Evaluating a multigene environmental DNA approach for biodiversity assessment

Drummond, Alexei J.; Newcomb, Richard D.; Buckley, Thomas R.; Xie, Donghua; Dopheide, Andrew; Potter, Benjamin C. M.; Heled, Joseph; Ross, Howard A.; Tooman, Leah; Grosser, Stefanie; Park, Duckchul; Demetras, Nicholas J.; Stevens, Mark I.; Russell, James C.; Anderson, Sandra; Carter, Anna; Nelson, Nicola J.

doi:10.1186/s13742-015-0086-1

Cited by 141 publications

(153 citation statements)

References 54 publications

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“…Initial metabarcoding applications have mostly tackled the substantial technical hurdles of sampling DNA under field conditions -the 'proof of concept' (e.g. Drummond et al 2015). To now benefit from the rich information DNA metabarcoding can provide, robust sampling designs are needed, built on a quantitative understanding of spatial variability among samples, detection probabilities (e.g.…”

Section: Methodological Uncertainties Associated With Dna Metabarcodingmentioning

confidence: 99%

“…As is typical for the initial uptake of any technology, early applications (e.g. Drummond et al 2015) have focused on exploring the method. As our understanding of the properties of these methods evolves, there is an increasing need to move beyond this and into applications that provide rich information for a range of purposes, including conservation planning and land management decisions .…”

Section: Future Research Directionsmentioning

confidence: 99%

“…For example, a single soil-based sampling regime could be used to identify locally present above-and below-ground species at multiple trophic levels (e.g. Drummond et al 2015). Highly trained specialists are not needed for specimen identification, avoiding this typically labour-intensive process (e.g.…”

Section: General Benefits Of Dna Metabarcoding and Its Integration Wimentioning

confidence: 99%

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Using DNA meta barcoding to assess New Zealand's terrestrial biodiversity

Holdaway¹,

Wood²,

Dickie³

et al. 2017

NZ J Ecol

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High throughput DNA sequencing technology has enabled entire biological communities to be characterised from DNA derived from pools of organisms, such as bulk-collected invertebrates, or DNA extracted from environmental samples (e.g. soil). These DNA-based techniques have the potential to revolutionise biodiversity monitoring. One approach in particular, DNA metabarcoding, can provide unprecedented taxonomic breadth at a scale not practically achievable through the morphological identification of individual organisms. Here, we assess the current strengths and weaknesses of DNA metabarcoding techniques for biodiversity assessment. We argue that it is essential to integrate conventional monitoring methods with novel DNA methods, to validate methods, and to better use and interpret data. We present a conceptual framework for how this might be done, explore potential applications within national biodiversity assessment frameworks, Maori biodiversity monitoring and the primary sector, and highlight areas of current uncertainty and future research directions. Rapid developments in DNA sequencing technology and bioinformatics will make DNA-based community data increasingly accessible to ecologists, and there needs to be a corresponding shift in research focus from DNA metabarcoding method development and evaluation to real-world applications that provide rich information for a range of purposes, including conservation planning and land management decisions.

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Section: Methodological Uncertainties Associated With Dna Metabarcodingmentioning

confidence: 99%

Section: Future Research Directionsmentioning

confidence: 99%

Section: General Benefits Of Dna Metabarcoding and Its Integration Wimentioning

confidence: 99%

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Using DNA meta barcoding to assess New Zealand's terrestrial biodiversity

Holdaway¹,

Wood²,

Dickie³

et al. 2017

NZ J Ecol

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“…genomicobservatory.cs.auckland.ac.nz/) aimed at the characterisation (environmental and phylogenetically) of terrestrial species in a selected ecosystem, as a first national contribution to the GOs Network (Drummond et al 2015).…”

Section: 1)mentioning

confidence: 99%

Monitoring Changes in Genetic Diversity

Bruford

Davies

Dulloo

et al. 2016

The GEO Handbook on Biodiversity Observation Networks

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DNA is the most elemental level of biodiversity, drives the process of speciation, and underpins other levels of biodiversity, including functional traits, species and ecosystems. Until recently biodiversity indicators have largely overlooked data from the molecular tools that are available for measuring variation at the DNA level. More direct analysis of trends in genetic diversity are now feasible and are ready to be incorporated into biodiversity monitoring. This chapter explores the current state-of-the-art in genetic monitoring, with an emphasis on new molecular tools and the richness of data they provide to supplement existing approaches. We also briefly consider proxy approaches that may be useful for many-species, global scale monitoring cases.

