Evaluating genetic traceability methods for captive bred marine fish and their applications in fisheries management and wildlife forensics

Growing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in the aquaculture production. Consequently, more captive bred fish are released into the wild through accidental escape or deliberate restocking, stock enhancement and sea ranching programs. The increased mixing of captive bred fish with wild conspecifics may affect the ecological and/or genetic integrity of wild fish populations. From a fisheries management perspective unambiguous identification tools for captive bred fish will be highly valuable to manage risks. Additionally there is great potential to use these tools in wildlife forensics (i.e. tracing back escapees to their origin and determining mislabelling of seafood products). Using SNP data from captive bred and wild populations of Atlantic cod (Gadus morhua L.) and sole (Solea solea L.), we explored the efficiency of population and parentage assignment techniques for the identification and tracing of captive bred fish. Simulated and empirical data were used to correct for stochastic genetic effects. Overall, parentage assignment performed well when a large effective population size characterizes the broodstock and escapees originate from early generations of captive breeding. Consequently, parentage assignments are particularly useful from a fisheries management perspective to monitor the effects of deliberate releases of captive bred fish on wild populations. Population assignment proved to be more efficient after several generations of captive breeding, which makes it a useful method in forensic applications for well-established aquaculture species. We suggest the implementation of a case by case strategy when choosing the best method

Development of a genetic tool for product regulation in the diverse British pig breed market

<p>Abstract</p> <p>Background</p> <p>The application of DNA markers for the identification of biological samples from both human and non-human species is widespread and includes use in food authentication. In the food industry the financial incentive to substituting the true name of a food product with a higher value alternative is driving food fraud. This applies to British pork products where products derived from traditional pig breeds are of premium value. The objective of this study was to develop a genetic assay for regulatory authentication of traditional pig breed-labelled products in the porcine food industry in the United Kingdom.</p> <p>Results</p> <p>The dataset comprised of a comprehensive coverage of breed types present in Britain: 460 individuals from 7 traditional breeds, 5 commercial purebreds, 1 imported European breed and 1 imported Asian breed were genotyped using the PorcineSNP60 beadchip. Following breed-informative SNP selection, assignment power was calculated for increasing SNP panel size. A 96-plex assay created using the most informative SNPs revealed remarkably high genetic differentiation between the British pig breeds, with an average F_ST of 0.54 and Bayesian clustering analysis also indicated that they were distinct homogenous populations. The posterior probability of assignment of any individual of a presumed origin actually originating from that breed given an alternative breed origin was > 99.5% in 174 out of 182 contrasts, at a test value of log(LR) > 0. Validation of the 96-plex assay using independent test samples of known origin was successful; a subsequent survey of market samples revealed a high level of breed label conformity.</p> <p>Conclusion</p> <p>The newly created 96-plex assay using selected markers from the PorcineSNP60 beadchip enables powerful assignment of samples to traditional breed origin and can effectively identify mislabelling, providing a highly effective tool for DNA analysis in food forensics.</p

Wildlife Law Enforcement's Use of “<i>the Money Shot</i>”:Creating a Visual Fallacy and Generating Wider Legal and Forensic Implications

Alarmingly, it appears that wildlife law enforcement organizations in some countries are routinely photographing suspected poachers and traffickers holding or placed alongside unprotected evidence that has been recovered during the apprehension of these individuals. Photographs are commonly taken showing clearly identifiable suspects with recovered wildlife products and other associated items that would be regarded as evidence. These images are subsequently being posted on social media platforms prior to the suspects appearing in court or being formally convicted of any offense. Not only does this practice have implications from a human rights perspective, but it also poses a risk to the validity and robustness of any subsequent forensic analysis. More broadly, these procedural practices could also inhibit future capacity and capability investments by international donors due to perceived human rights issues, poor evidence management procedures, and the inherent risks of miscarriages of justice occurring due to visual/pictorial fallacy and/or cognitive contextual priming. In this paper, we highlight the prevalence of these images through results of online research, discuss the risks of the “money shot,” and call on the wildlife law enforcement community to stop this practice

Genomic data reveals strong differentiation and reduced genetic diversity in island golden eagle populations

