A comparison of electrofishing methods and fyke netting to produce reliable abundance and size metrics

Porreca, Anthony P.; Pederson, Charles L.; Laursen, Jeffrey R.; Colombo, Robert E.

doi:10.1080/02705060.2013.810555

Cited by 15 publications

(14 citation statements)

References 8 publications

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“…Detection probability via conventional fishing methods (such as nets, pods, traps or electrofishing techniques) is often low (Radinger et al ., 2019). High mobility, as well as low density and/or the cryptic behaviour of these organisms, can also lead to lower detection probabilities of many key target species (MacKenzie & Royle, 2005; Maxwell & Jennings, 2005; Britton et al ., 2011; Porreca et al ., 2013). This may in turn increase the risk of nondetection error and its associated problems ( i.e ., so called false‐negative detections) (Gu & Swihart, 2004).…”

Section: Introductionmentioning

confidence: 99%

Reliable eDNA detection and quantification of the European weather loach (Misgurnus fossilis)

Brys

Halfmaerten

Neyrinck

et al. 2020

Journal of Fish Biology

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The European weather loach (Misgurnus fossilis) is a cryptic and poorly known fish species of high conservation concern. The species is experiencing dramatic population collapses across its native range to the point of regional extinction. Although environmental DNA (eDNA)‐based approaches offer clear advantages over conventional field methods for monitoring rare and endangered species, accurate detection and quantification remain difficult and quality assessment is often poorly incorporated. In this study, we developed and validated a novel digital droplet PCR (ddPCR) eDNA‐based method for reliable detection and quantification, which allows accurate monitoring of M. fossilis across a number of habitat types. A dilution experiment under laboratory conditions allowed the definition of the limit of detection (LOD) and the limit of quantification (LOQ), which were set at concentrations of 0.07 and 0.14 copies μl–1, respectively. A series of aquarium experiments revealed a significant and positive relationship between the number of individuals and the eDNA concentration measured. During a 3 year survey (2017–2019), we assessed 96 locations for the presence of M. fossilis in Flanders (Belgium). eDNA analyses on these samples highlighted 45% positive detections of the species. On the basis of the eDNA concentration per litre of water, only 12 sites appeared to harbour relatively dense populations. The other 31 sites gave a relatively weak positive signal that was typically situated below the LOQ. Combining sample‐specific estimates of effective DNA quantity (Qe) and conventional field sampling, we concluded that each of these weak positive sites still likely harboured the species and therefore they do not represent false positives. Further, only seven of the classified negative samples warrant additional sampling as our analyses identified a substantial risk of false‐negative detections (i.e., type II errors) at these locations. Finally, we illustrated that ddPCR outcompetes conventional qPCR analyses, especially when target DNA concentrations are critically low, which could be attributed to a reduced sensitivity of ddPCR to inhibition effects, higher sample concentrations being accommodated and higher sensitivity obtained.

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Section: Introductionmentioning

confidence: 99%

Reliable eDNA detection and quantification of the European weather loach (Misgurnus fossilis)

Brys

Halfmaerten

Neyrinck

et al. 2020

Journal of Fish Biology

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“…Aquatic biodiversity estimates obtained from conventional monitoring surveys are known to be influenced by the type of sampling method used (Kennard et al 2006, Porreca et al 2013, Bower et al 2014, the sampling season (Fischer andQuist 2014, Jurajda et al 2009) and the sampling effort (Reid and Haxton 2017, Pritt and Frimpong 2014, Ebner et al 2008. In order to obtain robust biodiversity estimates, a thorough understanding of the potential biases of survey methods is essential (Gotelli andColwell 2001, Schmidt 2005).…”

Section: Introductionmentioning

confidence: 99%

Monitoring riverine fish communities through eDNA metabarcoding: determining optimal sampling strategies along an altitudinal and biodiversity gradient

Bylemans

Gleeson

Lintermans

et al. 2018

MBMG

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Monitoring aquatic biodiversity through DNA extracted from environmental samples (eDNA) combined with high-throughput sequencing, commonly referred to as eDNA metabarcoding, is increasing in popularity within the scientific community. However, sampling strategies, laboratory protocols and analytical pipelines can influence the results of eDNA metabarcoding surveys. While the impact of laboratory protocols and analytical pipelines have been extensively studied, the importance of sampling strategies on eDNA metabarcoding surveys has not received the same attention. To avoid underestimating local biodiversity, adequate sampling strategies (i.e. sampling intensity and spatial sampling replication) need to be implemented. This study evaluated the impact of sampling strategies along an altitudinal and biodiversity gradient in the upper section of the Murrumbidgee River (Murray-Darling Basin, Australia). An eDNA metabarcoding survey was used to determine the local fish biodiversity and evaluate the influence of sampling intensity and spatial sampling replication on the biodiversity estimates. The results show that optimal eDNA sampling strategies varied between sites and indicate that river morphology, species richness and species abundance affect the optimal sampling intensity and spatial sampling replication needed to accurately assess the fish biodiversity. While the generality of the patterns will need to be confirmed through future studies, these findings provide a basis to guide future eDNA metabarcoding surveys in river systems.

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“…electrofishing, fyke netting, bait trapping) suffer from low sensitivity and detection biases (Britton et al 2011b;Lintermans 2015;Maxwell and Jennings 2005;Porreca et al 2013). Consequently, the ability to make well informed management decisions based on species distribution data obtained from these surveys is challenging (Britton et al 2011b;Campbell et al 2009).…”

Section: Introductionmentioning

confidence: 97%

Improving the containment of a freshwater invader using environmental DNA (eDNA) based monitoring

et al. 2016

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On-ground management actions targeting invasive and/or native species are often undertaken based on incomplete and biased distribution data for the species of interest. Once an invasive species becomes established, containment can provide an effective management option to conserve native biodiversity only if it is implemented beyond the outer distribution limits of the species of interest. Determining these outer distribution limits is currently difficult for freshwater fish species because of the low sensitivity and biases associated with conventional monitoring methods. The improved sensitivity of environmental DNA-based surveys makes them particularly useful to determine these outer distribution limits. In this study, we used conventional monitoring methods and eDNA-based monitoring using real-time PCR to determine the spread of the invasive redfin perch (Perca fluviatilis) in an intermittent river system. This voracious predatory fish is responsible for the continued decline of several threatened and vulnerable species within Australia. We found that eDNA detection rates were high in our study system, when redfin perch presence was confirmed by conventional monitoring, compared to previously published works. Additionally we describe how the combination of conventional and eDNAbased monitoring can improve redfin perch distribution data compared to conventional monitoring alone. This improvement has subsequently been used to inform management and determine the optimal location for the construction of an exclusion barrier.

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A comparison of electrofishing methods and fyke netting to produce reliable abundance and size metrics

Cited by 15 publications

References 8 publications

Reliable eDNA detection and quantification of the European weather loach (Misgurnus fossilis)

Reliable eDNA detection and quantification of the European weather loach (Misgurnus fossilis)

Monitoring riverine fish communities through eDNA metabarcoding: determining optimal sampling strategies along an altitudinal and biodiversity gradient

Improving the containment of a freshwater invader using environmental DNA (eDNA) based monitoring

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