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“…High Throughput Sequencing (HTS) of amplicons generated from bulk extracts of environmental samples can be used to rapidly generate biodiversity information from terrestrial Antarctic habitats [16]. With such metabarcoding methods (sensu [21]), morphologically conserved species are rapidly distinguished in parallel from substrates such as soil, snow or water [22][23][24][25], using simple sampling procedures and laboratory workflows [23,26]. In Antarctica, HTS based metabarcoding studies have investigated viruses [27], bacteria [17,28,29] and predominantly unicellular, fungal or algal, eukaryotes [18,26,30].…”

mentioning

confidence: 99%

Ground-truthing Phylotype Assignments for Antarctic Invertebrates

Czechowski¹,

Clarke²,

Cooper³

et al. 2017

DNA Barcodes

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taxonomy determination did not outperform metabarcoding approaches. Our study demonstrates how barcoding markers can be tested prior to their application to specific taxonomic groups, and that taxonomy fidelity of markers needs to be validated in relation to environment, taxa, and available reference information. Keywords:environmental DNA, metataxonomic, mitochondrial cytochrome c oxidase I, COI, 18S rDNA, Illumina, 454, biodiversity survey IntroductionBiodiversity information from Antarctic terrestrial habitats is important for estimating the effects of environmental change on Antarctic ecosystems [1,2], conservation management in light of increasing threats from nonindigenous invasive species [3], and investigations on the historic effect of glacial constraints on the evolution of Antarctic biotas over millions of years [4]. Undertaking such biodiversity research in terrestrial Antarctica is challenging due to the logistics of accessing remote locations in a harsh environment [5]. In recent years, biodiversity information for terrestrial Antarctic plant life has improved due to compilation of occurrence records from smaller-scale studies into easily accessible databases, and may in the future be easier to obtain through remote sensing technology [6,7]. However, the distribution and diversity of Antarctic invertebrates remains understudied [8,9] despite their important role in nutrient cycling and soil formation [10].Deficient biodiversity information for terrestrial Antarctic invertebrates is caused by the persistence of slow and inefficient survey methods. Antarctic springtails, mites, tardigrades, nematodes and rotifers are morphologically conserved, but still frequently analyzed with morphological approaches, requiring highly skilled taxonomists -time required to identify such invertebrates can be considered inversely proportional to their size [11][12][13][14]. Not reliant on morphological identification, DNA- Abstract: Biodiversity information from Antarctic terrestrial habitats helps conservation efforts, but the distribution and diversity particularly of microinvertebrates remains poorly understood. Springtails, mites, tardigrades, nematodes and rotifers are difficult to identify using morphological features, hence DNAbased metabarcoding methods are well suited for their study. We compared taxonomy assignments of a high throughput sequencing metabarcoding approach using one ribosomal DNA (18S rDNA) and one mitochondrial DNA (cytochrome c oxidase subunit I -COI) marker with morphological reference data. Specifically, we compared metabarcoding or morphological taxonomic assignments on multiple taxonomic levels in an artificial DNA blend containing Australian invertebrates, and in seven extracts of Antarctic soils containing known micro-faunal taxa. Avoiding arbitrary application of metabarcoding analysis parameters, we calibrated those parameters with metabarcoding data from non-Antarctic soils. Metabarcoding approaches employing 18S rDNA and COI markers enabled detection of small and cryptic Antarctic i...

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Evaluating a multigene environmental DNA approach for biodiversity assessment

Cited by 141 publications

References 54 publications

Using DNA meta barcoding to assess New Zealand's terrestrial biodiversity

Using DNA meta barcoding to assess New Zealand's terrestrial biodiversity

Monitoring Changes in Genetic Diversity

Ground-truthing Phylotype Assignments for Antarctic Invertebrates

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