Understanding population structure and the extent and distribution of genetic diversity are recognised as central issues in endangered species research, with broad implications for effective conservation management. Advances in whole genome sequencing (WGS) techniques provide greater resolution of genome-wide genetic diversity and inbreeding. Subspecies of golden eagles (Aquila chrysaetos) in Scotland (A. c. chrysaetos) and Japan (A. c. japonica) are endangered; it is therefore important to understand genetic diversity and inbreeding of these small island populations to increase the chances of conservation success. We investigated this using WGS data from golden eagles in Scotland, continental Europe, Japan, and the USA. Following determination of population genetic structure, analysis of heterozygosity and nucleotide diversity revealed reduced levels of genetic diversity together with runs of homozygosity (ROH), suggesting evidence of inbreeding due to recent shared parental ancestry in the island populations. These results highlight the need to consider genetic reinforcement of small isolated golden eagle populations from neighbouring outbred populations, alongside existing efforts to boost population size through within-island conservation translocations and captive breeding programmes

Nanopore sequencing in non-human forensic genetics

The past decade has seen a rapid expansion of non-human forensic genetics coinciding with the development of 2nd and 3rd generation DNA sequencing technologies. Nanopore sequencing is one such technology that offers massively parallel sequencing at a fraction of the capital cost of other sequencing platforms. The application of nanopore sequencing to species identification has already been widely demonstrated in biomonitoring studies and has significant potential for non-human forensic casework, particularly in the area of wildlife forensics. This review examines nanopore sequencing technology and assesses its potential applications, advantages and drawbacks for use in non-human forensics, alongside other next-generation sequencing platforms and as a possible replacement to Sanger sequencing. We assess the specific challenges of sequence error rate and the standardisation of consensus sequence production, before discussing recent progress in the validation of nanopore sequencing for use in forensic casework. We conclude that nanopore sequencing may be able to play a considerable role in the future of non-human forensic genetics, especially for applications to wildlife law enforcement within emerging forensic laboratories

SNP discovery using next generation transcriptomic sequencing in Atlantic herring (Clupea harengus)

The introduction of Next Generation Sequencing (NGS) has revolutionised population genetics, providing studies of non-model species with unprecedented genomic coverage, allowing evolutionary biologists to address questions previously far beyond the reach of available resources. Furthermore, the simple mutation model of Single Nucleotide Polymorphisms (SNPs) permits cost-effective high-throughput genotyping in thousands of individuals simultaneously. Genomic resources are scarce for the Atlantic herring (Clupea harengus), a small pelagic species that sustains high revenue fisheries. This paper details the development of 578 SNPs using a combined NGS and high-throughput genotyping approach. Eight individuals covering the species distribution in the eastern Atlantic were bar-coded and multiplexed into a single cDNA library and sequenced using the 454 GS FLX platform. SNP discovery was performed by de novo sequence clustering and contig assembly, followed by the mapping of reads against consensus contig sequences. Selection of candidate SNPs for genotyping was conducted using an in silico approach. SNP validation and genotyping were performed simultaneously using an Illumina 1,536 GoldenGate assay. Although the conversion rate of candidate SNPs in the genotyping assay cannot be predicted in advance, this approach has the potential to maximise cost and time efficiencies by avoiding expensive and time-consuming laboratory stages of SNP validation. Additionally, the in silico approach leads to lower ascertainment bias in the resulting SNP panel as marker selection is based only on the ability to design primers and the predicted presence of intron-exon boundaries. Consequently SNPs with a wider spectrum of minor allele frequencies (MAFs) will be genotyped in the final panel. The genomic resources presented here represent a valuable multi-purpose resource for developing informative marker panels for population discrimination, microarray development and for population genomic studies in the wild

Evaluation of Impact of Population Management on Genetic Parameters of Selected Spiral-horned Antelopes

The rapid loss of biodiversity and the associated reduction and fragmentation of habitats means that ex situ populations have become an important part of species conservation. These populations, which are often established from a small number of founders, require careful management to avoid the negative effects of genetic drift and inbreeding. Although the inclusion of molecular data is recommended, their availability for captive breeding management remains limited. The aim of this study was to evaluate the relationship between the levels of genetic diversity in six spiral-horned antelope taxa bred under human care and their respective management strategies, conservation status, demography, and geographic origin, using 10 nuclear DNA microsatellite loci and mitochondrial control region DNA sequences. Our findings include associations between genetic diversity and management intensity but also with the diversity and contribution of wild populations to captive founders, with some populations apparently composed of animals from divergent wild lineages elevating captive genetic diversity. When population sizes are large, the potential advantages of maximizing genetic diversity in widely outcrossed populations may need careful consideration with respect to the potential disruption of adaptive diversity. Genetic data serve as a robust tool for managing captive populations, yet their interpretation necessitates a comprehensive understanding of species biology and history.</p

