2019
DOI: 10.1101/578591
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Studying ecosystems with DNA metabarcoding: lessons from aquatic biomonitoring

Abstract: 27An ongoing challenge for ecological studies has been the collection of data with high precision 28and accuracy at a sufficient scale to detect effects relevant to management of critical global 29 change processes. A major hurdle for many workflows has been the time-consuming and 30 challenging process of sorting and identification of organisms, but the rapid development of 31 DNA metabarcoding as a biodiversity observation tool provides a potential solution. As high-32 throughput sequencing becomes more rapi… Show more

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Cited by 15 publications
(14 citation statements)
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“…As showcased in recent literature, DNA metabarcoding has gained significant popularity in various ecological studies where biodiversity in a habitat or a sample is investigated (Bik et al, 2012; Yu et al, 2012; J. Gibson et al, 2014, 2015; Creer et al, 2016; Leese et al, 2016; Bush et al, 2017; Porter & Hajibabaei, 2018c; Bush et al, Submitted). In this study we show that the optimal choice of amplicon(s) ought to be based on the objective of the study: optimizing richness, optimizing the differentiation of samples based on sites/conditions, or optimizing the detection of target taxa.…”
Section: Discussionmentioning
confidence: 99%
“…As showcased in recent literature, DNA metabarcoding has gained significant popularity in various ecological studies where biodiversity in a habitat or a sample is investigated (Bik et al, 2012; Yu et al, 2012; J. Gibson et al, 2014, 2015; Creer et al, 2016; Leese et al, 2016; Bush et al, 2017; Porter & Hajibabaei, 2018c; Bush et al, Submitted). In this study we show that the optimal choice of amplicon(s) ought to be based on the objective of the study: optimizing richness, optimizing the differentiation of samples based on sites/conditions, or optimizing the detection of target taxa.…”
Section: Discussionmentioning
confidence: 99%
“…A key difference between our sampling approaches was that the standard CABIN wetland protocol (19) provided estimates of relative abundance based on counts from a subset of each sample, whereas sequences identified using DNA metabarcoding were converted to presence-absence data (13, 28). In addition, CABIN identified 74 families based on morphological features, but metabarcoding could identify 109 families, as well as 263 genera (see Supplement 1 and Fig.…”
Section: Resultsmentioning
confidence: 99%
“…In fact, only the presence-absence DNA metabarcoding models identified significant relationships with the major environmental covariates of this region (16). These effects could be estimated precisely because detectability, and thereby sampling efficiency, was higher for so many taxa using DNA metabarcoding (13). We also used the occupancy model framework to compare detectability of each taxon with different primers, a more robust measure of their complementarity than lists of taxa observed.…”
Section: Discussionmentioning
confidence: 99%
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“…Biomonitoring by metabarcoding has been advocated for arthropods because these methods have the potential to be much faster and less costly than identifications obtained by morphology (Hajibabaei et al 2011, Baird and Hajibabaei 2012, Watts et al 2019. Metabarcoding methods are already being adopted for biomonitoring of invertebrates (Gibson et al 2015, Hajibabaei et al 2016, Bush et al 2019. Identifications obtained through metabarcoding should be of better taxonomic resolution in Alaska, where a deliberate effort has been made to construct a reference library of DNA barcode sequences useful for species identifications of terrestrial arthropods (Sikes et al 2017), than in regions where such libraries are lacking (see Watts et al 2019).…”
Section: Introductionmentioning
confidence: 99%