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Abstract: The ability to determine authenticity and provenance of fish and fish products throughout the international fish trade distribution chain is of paramount importance, and in many countries traceability in the fisheries sector is... more
Abstract: The ability to determine authenticity and provenance of fish and fish products throughout the international fish trade distribution chain is of paramount importance, and in many countries traceability in the fisheries sector is based on labelling rules. As shown by numerous fraud cases worldwide, however, and the relentless global problem of illegal, unreported and unregulated (IUU) fishing, independent control technologies are urgently needed to ensure appropriate implementation of traceability schemes. Here, we discuss opportunities and challenges arising from the rapid progress in research and technology pertinent to traceability. In support of an integrative approach, several technologies will be considered, though emphasis is placed on DNA technology as an approach witnessing major recent development.
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Research Interests: Evolutionary Biology, Genetics, Life history, Biology, Heredity, and 15 moreGenetic Diversity, Computer Simulation, Genetic Structure, Atlantic Ocean, Animals, Iberian Peninsula, Larval Dispersal, Brachyura, Genetic Differentiation, Estuary, Analysis of Variance, Larva, Linkage Disequilibrium, Genetic variation, and Carcinus Maenas
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The evolutionary consequences of an artificial introduction of the clupeid Limnothrissa miodon from Lake Tanganyika into Lake Kivu, East Africa were examined. In 1959, 57 400 fry (mixture of Limnothrissa and the related clupeid,... more
The evolutionary consequences of an artificial introduction of the clupeid Limnothrissa miodon from Lake Tanganyika into Lake Kivu, East Africa were examined. In 1959, 57 400 fry (mixture of Limnothrissa and the related clupeid, Stolothrissa tanganicae), were released into Lake Kivu to boost fisheries production. Comparisons were made between respective source and transplant populations 34 years later (1993) using morphometrics (‘truss’ method), allozymes (29 enzyme-coding loci) and mitochondrial (mt) DNA variation (RFLP analysis of PCR-amplified ND5/6 genes). Significant morphological and genetic differentiation between source and transplant samples was detected, with a distinct clustering of Kivu Limnothrissa on respective dendrograms, especially at the morphometric and mtDNA levels. Differentiation within Lake Tanganyika was, however, consistently higher than that between lakes. Allozymic diversity was similar in samples from both lakes (Lake Tanganyika: heterozygosity = 0.0658, mean number of alleles=1.44; Lake Kivu: heterozygosity = 0.0655; mean number of alleles = 1.48), however, a significantly lower mtDNA haplotype diversity was detected in Lake Kivu (Lake Tanganyika: 0.905; Lake Kivu: 0.755). Data suggest that high post-introduction mortality and various demographic factors reduced the effective population size of the introduced population to tens rather than thousands of individuals, resulting in a reduction in genetic diversity and founder effect.
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Research Interests: Evolutionary Biology, Genetics, Biology, Metagenomics, Medicine, and 14 moreBiological Sciences, Phylogeny, Environmental Sciences, Animals, Polymerase Chain Reaction, Pyrosequencing, Artifacts, Nucleic Acids, Species Richness, Nematoda, Genetic variation, Base Sequence, Amplicon, and Molecular Sequence Data
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ABSTRACT Cyclostomata bryozoa are thought to reproduce via polyembryony, a clonal replication of a fertilized egg. To test this hypothesis and to assess the impact of their reproductive strategy on the structure of populations, we... more
ABSTRACT Cyclostomata bryozoa are thought to reproduce via polyembryony, a clonal replication of a fertilized egg. To test this hypothesis and to assess the impact of their reproductive strategy on the structure of populations, we isolated microsatellite markers in Crisia denticulata (Cyclostomata, Stenolemata), using an initial enrichment step with random amplified polymorphic DNA (RAPD) primers. A total of nine microsatellites, one tetra- and eight dinucleotides repeats were isolated; seven were found to be polymorphic in a test sample of 30 individuals, with allele numbers/locus varying from 2 to 6. The tetranucleotide locus showed heterozygote deficiency. These primers did not amplify the DNA of Crisia eburnea.
