Successful molecular detection studies require clear communication among diverse research partners

Mosher, Brittany A.; Bernard, Riley F.; Lorch, Jeffrey M.; Miller, David A. W.; Richgels, Katherine L. D.; White, C. Le Ann; Grant, Evan H. Campbell

doi:10.1002/fee.2141

Cited by 19 publications

(21 citation statements)

References 51 publications

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“…In addition, the lack of clear communication of novel genetic methods and results (including transparency and reproducibility) to relevant stakeholders can be prohibitive in translating these findings to appropriate management and eradication action on the ground (Mosher et al , Ward et al ). These communication challenges have been well documented in relation to the marine sector (e.g.…”

Section: Resultsmentioning

confidence: 99%

Genetic tools in the management of invasive mammals: recent trends and future perspectives

2020

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Invasive non‐native species are now considered to be one of the greatest threats to biodiversity worldwide. Therefore, efficient and cost‐effective management of species invasions requires robust knowledge of their demography, ecology and impacts, and genetic‐based techniques are becoming more widely adopted in acquiring such knowledge. We focus on the use of genetic tools in the applied management of mammalian invasions globally, as well as on their inherent advantages and disadvantages. We cover tools that are used in: 1) detecting and monitoring mammalian invaders; 2) identifying origins and invasive pathways; 3) assessing and quantifying the negative impacts of invaders; and 4) population management and potential eradication of invasive mammals. We highlight changes in sequencing technologies, including how the use of techniques such as Sanger sequencing and microsatellite genotyping, for monitoring and tracing invasive pathways respectively, are now giving way to the use of high‐throughput sequencing methods. These include the emergence of environmental DNA (eDNA) metabarcoding for the early detection of invasive mammals, and single nucleotide polymorphisms or whole genomes to trace the sources of invasive populations. We are now moving towards trials of genome‐editing techniques and gene drives to control or eradicate invasive rodents. Genetic tools can provide vital information that may not be accessible with non‐genetic methods, for the implementation of conservation policies (e.g. early detection using systematic eDNA surveillance, the identification of novel pathogens). However, the lack of clear communication of novel genetic methods and results (including transparency and reproducibility) to relevant stakeholders can be prohibitive in translating these findings to appropriate management actions. Geneticists should engage early with stakeholders to co‐design experiments in relation to management goals for invasive mammals.

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Section: Resultsmentioning

confidence: 99%

Genetic tools in the management of invasive mammals: recent trends and future perspectives

2020

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“…As with any study, defining the question to be addressed is the first step and the design of the eDNA assay depends upon the scope of the study 26 . For instance, if the goal of the research or survey is to detect one or a few species, a targeted probe-based assay is best.…”

Section: Discussionmentioning

confidence: 99%

“…For instance, the design of multiple assays for testing may be limited by sequence availability, and compromise may be necessary on aspects of assay performance. These choices must be guided by the goals of the study and must be reported with the results 26 .…”

Section: Discussionmentioning

confidence: 99%

Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications

Klymus

Ramos

Thompson

et al. 2020

JoVE

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New, non-invasive methods for detecting and monitoring species presence are being developed to aid in fisheries and wildlife conservation management. The use of environmental DNA (eDNA) samples for detecting macrobiota is one such group of methods that is rapidly becoming popular and being implemented in national management programs. Here we focus on the development of species-specific targeted assays for probe-based quantitative PCR (qPCR) applications. Using probebased qPCR offers greater specificity than is possible with primers alone. Furthermore, the ability to quantify the amount of DNA in a sample can be useful in our understanding of the ecology of eDNA and the interpretation of eDNA detection patterns in the field. Careful consideration is needed in the development and testing of these assays to ensure the sensitivity and specificity of detecting the target species from an environmental sample. In this protocol we will delineate the steps needed to design and test probe-based assays for the detection of a target species; including creation of sequence databases, assay design, assay selection and optimization, testing assay performance, and field validation. Following these steps will help achieve an efficient, sensitive, and specific assay that can be used with confidence. We demonstrate this process with our assay designed for populations of the mucket (Actinonaias ligamentina), a freshwater mussel species found in the Clinch River, USA.

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“…The advantages of using (e)DNA metabarcoding in NIS surveillance can be obvious for researchers dealing with it, but may seem much more complex and difficult for environmental managers and stakeholders who are new or untrained in DNA-based methods. Thus, it is particularly important to keep the interest and trust of end-users (Darling 2019, Mosher et al 2020, Sepulveda et al 2020. For that, it is vital for end-users to be able to: recognize both the power and the limitations of existing tools; to know how (e)DNA metabarcoding works and what are the limitations of the technique and, finally, what can the technique offer to environmental managers beyond what current methodologies already do (Darling 2019).…”

Section: Final Considerationsmentioning

confidence: 99%

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

Duarte

Vieira

Lavrador

et al. 2020

Preprint

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17In coastal ecosystems, non-indigenous species (NIS) are recognized as a major threat to 18 biodiversity, ecosystem functioning and socio-economic activities. Here we present a systematic 19 review on the use of metabarcoding for NIS surveillance in marine and coastal ecosystems, 20 through the analysis of 42 publications. Metabarcoding has been mainly applied to environmental 21 DNA (eDNA) from water samples, but also to DNA extracted from bulk organismal samples. 22 2 seeking the best approach for detecting the broadest range of species, while minimizing the 38 chances of false positives and false negatives detection. 39 40 Keywords: Marine and coastal ecosystems; non-indigenous species; biosurveillance; (e)DNA 41 metabarcoding 42 43

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Successful molecular detection studies require clear communication among diverse research partners

Cited by 19 publications

References 51 publications

Genetic tools in the management of invasive mammals: recent trends and future perspectives

Genetic tools in the management of invasive mammals: recent trends and future perspectives

Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications

Status and prospects of marine NIS detection and monitoring through (e)DNA metabarcoding

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