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Simpson TJS, Wellington CM, Lukehurst SS, Huerlimann R, Veilleux H, Snow M, Dias J, McDonald JI. Development of a real-time PCR (qPCR) method for the identification of the invasive paddle crab Charybdis japonica ( Crustacea, Portunidae). PeerJ 2023; 11:e15522. [PMID: 37334135 PMCID: PMC10269569 DOI: 10.7717/peerj.15522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/17/2023] [Indexed: 06/20/2023] Open
Abstract
Crabs can be transported beyond their native range via anthropogenic-mediated means such as aquarium trade, live seafood trade and shipping. Once introduced into new locations, they can establish persisting populations and become invasive, often leading to negative impacts on the recipient environment and native species. Molecular techniques are increasingly being used as complementary tools in biosecurity surveillance and monitoring plans for invasive species. Molecular tools can be particularly useful for early detection, rapid identification and discrimination of closely related species, including when diagnostic morphological characters are absent or challenging, such as early life stages, or when only part of the animal is available. In this study, we developed a species-specific qPCR assay, which targets the cytochrome c oxidase subunit 1 (CO1) region of the Asian paddle crab Charybdis japonica. In Australia, as well as many parts of the world, this species is considered invasive and routine biosecurity surveillance is conducted to reduce the risk of establishment. Through rigorous testing of tissue from target and non-target species we demonstrate that this assay is sensitive enough to detect as little as two copies per reaction and does not cross amplify with other closely related species. Field samples and environmental samples spiked with C. japonica DNA in high and low concentrations indicate that this assay is also a promising tool for detecting trace amounts of C. japonica eDNA in complex substrates, making it a useful complementary tool in marine biosecurity assessments.
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Affiliation(s)
- Tiffany JS Simpson
- Conservation and Fisheries Directorate, Ascension Island Government, Georgetown, Ascension Island, South Atlantic, United Kingdom
- Trace and Environmental DNA (TrEnD) Laboratory, Curtin University of Technology, Perth, Western Australia, Australia
| | - Claire M. Wellington
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development (DPIRD), Perth, Western Australia, Australia
| | - Sherralee S. Lukehurst
- Trace and Environmental DNA (TrEnD) Laboratory, Curtin University of Technology, Perth, Western Australia, Australia
- School of Biological Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Roger Huerlimann
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Heather Veilleux
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
- Ecometrix Incorporated, Mississauga, Ontario, Canada
| | - Michael Snow
- Genotyping Australia, Perth, Western Australia, Australia
| | - Joana Dias
- School of Biological, Environmental and Earth Sciences, University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
| | - Justin I. McDonald
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development (DPIRD), Perth, Western Australia, Australia
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Picard MH, Zaiko A, Tidy AM, Kelly DJ, Thomson-Laing G, Wilkinson SP, Pochon X, Vandergoes MJ, Hawes I, Wood SA. Optimal sample type and number vary in small shallow lakes when targeting non-native fish environmental DNA. PeerJ 2023; 11:e15210. [PMID: 37151294 PMCID: PMC10162041 DOI: 10.7717/peerj.15210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 03/20/2023] [Indexed: 05/09/2023] Open
Abstract
Non-native fish have been shown to have deleterious impacts on freshwater ecosystems in New Zealand. Early detection is critical for their effective management. Traditional capture-based techniques may not detect newly introduced fish, especially if they are present in low abundance. Molecular techniques that target environmental DNA (eDNA) have been shown, in many instances, to be more sensitive, cost-effective and require lower sampling effort. However, appropriate sampling strategies are needed to ensure robust and interpretable data are obtained. In this study we used droplet digital PCR assays to investigate the presence of two non-native fish in New Zealand, the European perch (Perca fluviatilis) and rudd (Scardinius erythrophthalmus) in three small lakes. Samples were collected from water and surface sediment at near-shore and mid-lake sites. Probabilistic modelling was used to assess the occupancy of fish eDNA and develop guidance on sampling strategies. Based on the detection probability measures from the present study, at least six sites and five replicates per site are needed to reliably detect fish eDNA in sediment samples, and twelve sites with eight replicates per site for water samples. The results highlight the potential of developing monitoring and surveillance programs adapted to lakes, that include the use of assays targeting eDNA. This study focused on small shallow lakes, and it is likely that these recommendations may vary in larger, deeper, and more geomorphologically complex lakes, and this requires further research.
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Affiliation(s)
- Maïlys H.V. Picard
- School of Biological Sciences, Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
| | - Anastasija Zaiko
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Warkworth, New Zealand
| | | | - David J. Kelly
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
| | | | | | - Xavier Pochon
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Warkworth, New Zealand
| | | | - Ian Hawes
- School of Biological Sciences, Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
| | - Susanna A. Wood
- Coastal and Freshwater, Cawthron Institute, Nelson, New Zealand
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Rojahn J, Gleeson D, Furlan EM. Monitoring post-release survival of the northern corroboree frog, Pseudophryne pengilleyi, using environmental DNA. WILDLIFE RESEARCH 2018. [DOI: 10.1071/wr17179] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Translocations are becoming an increasingly important conservation tool to combat rising levels of species extinction. Unfortunately, many translocation efforts fail; yet, the timing and cause of failure often remain unknown. Monitoring individuals in the days and weeks following release can provide valuable information on their capacity to survive this initial hurdle. In Australia, breeding programs have been established for the endangered northern corroboree frog, Pseudophryne pengilleyi, to enable reintroduction to the wild via captive-reared individuals, typically, early life stages such as eggs or juvenile frogs that cannot be monitored via traditional survey methods that target adult frogs (e.g. shout–response). Environmental DNA (eDNA) detects trace amounts of DNA that organisms release into their environment and could provide a means to infer population persistence for wildlife releases and translocations.
Aims
In the present study, we aim to develop an eDNA assay capable of detecting both sexes of P. pengilleyi across multiple life stages, and use it to monitor their survival.
Methods
An eDNA assay was developed to target the two corroboree frog species (P. pengilleyi and P. corroboree, the southern corroboree frog) and was tested for its sensitivity and specificity in silico and in vitro. Pseudophryne pengilleyi eggs were released into three naturally occurring ponds and water samples were, subsequently, collected from each pond on several occasions over a period of 78 days. Quantitative polymerase chain reaction was used to detect P. pengilleyi eDNA from water samples.
Key Results
The developed assay was shown to be sensitive and specific to corroboree frogs. eDNA monitoring of reintroduced P. pengilleyi detected the species’ DNA at three of three release ponds and DNA remained detectable until at least 78 days post-release at two of three ponds.
Conclusions
We show how the development of a corroboree frog-specific assay allowed us to monitor the post-release survival of P. pengilleyi in naturally occurring pools.
Implications
eDNA surveys may provide a useful tool to monitor post-release survival of translocated populations in a non-invasive manner, with the potential to identify the timing and causes of failure. Such knowledge can be used to inform the management of translocated populations and future release strategies.
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Bylemans J, Furlan EM, Pearce L, Daly T, Gleeson DM. Improving the containment of a freshwater invader using environmental DNA (eDNA) based monitoring. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1203-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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