The true picture of environmental DNA, a case study in harvested fishponds

Blabolil, Petr; Griffiths, Nathan P.; Hänfling, Bernd; Jůza, Tomáš; Draštík, Vladislav; Knežević-Jarić, Jelena; Santos, Romulo dos; Mrkvička, Tomáš; Peterka, Jiří

doi:10.1016/j.ecolind.2022.109241

Cited by 2 publications

(4 citation statements)

References 65 publications

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Section: Optimising Single-site Replicationsupporting

confidence: 59%

“…It should be noted that while increasing PCR replication improves the probability of detection, as observed in our case-study, in metabarcoding studies detectability is also influenced by sample read depth (Shirazi et al ., 2021). Many eDNA metabarcoding studies pool PCR replicates as one multiplex (Blabolil et al ., 2022; Griffiths et al ., 2020; Hänfling et al ., 2016). However, relative sample read depth should be considered when pooling many PCR replicates, as significant reductions in read depth may hamper the increased detectability gained from adding additional replicates.…”

Section: Discussionmentioning

confidence: 99%

“…However, relative sample read depth should be considered when pooling many PCR replicates, as significant reductions in read depth may hamper the increased detectability gained from adding additional replicates. In our study, three PCR replicates were pooled and ran for each sample, as is standard with this 12S workflow (Blabolil et al ., 2022; Di Muri et al ., 2020; Griffiths et al ., 2020; Hänfling et al ., 2016). While this means that individually sequenced PCR replicates had comparatively increased read depth, this is not a concern, since the primary application of these were to confirm the conditional probabilities of presence in sample replicates (p s ) and detection in PCR replicates (p r ).…”

Section: Discussionmentioning

confidence: 99%

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Proving a negative; estimating species ‘Confidence in Absence for Decision-Making’ (CIADM) using environmental DNA monitoring

Griffiths,

Hänfling,

Cattaneo

et al. 2024

Preprint

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Policy-driven decision-making is an important aspect of environmental management globally, often focused on protecting priority species. However, declining trends in freshwater biodiversity have resulted in a lack of up-to-date knowledge regarding the distribution of rare and elusive species. Furthermore, when dealing with priority species, it is sometimes more important to provide a confident assessment of absence, than merely confirm their presence. Without such confident assessments, resource intensive management plans may be misplaced, and not adequately targeted to conserve important remaining populations. Here, we present a framework to estimate confidence in absence, referred to as ′Confidence in Absence for Decision-Making ′ (CIADM), based on single-visit environmental DNA metabarcoding data obtained from water samples. It uses a case study of European eel presence / absence upstream of 44 water pumping stations, given their critically endangered status and the legislative drivers for remediation (EC Eel Regulation 1100/2007, Eels (England and Wales) Regulation 2009). Through a high degree of biological (sample) and technical (PCR) replication, we retrospectively assigned ′confidence in absence′ values and proposed various strategies to achieve the required confidence levels in future surveys. Our findings indicate that 17 out of 44 pumping stations tested positive for eel, and we were able to assign a >99% confidence level that the remaining 27 sites were negative for eel DNA at the time of sampling. Increasing both biological and technical replication increased ′confidence in absence′ values. For example, using three PCR replicates per sample, required four replicate biological samples to achieve >95% and six to achieve >99% confidence in eel absence given non-detection. However, we estimate that by using seven PCR replicates per sample a >99% confidence in eel absence following non-detection could be achieved with only three replicate biological samples. Furthermore, we found that eel positive sites had significantly higher species richness, and fish communities differed between eel positive and eel negative sites. This study highlights the importance of optimising workflow specific replication, and provides an adaptable framework to produce confidence estimations of priority species absence given non-detection.

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Section: Optimising Single-site Replicationsupporting

confidence: 59%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Proving a negative; estimating species ‘Confidence in Absence for Decision-Making’ (CIADM) using environmental DNA monitoring

Griffiths,

Hänfling,

Cattaneo

et al. 2024

Preprint

Self Cite

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“…Studies have found that eDNA metabarcoding can reflect long-term (Hänfling et al, 2016) and contemporary (Di Muri et al, 2020) fish catch data in lentic systems. Further, in lentic systems, eDNA signal has been found to be more homogenous in autumn/winter compared to the summer, and as a result detection probability is increased (Blabolil et al, 2022;Handley et al, 2019). Numerous studies have also found eDNA metabarcoding to yield high sensitivity in lotic systems (Griffiths et al, 2020;Hallam et al, 2021;McColl-Gausden et al, 2021;McDevitt et al, 2019;Muha et al, 2021;Pont et al, 2018), but detectability in rivers can be more unpredictable.…”

Section: Introductionmentioning

confidence: 99%

Seasonal changes in fish eDNA signal vary between contrasting river types

Griffiths,

Bolland,

Wright

et al. 2024

Preprint

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Due to the societal reliance on goods and services provided by river systems, and their close proximity to settlements, few modern-day rivers are without significant anthropogenic modifications. The natural river hydrology is often altered as a consequence of pumping water for flood alleviation, retaining water for irrigation and modifying channels for navigation. In recent years, water pumping stations have been found to have several adverse impacts, including fish mortality (direct and indirect) and habitat fragmentation. More broadly, modern-day river systems face a myriad of anthropogenic flow and channel modifications, with varying impacts on different fish life stages. To manage such risks in line with policy, knowledge of the overall fish community and priority species present is required. It is therefore important to understand the robustness of developing survey strategies across differently managed river systems. This study investigates the seasonal patterns of environmental DNA (eDNA) metabarcoding detections from water samples, taken across three differently managed river types over a one-year period. We observed some significant seasonal variation in detection rates and fish communities; however, this variation was not consistent among river types. Despite this, we found comparatively poor fish communities upstream of pumping stations all year-round, with pumped catchments containing significantly fewer species than the adjacent main river channel and our regional control site. Finally, we highlight that seasonal variation in detectability for the overall fish community may not always reflect that of priority species. In our case, we found favourable European eel (Anguilla anguilla) detection in the summer months across all river types. It is therefore recommended that rather than focusing on overall detectability, policy driven targeted surveys should be designed with priority species ecology in mind.

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The true picture of environmental DNA, a case study in harvested fishponds

Cited by 2 publications

References 65 publications

Proving a negative; estimating species ‘Confidence in Absence for Decision-Making’ (CIADM) using environmental DNA monitoring

Proving a negative; estimating species ‘Confidence in Absence for Decision-Making’ (CIADM) using environmental DNA monitoring

Seasonal changes in fish eDNA signal vary between contrasting river types

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