Environmental DNA‐based methods detect the invasion front of an advancing signal crayfish population

Greenhalgh, Jack; Collins, Rupert A.; Edgley, Duncan E.; Genner, Martin J.; Hindle, Jan; Jones, Gareth; Loughlin, Lesley; O’donnel, Maire; Sweet, Michael; Battarbee, Richard W.

doi:10.1002/edn3.280

Cited by 6 publications

(4 citation statements)

References 74 publications

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“…Our results indicate that eDNA-based surveys can be effective tools for detecting and mapping invasive and endangered crayfish species, supporting other studies with similar results (Baudry et al, 2021;Cowart et al, 2018;Greenhalgh et al, 2022;Harper et al, 2018;Robinson et al, 2018;Tréguier et al, 2014;Troth et al, 2020Troth et al, , 2021.…”

Section: Discussionsupporting

confidence: 90%

“…Our results indicate that eDNA‐based surveys can be effective tools for detecting and mapping invasive and endangered crayfish species, supporting other studies with similar results (Baudry et al., 2021; Cowart et al., 2018; Greenhalgh et al., 2022; Harper et al., 2018; Robinson et al., 2018; Tréguier et al., 2014; Troth et al., 2020, 2021). In this case, combining manual searches and eDNA‐based information using an occupancy model enabled us to confidently determine the presence of P .…”

Section: Discussionsupporting

confidence: 89%

“…Advances in molecular techniques have enabled the detection of crayfish species using environmental DNA (eDNA) from water samples (Dunn et al., 2017; Ficetola et al., 2008; Greenhalgh et al., 2022; Harper et al., 2018; Robinson et al., 2018; Tréguier et al., 2014; Troth et al., 2020, 2021). With careful design of sampling and stringent analysis of data, eDNA‐based surveys can map the distributions of invasive crayfish and provide a valuable framework for evidence‐based conservation efforts (Burian et al., 2021; Cowart et al., 2018).…”

Section: Introductionmentioning

confidence: 99%

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Environmental DNA can inform the trade‐off between proactive and reactive strategies for crayfish conservation

Greenhalgh,

Banks,

Collins

et al. 2024

Environmental DNA

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The introduction of the signal crayfish Pacifastacus leniusculus to British rivers has led to ecological degradation and the decline of the native white‐clawed crayfish Austropotamobius pallipes. To manage and mitigate the impact of the signal crayfish, conservation agencies and government bodies employ multiple conservation strategies. These take the form of proactive native crayfish breeding and stocking programs and reactive invasive crayfish control programs. Here, we used eDNA to assess the populations of native and invasive crayfish species across 50 sites in 10 river catchments in Norfolk, United Kingdom (UK). The sites were chosen to enable assessment of the potential of eDNA to inform proactive and reactive crayfish conservation strategies. Three of the catchments sampled were selected to assess the success of recent A. pallipes reintroduction, whereas the remaining seven were selected to better understand the distribution of each species at the landscape scale. Combining results of eDNA‐based methods with net searches within an occupancy model enabled us to confidently determine the presence of P. leniusculus at eight sites, and A. pallipes at three sites, which was more than visual searches alone (five and two study sites, respectively). Neither eDNA nor net searches detected A. pallipes at sites where A. pallipes had been reintroduced. We recommend that practitioners using eDNA‐based surveys for management and conservation of crayfish should consider: (1) designing eDNA surveys with an emphasis on large spatial scales to comprehensively describe the distributions of native and invasive crayfish in a region of interest; (2) work with local conservation organizations and/or government bodies to inform the selection of study sites to generate results that are meaningful to real‐world conservation actions; and (3) use results from eDNA‐based crayfish surveys to target limited conservation resources to appropriate proactive and/or reactive conservation actions.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionsupporting

confidence: 89%

Section: Introductionmentioning

confidence: 99%

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Environmental DNA can inform the trade‐off between proactive and reactive strategies for crayfish conservation

Greenhalgh,

Banks,

Collins

et al. 2024

Environmental DNA

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“…The use of eDNA as a method for the cost-effective and non-intrusive monitoring and management of invasive species and species at risk has seen increasing attention and standardization in recent years (Abbott et al 2021; Fediajevaite et al 2021). The concomitant detection of invasive/native species can help to delineate the invasion front of an invasive species (Keller et al 2022) and capture shifting dynamics of the river ecosystem (Greenhalgh et al 2022), for example the increasing detection in time and space of dreissenid mussels to the detriment of local native species (Ricciardi, Whoriskey, and Rasmussen 1996).…”

