Development of an environmental DNA assay for detecting multiple shark species involved in human–shark conflicts in Australia

Rooyen, Anthony van; Miller, Adam D.; Clark, Zach; Sherman, Craig D. H.; Butcher, Paul A.; Rizzari, Justin R.; Weeks, Andrew R.

doi:10.1002/edn3.202

Cited by 6 publications

(2 citation statements)

References 39 publications

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“…Total genomic DNA was extracted from Sterivex ® filters using a DNeasy Blood & Tissue Kit (Qiagen) following the procedure outlined in Rooyen et al (2021). A single polymerase chain reaction (PCR) assay was used to amplify vertebrate DNA (including fish, amphibian and bird DNA) from the extracted eDNA samples.…”

Section: Edna Extraction and Amplificationmentioning

confidence: 99%

Contrasting patterns of biodiversity across wetland habitats using single‐time‐point environmental DNA surveys

Coleman,

Matthews,

Sherman

et al. 2023

Aquatic Conservation

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Wildlife surveys are central to the conservation and restoration management of wetland habitats; however, the often laborious and costly nature of traditional survey methods can constrain the spatial and temporal extent and replication of survey efforts. Environmental DNA (eDNA) technologies now provide the opportunity to reduce some of these limitations, but applications in temporary and permanent freshwater marshes and meadows (herein referred to as ‘wetland habitats’) remain limited. This study investigates the performance of single‐time‐point eDNA surveys for characterizing fish, amphibian and bird assemblages of wetland habitats in south‐eastern Australia. Comparisons were made between coastal and inland wetlands, between wetlands of varying condition and between eDNA and traditional surveys. Findings show that eDNA surveys can provide comprehensive descriptions of faunal assemblages associated with wetland habitats, with resolution similar to that provided by traditional survey approaches. Analyses also revealed significant differences in patterns of biodiversity between wetland types (coastal vs. inland) but not between wetland habitats varying in condition. Overall, this study confirms that eDNA surveys provide a reliable option for undertaking wetland biodiversity assessments aimed at improving biodiversity data coverage for otherwise data deficient wetlands.

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Section: Edna Extraction and Amplificationmentioning

confidence: 99%

Contrasting patterns of biodiversity across wetland habitats using single‐time‐point environmental DNA surveys

Coleman,

Matthews,

Sherman

et al. 2023

Aquatic Conservation

Self Cite

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“…eDNA sampling is therefore particularly relevant for the study of chondrichthyans, as they are often present in low abundances. To date, targeted eDNA assays have been developed for different threatened chondrichthyan species, including sharks (Lafferty et al, 2018; Postaire et al, 2020; Schweiss et al, 2020; Budd et al, 2021; Cooper et al, 2021; van Rooyen et al, 2021; Jenrette et al, 2023) and rays (Simpfendorfer et al, 2016; Gargan et al, 2017; Weltz et al, 2017; Lehman et al, 2020). No eDNA barcoding studies have yet been conducted on the Mediterranean angel sharks, although there is a clear need to better assess their current status using appropriate non‐destructive methods (Ellis et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

An environmental DNA assay for the detection of Critically Endangered angel sharks (Squatina spp.)

Faure,

Manel,

Macé

et al. 2023

Aquatic Conservation

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The three sympatric angel shark species occurring in the Mediterranean – Squatina squatina (the angelshark), Squatina aculeata (the sawback angelshark), and Squatina oculata (the smoothback angelshark) – are all classed as Critically Endangered on the International Union for Conservation of Nature (IUCN) Red List. There is a clear need to better quantify their current status, using appropriate non‐destructive methods, to help inform future conservation measures. This study introduces an environmental DNA (eDNA) assay able to detect and distinguish S. aculeata, S. oculata, and S. squatina in the Mediterranean Sea by combining probe‐based quantitative polymerase chain reaction (qPCR) technology and Sanger sequencing. The assay targets a 173‐bp barcode in the mitochondrial cytochrome c oxidase I (COI) gene. It was tested in silico, in vitro on tissue‐extracted DNA, and on eDNA extracted from filtration samples. This genus‐specific assay was applied to detect the presence of S. squatina in eDNA samples collected in Corsica, France. The target barcode was found in seven of 76 eDNA samples, revealing the presence of S. squatina in north‐western Corsica, where the shark has never been observed, and confirming its existence on the eastern coast. The study also demonstrates that using eDNA sampling, based on 30 L of seawater filtered close to the substrate with a waterproof peristaltic pump, it was possible to detect the eDNA of this rare benthic species. The results of detection can help identify critical areas for angel shark conservation and facilitate the development of local public awareness initiatives. This novel qPCR assay should be used for future applications in the Mediterranean and eastern Atlantic targeting angel sharks to better identify the remaining populations. In this study the qPCR assay was applied for S. squatina eDNA, but application to S. aculeata and S. oculata still needs to be validated in the field.

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The influence of bait position on the catch of target and non-target sharks in a SMART drumline bather protection program

Lipscombe

Scott²,

Morris³

et al. 2023

Fisheries Research

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Development of an environmental DNA assay for detecting multiple shark species involved in human–shark conflicts in Australia

Cited by 6 publications

References 39 publications

Contrasting patterns of biodiversity across wetland habitats using single‐time‐point environmental DNA surveys

Contrasting patterns of biodiversity across wetland habitats using single‐time‐point environmental DNA surveys

An environmental DNA assay for the detection of Critically Endangered angel sharks (Squatina spp.)

The influence of bait position on the catch of target and non-target sharks in a SMART drumline bather protection program

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