Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system

Shaw, Jennifer L.; Clarke, Laurence J.; Wedderburn, Scotte D.; Barnes, Thomas C.; Weyrich, Laura S.; Cooper, Alan

doi:10.1016/j.biocon.2016.03.010

Cited by 272 publications

(298 citation statements)

References 36 publications

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“…The sum of the detections for each genus (i.e., presence/absence) has been combined for all primer sets variable seabed characteristics, which play an important role in distribution of megafauna as they impact several factors, including larval settlement, anchorages, and shelter (Kedra, Renaud, Andrade, Goszczko, & Ambrose, 2013;Preez, Curtis, & Clarke, 2016). Our observations of distinct patterns of community structure depicted using either COI and 18S primer sets are consistent with several studies that have shown an effect of markers on the detection rate of marine invertebrates (Djurhuus et al, 2018;Drummond et al, 2015;Elbrecht et al, 2017;Kelly et al, 2017;Shaw et al, 2016). Variation in eDNA community structure was intermediate between the variation observed using the two different species collection approaches.…”

Section: Overall Biodiversity and Community Structuresupporting

confidence: 90%

Comparing eDNA metabarcoding and species collection for documenting Arctic metazoan biodiversity

et al. 2019

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Background: Arctic biodiversity has long been poorly documented and is now facing rapid transformations due to ongoing climate change and other impacts, including shipping activities. These changes are placing marine coastal invertebrate communities at greater risk, especially in sensitive areas such as commercial ports. Preserving biodiversity is a significant challenge, going far beyond the protection of charismatic species and involving suitable knowledge of the spatiotemporal organization of species. Therefore, knowledge of alpha, beta, and gamma biodiversity is of great importance to achieve this objective, particularly when partnered with new cost-effective approaches to monitor biodiversity. Method and results:This study compares metabarcoding of COI mitochondrial and 18S rRNA genes from environmental DNA (eDNA) water samples with standard invertebrate species collection methods to document community patterns at multiple spatial scales. Water samples (250 ml) were collected at three different depths within three Canadian Arctic ports: Churchill, MB; Iqaluit, NU; and Deception Bay, QC. From these samples, 202 genera distributed across more than 15 phyla were detected using eDNA metabarcoding, of which only 9%-15% were also identified through species collection at the same sites. Significant differences in taxonomic richness and community composition were observed between eDNA and species collections at both local and regional scales. This study shows that eDNA dispersion in the Arctic Ocean reduces beta diversity in comparison with species collections while emphasizing the importance of pelagic life stages for eDNA detection. Conclusion:The study also highlights the potential of eDNA metabarcoding to assess large-scale Arctic marine invertebrate diversity while emphasizing that eDNA and species collection should be considered as complementary tools to provide a more holistic picture of coastal marine invertebrate communities. K E Y W O R D SArctic, beta diversity, biodiversity, eDNA, marine invertebrates, metabarcoding | 343 LEDUC Et aL.

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Section: Overall Biodiversity and Community Structuresupporting

confidence: 90%

Comparing eDNA metabarcoding and species collection for documenting Arctic metazoan biodiversity

et al. 2019

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“…Thus detection of Alabama and Gulf sturgeon is likely from recent DNA rather than long-term persistence. DNA transfer by vectors (Shaw et al, 2016) such as predators and wetland birds is unlikely for large fish such as the Alabama and Gulf sturgeon. However, DNA transfer from boats and water currents is a possibility.…”

Section: Discussionmentioning

confidence: 99%

Saving the doomed: Using eDNA to aid in detection of rare sturgeon for conservation (Acipenseridae)

Pfleger

Rider

Johnston

et al. 2016

Global Ecology and Conservation

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“…Thus, eDNA metabarcoding would be able to detect larvae that are often overlooked by alternative survey methods. Although the advantages of eDNA metabarcoding in species detection performance compared with alternative methods have been previously suggested18343536, prior to the present study, no comparisons had been conducted. The present study demonstrated that eDNA metabarcoding is a more time-efficient method for examining a whole fish community than a visual census, having a very high detection performance among the alternative methods18.…”

Section: Discussionmentioning

confidence: 99%

Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea

Yamamoto

Masuda

Sato

et al. 2017

Sci Rep

377

321

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Environmental DNA (eDNA) metabarcoding has emerged as a potentially powerful tool to assess aquatic community structures. However, the method has hitherto lacked field tests that evaluate its effectiveness and practical properties as a biodiversity monitoring tool. Here, we evaluated the ability of eDNA metabarcoding to reveal fish community structures in species-rich coastal waters. High-performance fish-universal primers and systematic spatial water sampling at 47 stations covering ~11 km2 revealed the fish community structure at a species resolution. The eDNA metabarcoding based on a 6-h collection of water samples detected 128 fish species, of which 62.5% (40 species) were also observed by underwater visual censuses conducted over a 14-year period. This method also detected other local fishes (≥23 species) that were not observed by the visual censuses. These eDNA metabarcoding features will enhance marine ecosystem-related research, and the method will potentially become a standard tool for surveying fish communities.

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Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system

Cited by 272 publications

References 36 publications

Comparing eDNA metabarcoding and species collection for documenting Arctic metazoan biodiversity

Comparing eDNA metabarcoding and species collection for documenting Arctic metazoan biodiversity

Saving the doomed: Using eDNA to aid in detection of rare sturgeon for conservation (Acipenseridae)

Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea

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