Section: Discussionmentioning

confidence: 99%

How to barcode (almost all) freshwater biodiversity

Tournayre,

Tian,

Lougheed

et al. 2023

Preprint

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Freshwater ecosystems are complex, diverse and face a variety of imminent threats that have led to changes in both ecosystem structure and function. It is urgent that we develop and standardize monitoring tools allowing for rapid and comprehensive assessment of freshwater communities to understand their changing dynamics and to inform conservation. Environmental DNA surveys offer a means to inventory and monitor aquatic diversity, yet most studies focus on one or a few taxonomic groups only. In this study, we sought to 1) identify thoroughly validated, cost-efficient primer pair combinations that maximize detection of broad swaths of freshwater diversity, and 2) facilitate future primer pair selection by creating a free online and user-friendly tool. We first evaluated the completeness of public reference sequence databases and the efficiency of 14 primer pairs using anin silicoapproach, and then performed eDNA surveys using five mock communities (mix of DNA from tissues), water samples from aquarium samples with known taxonomic composition, and finally water samples from freshwater systems in Eastern Canada. We highlight the power of eDNA-based metabarcoding for reconstructing freshwater communities, including prey, parasite, pathogen, invasive, and declining species. Our work reveals the importance of the marker choice on species resolution, as well as the importance of degenerate primers, the length of the target fragment and the filtering parameters on detection success in water eDNA samples. Our new online tool SNIPe revealed that 13 to 14 primer pairs are necessary to recover 100% of the species in water samples (aquarium and natural systems), but four primer pairs are sufficient to recover almost 75% of taxa with little overlap. These results highlight the usefulness of eDNA for freshwater monitoring and should prompt more studies on tools to survey all-inclusive communities.

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Enhancing metabarcoding of freshwater biotic communities: A new online tool for primer selection and exploring data from 14 primer pairs

Tournayre,

Tian,

Lougheed

et al. 2024

Environmental DNA

View full text Add to dashboard Cite

Freshwater ecosystems are complex, diverse, and face multiple imminent threats that have led to changes in both structure and function. It is urgent that we develop and standardize monitoring tools that allow for rapid and comprehensive assessment of freshwater communities to understand their changing dynamics and inform conservation. Environmental DNA surveys offer a means to inventory and monitor aquatic diversity, yet most studies focus on one or a few taxonomic groups because of technical challenges. In this study, we (1) create an eDNA metabarcoding dataset (natural water bodies) with 14 validated primer pairs; (2) create a free online, user‐friendly tool for primer selection that can be used for any metabarcoding data (SNIPe); and (3) using SNIPe, explore our dataset to derive subsets of informative, cost‐effective primer pairs that maximize detection of freshwater diversity. We first evaluated the completeness of public reference sequence databases and the efficiency of 14 primer pairs in silico, in vitro on five mock communities (mix of DNA from tissues of select taxa), in vivo on water samples from aquarium samples with known taxonomic composition, and finally in vivo on water samples from freshwater systems in Eastern Canada. Results from analyses using SNIPe revealed that 13 or 14 primer pairs are necessary to recover 100% of the species in water samples (natural systems), but that four primer pairs are sufficient to recover almost 75% of taxa with little overlap. Our work highlights the power of eDNA metabarcoding for reconstructing freshwater communities, including prey, parasite, pathogen, invasive, and declining species. It also emphasizes the importance of marker choice on species resolution, and primer characteristics and filtering parameters on detection success and accuracy of biodiversity estimates. Together, these results highlight the usefulness of eDNA for freshwater monitoring and should prompt more studies of tools to survey all communities.

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Environmental DNA‐based methods detect the invasion front of an advancing signal crayfish population

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 6 publications

References 74 publications

Environmental DNA can inform the trade‐off between proactive and reactive strategies for crayfish conservation

Environmental DNA can inform the trade‐off between proactive and reactive strategies for crayfish conservation

How to barcode (almost all) freshwater biodiversity

Enhancing metabarcoding of freshwater biotic communities: A new online tool for primer selection and exploring data from 14 primer pairs

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