A new tool in the toolbox for large-scale, high-throughput fisheries mark-recapture studies using genetic identification (original) (raw)
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DNA-analysis to monitor fisheries and aquaculture: Too costly?
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Evidence from DNA-analysis is commonplace in human criminal investigations, and while it is increasingly being used in wildlife crime, to date, its application to control and enforcement activities in fisheries and aquaculture has only been sporadic. Contemporary DNA-analysis tools are capable of addressing a broad range of compliance issues, species identification, mislabelling of fish products, determining the origin of catches and the farm of origin of aquaculture escapees. Such applications have the potential to ensure traceability along the fish product supply chain and to combat consumer fraud and Illegal, Unreported and Unregulated fishing. Nevertheless, DNAanalysis is not yet used routinely in investigations into compliance with fisheries and aquaculture legislation. One potential reason for this is that DNA-analysis techniques may have been regarded as too expensive. However, costs have plummeted over the past decade prompting us to objectively assess whether the costs associated with routine use of DNA-analysis techniques for fisheries and aquaculture control and enforcement activities do constitute an impediment. Based on a number of recent fisheries and aquaculture compliance investigations that incorporated DNA-analysis, our results indicate that the use of genetic analysis was justified and worthwhile in all cases examined. We therefore conclude that the costs associated with DNA-analysis do not represent a barrier to the routine adoption of DNA-analysis techniques in fisheries and aquaculture compliance investigations. Thus, control and enforcement agencies should be encouraged to use such techniques routinely.
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Nature …, 2012
Illegal, unreported and unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch certificates and eco-labels are urgently needed. Here we show that, by using geneassociated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93-100% of individuals could be correctly assigned to origin in policy-driven case studies. We show how case-targeted single nucleotide polymorphism assays can be created and forensically validated, using a centrally maintained and publicly available database. our results demonstrate how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide.
Foods
The decline in wild-caught fisheries paired with increasing global seafood demand is pushing the need for seafood sustainability to the forefront of national and regional priorities. Validation of species identity is a crucial early step, yet conventional monitoring and surveillance tools are limited in their effectiveness because they are extremely time-consuming and require expertise in fish identification. DNA barcoding methods are a versatile tool for the genetic monitoring of wildlife products; however, they are also limited by requiring individual tissue samples from target specimens which may not always be possible given the speed and scale of seafood operations. To circumvent the need to individually sample organisms, we pilot an approach that uses forensic environmental DNA (eDNA) metabarcoding to profile fish species composition from the meltwater in fish holds on industrial and artisanal fishing vessels in Ecuador. Fish identified genetically as present were compared to t...
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Fisheries enforcement relies on visual catch identification and quantification at sea or when landed. Silage (fish dissolved in acid) and fish blocks (block frozen fish) are promising methods for on-board processing and storage of low-value catches. We examined the use of non-destructive sampling and two DNA-based methods, quantitative PCR (qPCR) and metabarcoding, to assess species composition and relative abundance in industrial grade experimental silage and fish blocks. We demonstrate the ability to identify and quantify DNA from fish species in both products. qPCR analysis of small silage samples collected over 21 days detected all target control species. DNA from one species (Atlantic wolffish) was consistently overrepresented while, for three species of gadoids (Atlantic cod, haddock and whiting), the DNA content matched input tissue proportions with high accuracy. qPCR and metabarcoding of fish blocks, sampled as run-off water and exterior swabs, provided consistent species d...
Environmental DNA as an effective tool for detection of imperiled fishes
Environmental Biology of Fishes, 2015
Detection of aquatic species is imperfect, especially if the species is rare and exhibits spatial and temporal variability. Many fish species require a number of sampling trips before detection is positive. And yet, information on species persistence is critical for effective conservation efforts. New forensic genetic techniques, such as environmental DNA (eDNA), have been developed and successfully used to validate the presence of exotic aquatic species in new areas. We compared detection of a federally listed, threatened, migratory fish species the Slackwater darter (Etheostoma boschungi); using eDNA to concomitantly collected field collections. Detection probabilities for this species are variable, but consistently low in recent collections. Our results indicated that detection using eDNA was vastly more effective than traditional sampling at confirming the presence of the Slackwater darter. Positive detection at non-breeding sites was half of the detection rate at breeding sites, most likely to the greater area available in non-breeding streams. These data suggest that eDNA is an effective tool for quickly evaluating a relatively large number of sites for the presence of rare aquatic species.
Applications of DNA barcoding to fish landings: authentication and diversity assessmente
ZooKeys, 2013
DNA barcoding methodologies are being increasingly applied not only for scientific purposes but also for diverse real-life uses. Fisheries assessment is a potential niche for DNA barcoding, which serves for species authentication and may also be used for estimating within-population genetic diversity of exploited fish. Analysis of single-sequence barcodes has been proposed as a shortcut for measuring diversity in addition to the original purpose of species identification. Here we explore the relative utility of different mitochondrial sequences (12S rDNA, COI, cyt b, and D-Loop) for application as barcodes in fisheries sciences, using as case studies two marine and two freshwater catches of contrasting diversity levels. Ambiguous catch identification from COI and cyt b was observed. In some cases this could be attributed to duplicated names in databases, but in others it could be due to mitochondrial introgression between closely related species that may obscure species assignation from mtDNA. This last problem could be solved using a combination of mitochondrial and nuclear genes. We suggest to simultaneously analyze one conserved and one more polymorphic gene to identify species and assess diversity in fish catches.
Molecular Ecology Resources, 2019
Although environmental DNA shed from an organism is now widely used for species detection in a wide variety of contexts, mobilizing environmental DNA for management requires estimation of population size and trends in addition to assessing presence or absence. However, the efficacy of environmental-DNA-based indices of abundance for long-term population monitoring have not yet been assessed. Here we report on the relationship between six years of mark-recapture population estimates for eulachon (Thaleichthys pacificus) and 'eDNA rates,' which are calculated from the product of stream flow and DNA concentration. Eulachon are a culturally and biologically important anadromous fish that have significantly declined in the southern part of their range but were historically rendered into oil and traded. Both the peak eDNA rate and the area under the curve of the daily eDNA rate were highly predictive of the mark-recapture population estimate, explaining 84.96% and 92.53% of the deviance respectively. Even in the absence of flow correction, the peak of the daily eDNA concentration explained an astonishing 89.53% while the area under the curve explained 90.74% of the deviance. These results support the use of eDNA to monitor eulachon population trends and represent a >80% cost savings over mark-recapture, which could be further increased with automated water sampling, reduced replication, and focused temporal sampling. Due to its logistical ease and affordability, eDNA sampling can facilitate monitoring a larger number of rivers and in remote locations where mark-recapture is infeasible.