Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, <i>Dreissena rostriformis bugensis</i> in flowing water

Blackman, Rosetta C.; Ling, Kar Keun Sean; Harper, Lynsey R.; Shum, Peter; Hänfling, Bernd; Handley, Lori Lawson

doi:10.1002/ece3.6921

Cited by 31 publications

(48 citation statements)

References 74 publications

(122 reference statements)

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“…Biodiversity studies increasingly use environmental DNA (eDNA)‐based methods to assess community patterns (Cordier et al, 2020; Dornelas et al, 2019), to discover rare organisms (Jerde et al, 2011), and to detect invasive species (Holman et al, 2019). Comparisons between non‐molecular and eDNA biodiversity surveys have consistently shown that eDNA surveys are highly sensitive and can detect species accurately at a reduced cost (Blackman et al, 2020; Borrell et al, 2017; Deiner et al, 2017). However, rigorous optimization and methodological standardization are necessary to correctly interpret data generated from eDNA surveys (Agersnap et al, 2017; Goldberg et al, 2016; Zinger et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…An unexplored question is to what extent the results of the above single‐species studies (qPCR‐based) also apply to metabarcoding experiments. Some work has directly compared the sensitivity of qPCR and metabarcoding using non‐specific primers (Blackman et al, 2020; Bylemans et al, 2019; Harper et al, 2018; Simmons et al, 2016; Wood et al, 2019). In all these studies, the qPCR assays were shown to be more sensitive for the detection of the study species.…”

Section: Introductionmentioning

confidence: 99%

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How does eDNA decay affect metabarcoding experiments?

2021

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Biodiversity studies increasingly use environmental DNA (eDNA)based methods to assess community patterns (Cordier et al., 2020;Dornelas et al., 2019), to discover rare organisms (Jerde et al., 2011), and to detect invasive species (Holman et al., 2019).Comparisons between non-molecular and eDNA biodiversity surveys have consistently shown that eDNA surveys are highly sensitive and can detect species accurately at a reduced cost (Blackman

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

How does eDNA decay affect metabarcoding experiments?

2021

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“…Previous work has identified that NNS can be detected using eDNA metabarcoding [37,39], but these surveys aimed at detecting any NNS rather than a specific set of target taxa. Several studies have identified that general target metabarcoding primers show lower reliability and sensitivity compared to species-specific quantitative PCR assays [95,96]. Additionally, previous work has identified that in some cases different bioinformatic methods carry variable sensitivity [97], although this effect is fairly minimal in this dataset (see electronic supplementary material, note 3).…”

Section: Discussionmentioning

confidence: 89%

Managing human-mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species

Holman

Parker-Nance

Bruyn

et al. 2022

Phil. Trans. R. Soc. B

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The use of molecular tools to manage natural resources is increasingly common. However, DNA-based methods are seldom used to understand the spatial and temporal dynamics of species' range shifts. This is important when managing range shifting species such as non-native species (NNS), which can have negative impacts on biotic communities. Here, we investigated the ascidian NNS Ciona robusta , Clavelina lepadiformis , Microcosmus squamiger and Styela plicata using a combined methodological approach. We first conducted non-molecular biodiversity surveys for these NNS along the South African coastline, and compared the results with historical surveys. We detected no consistent change in range size across species, with some displaying range stability and others showing range shifts. We then sequenced a section of cytochrome c oxidase subunit I (COI) from tissue samples and found genetic differences along the coastline but no change over recent times. Finally, we found that environmental DNA metabarcoding data showed broad congruence with both the biodiversity survey and the COI datasets, but failed to capture the complete incidence of all NNS. Overall, we demonstrated how a combined methodological approach can effectively detect spatial and temporal variation in genetic composition and range size, which is key for managing both thriving NNS and threatened species. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’.

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“…Previous work has identified that NNS can be detected using eDNA metabarcoding [32, 34], but these surveys aimed at detecting any NNS rather than a specific set of target taxa. Several studies have identified that general target metabarcoding primers show lower reliability and sensitivity compared to species-specific quantitative PCR assays [93, 94]. Additionally, previous work has identified that in some cases different bioinformatic methods carry variable sensitivity [95], although this effect is fairly minimal in this dataset (see Supplementary Note 3).…”

Section: Discussionmentioning

confidence: 86%

Managing human mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species

Holman

Parker-Nance

Bruyn

et al. 2021

Preprint

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The use of molecular methods to manage natural resources is increasingly common. However, DNA-based methods are seldom used to understand the spatial and temporal dynamics of species' range shifts. This is important when managing range-shifting species such as non-native species (NNS), which can have negative impacts on biotic communities. Here we investigated the range-shifting NNS Ciona robusta, Clavelina lepadiformis, Microcosmus squamiger and Styela plicata using a combined methodological approach. We first conducted non-molecular biodiversity surveys for these NSS along the South African coastline, and compared the results with historical surveys. We detected no consistent change in range size across species, with some displaying range stability and others showing range shifts. We then sequenced a section of cytochrome c oxidase subunit I (COI) from tissue samples and found genetic differences along the coastline but no change over recent times. Finally, we found that environmental DNA metabarcoding data showed broad congruence with both the non-molecular biodiversity and the COI datasets, but failed to capture complete incidence of all NSS. Overall, we demonstrated how a combined methodological approach can effectively detect spatial and temporal variation in genetic composition and range size, which is key for managing biodiversity changes of both threatened and NSS.

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Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 31 publications

References 74 publications

How does eDNA decay affect metabarcoding experiments?

How does eDNA decay affect metabarcoding experiments?

Managing human-mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species

Managing human mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species

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