The ecologist's field guide to sequence‐based identification of biodiversity

By S. Creer, K. Deiner, Serita Frey, D. Porazinska, P. Taberlet, W. Thomas, C. Potter, Holly M. Bik. 2016

358 citations recorded by the source corpus.

The past 100 years of ecological research has seen substantial progress in understanding the natural world and likely effects of change, whether natural or anthropogenic. Traditional ecological approaches underpin such advances, but would additionally benefit from recent developments in the sequence‐based quantification of biodiversity from the fields of molecular ecology and genomics. By building on a long and rich history of molecular taxonomy and taking advantage of the new generation of DNA sequencing technologies, we are gaining previously impossible insights into alpha and beta diversity from all domains of life, irrespective of body size. While a number of complementary reviews are available in specialist journals, our aim here is to succinctly describe the different technologies available within the omics toolbox and showcase the opportunities available to contemporary ecologists to advance our understanding of biodiversity and its potential roles in ecosystems. Starting in the field, we walk the reader through sampling and preservation of genomic material, including typical taxonomy marker genes used for species identification. Moving on to the laboratory, we cover nucleic acid extraction approaches and highlight the principal features of using marker gene assessment, metagenomics, metatranscriptomics, single‐cell genomics and targeted genome sequencing as complementary approaches to assess the taxonomic and functional characteristics of biodiversity. We additionally provide clear guidance on the forms of DNA found in the environmental samples (e.g. environmental vs. ancient DNA) and highlight a selection of case studies, including the investigation of trophic relationships/food webs. Given the maturity of sequence‐based identification of prokaryotes and microbial eukaryotes, more exposure is given to macrobial communities. We additionally illustrate current approaches to genomic data analysis and highlight the exciting prospects of the publicly available data underpinning published sequence‐based studies. Given that ecology ‘has to count’, we identify the impact that molecular genetic analyses have had on stakeholders and end‐users and predict future developments for the fields of biomonitoring. Furthermore, we conclude by highlighting future opportunities in the field of systems ecology afforded by effective engagement between the fields of traditional and molecular ecology.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6cb5b8c4eb943806ddfd0ce408fe63b8cdc80a07

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Citations in the corpus

Dos and don'ts when inferring assembly rules from diversity patterns (2020, background): “One example is amplicon-based DNA analysis of environmental samples (i.e., metabarcoding data, environmental DNA; Creer et al., 2016; Taberlet et al., 2012).”
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities (2017, methodology): “…analysis, NDMS ordination, etc.), prior to hypothesis testing via downstream statistical analysis. identification of taxa over the past 40 years (Creer et al., 2016), the range of software solutions to analyse microbial metabarcoding data sets is unsurprisingly extensive (Bik et al., 2012).”
Long‐range PCR allows sequencing of mitochondrial genomes from environmental DNA (2017, background): “The use of DNA found in the environment (eDNA) to catalogue biodiversity is gaining momentum (Creer et al., 2016).”
A practical guide to DNA metabarcoding for entomological ecologists (2020, background): “Although undenatured ethanol is preferred for precipitation (Creer et al., 2016), its use may be constrained logistically or financially.”
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, background): “DNA templates that are GC-rich can also hamper DNA amplification as secondary structures are formed, such as DNA hairpins (Creer et al. 2016); these may block DNA polymerases from efficiently replicating GC-rich DNA sequences.”
“Pitfalls in relative abundance estimation using eDNA metabarcoding” (2018, background): “For the last decade, metabarcoding applicability in ecology ranged from species detection to biodiversity assessment and community ecology in several habitats (review Creer et al. 2016).”
Uses and Misuses of Environmental DNA in Biodiversity Science and Conservation (2018, methodology): “Its high detection capability and sensitivity along with reduced costs in comparison to those of traditional methods create an unprecedented opportunity to advance biodiversity monitoring and environmental management (Sutherland et al. 2013, Cristescu 2014, Kelly et al. 2014b).”
Non‐specific amplification compromises environmental DNA metabarcoding with COI (2019, methodology): “While PCR‐free methods are being actively investigated, it is clear that despite the limitations in quantification, the majority of environmental metabarcoding will be based around amplicon sequencing, at least for the medium term (Bista et al., 2018; Creer et al., 2016; Stat et al., 2017; Wilcox et”
DNA Sequencing as a Tool to Monitor Marine Ecological Status (2017, background): “…employed target regions (Dauble et al., 2012; Pawlowski et al., 2014; Cowart et al., 2015; Guo et al., 2015; Harada et al., 2015; Johnson and Martiny, 2015; Aylagas et al., 2016; Bucklin et al., 2016; Creer et al., 2016; Leray and Knowlton, 2016; Thompson et al., 2016; Trivedi et al., 2016).”