Gristhorpe Man: an Early Bronze Age log-coffin burial scientifically defined

© 2010 Antiquity PublicationsA log-coffin excavated in the early nineteenth century proved to be well enough preserved in the early twenty-first century for the fill armoury of modern scientific investigation to give its occupants and contents new identity, new origins and a new date. In many ways the interpretation is much the same as before: a local big man buried looking out to sea. Modern analytical techniques can create a person more real, more human and more securely anchored in history. This research team shows how.The project has been funded by grants from the British Academy, British Association for the Advancement of Science, Natural Environment Research Council, Royal Archaeological Institute and Scarborough Museums Trust. CJK’s participation in this project was funded by a Leverhulme Research Fellowship (RF/6/RFG/2008/0253)

Development of a qPCR assay for the quantification of canine autosomal DNA recovered from livestock attacks

The absence of a standardised method to quantify canine DNA recovered from livestock attacks leaves forensic providers without an important quality control step to help support their decision making. Typically used to normalise the amount of DNA for STR amplification, modern forensic DNA quantification approaches use qPCR of target genes and can also include an Internal Positive Controls (IPC) to determine the presence of PCR inhibitors. The co-amplification of livestock DNA alongside canine DNA has meant that previously developed qPCR methods are not suitable for use so a standardised approach is needed. This research describes the development of a Taq-man multiplex qPCR assay that simultaneously quantifies the autosomal MC1R and Y-specific SRY gene to determine the concentration of canine DNA recovered from attacked livestock. Data suggests that the method is robust and reproducible with no significant difference in the standard curves produced from multiple runs orfrom different DNA standards derived from different canines. Assay sensitivity of between 15 and 31 pg is consistent with other forensic quantification assays and also in line with the sensitivity of the two tested canine STR kits, Canine Genotype 2.1 Kit and CaDNAP Panels 1 and 2. The assay is highly specific to canines when tested against 163 different dogs representing 33 different breeds and no cross-amplification of non-target species’ DNA was observed even from livestock DNA tested at 31.25 ng/µl. This strongly suggests that any DNA detected on evidence collected from attacked livestock is canine. The assay also shows robust tolerance tocommon livestock inhibitors continuing to amplify when inhibitor-spiked DNA samples were tested. Both mixed and inhibited DNA samples underwent STR typing using two canine forensic STR kits with data showing the Canine Genotype 2.1 Kit displaying pronounced cross-amplification of livestock DNA and and/or extensive PCR inhibition leading to the complete loss of amplification when using this kit. Conversely the CaDNAP Panels 1 and 2 showed little cross-amplification of livestock DNA and improved inhibitor tolerance suggesting that thisapproach was better suited for the analysis of livestock attack samples. Findings are discussed and the impact of the observations on future work in this area are explored

Group Dynamics of Zebra and Wildebeest in a Woodland Savanna: Effects of Predation Risk and Habitat Density

.Using generalized linear models, we examined the relative importance of habitat type (differing in vegetation density), probability of encountering lion (based on utilization distribution of all individual lions in the reserve), and season in predicting group size and composition. We found that only in open scrub habitat, group size for both ungulate species increased with the probability of encountering lion. Group composition differed between the two species and was driven by habitat selection as well as predation risk. For both species, composition of groups was, however, dominated by males in open scrub habitats, irrespective of the probability of encountering lion.Distribution patterns of wildebeest and zebra groups at the landscape level directly support the theoretical and empirical evidence from a range of taxa predicting that grouping is favored in open habitats and when predation risk is high. Group composition reflected species-specific social, physiological and foraging constraints, as well as the importance of predation risk. Avoidance of high resource open scrub habitat by females can lead to loss of foraging opportunities, which can be particularly costly in areas such as KGR, where this resource is limited. Thus, landscape-level grouping dynamics are species specific and particular to the composition of the group, arising from a tradeoff between maximizing resource selection and minimizing predation risk