intergovernmental Platform on Biodiversity and Ecosystem Services.

show abstract

Section: Molecular-based Indicatorsmentioning

confidence: 99%

Recommendations for the Next Generation of Global Freshwater Biological Monitoring Tools

Jackson

Weyl

Altermatt

et al. 2016

Advances in Ecological Research

View full text Add to dashboard Cite

show abstract

“…For example, there are 129 papers in the ISI Web of Science Core Collection up to 2015 that use the phrase 'metabarcoding' but not our search terms. Additionally, studies using alternative or more descriptive terms such as paleoenvironmental DNA (Rawlence et al 2014) were not captured by our search terms meaning that research focusing on specific aspects of environmental DNA, such as ancient DNA may be underrepresented in our analysis.…”

Section: Methodsmentioning

confidence: 99%

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

109

112

View full text Add to dashboard Cite

Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil ® and PowerMax ® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil ® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater ® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

show abstract

“…First used in studies of palaeo-biodiversity (Herbert et al 2003), this approach has been shown to track the variation in the abundance of plants and domestic animals over the last six millennia, enabling the reconstruction of human impacts on alpine lakes through time (Giguet-Covex et al, 2014). The peats contained within many floodplain fills are also potential carriers for sedaDNA (Rawlence et al, 2014;Parducci et al, 2015). At present there are few studies but an ongoing research in Arctic Norway has recovered the sedaDNA of over species from small valley-floor ponds in the Veranger peninsula (Clarke et al in prep.).…”

Section: Accepted Manuscriptmentioning

confidence: 99%

Natural vs anthropogenic streams in Europe: History, ecology and implications for restoration, river-rewilding and riverine ecosystem services

Brown

Lespez

Sear

et al. 2018

Earth-Science Reviews

206

152

View full text Add to dashboard Cite

Using palaeoenvironmental DNA to reconstruct past environments: progress and prospects

Cited by 102 publications

References 187 publications

Recommendations for the Next Generation of Global Freshwater Biological Monitoring Tools

Recommendations for the Next Generation of Global Freshwater Biological Monitoring Tools

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Natural vs anthropogenic streams in Europe: History, ecology and implications for restoration, river-rewilding and riverine ecosystem services

Contact Info

Product

Resources

About