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Anthropogenic endocrine disruptors now contaminate all environments globally, with concomitant deleterious effects across diverse taxa. While most studies on endocrine disruption (ED) have focused on vertebrates, the superimposition of... more
Anthropogenic endocrine disruptors now contaminate all environments globally, with concomitant deleterious effects across diverse taxa. While most studies on endocrine disruption (ED) have focused on vertebrates, the superimposition of male sexual characteristics in the female dogwhelk, Nucella lapillus (imposex), caused by organotins, provides one of the most clearcut ecological examples of anthropogenically induced ED in aquatic ecosystems. To identify the underpinning mechanisms of imposex for this ‘nonmodel’ species, we combined Roche 454 pyrosequencing with custom oligoarray fabrication inexpensively to both generate gene models and identify those responding to chronic tributyltin (TBT) treatment. The results supported the involvement of steroid, neuroendocrine peptide hormone dysfunction and retinoid mechanisms, but suggested additionally the involvement of putative peroxisome proliferator–activated receptor (PPAR) pathways. Application of rosiglitazone, a well‐known vertebrate PPARγ ligand, to dogwhelks induced imposex in the absence of TBT. Thus, while TBT‐induced imposex is linked to the induction of many genes and has a complex phenotype, it is likely also to be driven by PPAR‐responsive pathways, hitherto not described in invertebrates. Our findings provide further evidence for a common signalling pathway between invertebrate and vertebrate species that has previously been overlooked in the study of endocrine disruption.
Research Interests: Biology, Environmental Monitoring, Medicine, Gene-environment interactions, Transcriptome, and 13 moreMolecular Ecology, Biological Sciences, Gastropoda, Endocrine disruptors, Female, Animals, Male, Disorders of sex development, Endocrine Disruption, Endocrine Disruptors, Imposex, Tributyltin, and Endocrine System
... punctuated by improvements in molecular and statistical techniques that produced an array of tools relevant to ecological and evolutionary studies such as assignment tests, estimates of effective population size, fine-scale population... more
... punctuated by improvements in molecular and statistical techniques that produced an array of tools relevant to ecological and evolutionary studies such as assignment tests, estimates of effective population size, fine-scale population structure, kinship analyses (eg Helyar et al. ...
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ABSTRACT
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The endangered fish species Anaecypris hispanica is restricted to eight disjunct populations in the Portuguese Guadiana drainage. The genetic structure of these populations was studied in order to determine levels of genetic variation... more
The endangered fish species Anaecypris hispanica is restricted to eight disjunct populations in the Portuguese Guadiana drainage. The genetic structure of these populations was studied in order to determine levels of genetic variation within and among populations and suggest implications for conservation of the species. Based on five microsatellite loci, the null hypothesis of population homogeneity was tested. Tests for
Research Interests: Conservation Genetics, Biology, Endangered Species, Genetic Diversity, Biological Sciences, and 12 morePopulation structure, Environmental Sciences, Population, Biological Conservation, Genetic Structure, Genetic Population Structure, Microsatellite, Population Size, Genetic Differentiation, Genetic variation, Genetic Variability, and microsatellite loci
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Understanding population connectivity and genetic diversity is of fundamental importance to conservation. However, in globally threatened marine megafauna, challenges remain due to their elusive nature and wide-ranging distributions. As... more
Understanding population connectivity and genetic diversity is of fundamental importance to conservation. However, in globally threatened marine megafauna, challenges remain due to their elusive nature and wide-ranging distributions. As overexploitation continues to threaten biodiversity across the globe, such knowledge gaps compromise both the suitability and effectiveness of management actions. Here, we use a comparative framework to investigate genetic differentiation and diversity of manta rays, one of the most iconic yet vulnerable groups of elasmobranchs on the planet. Despite their recent divergence, we show how oceanic manta rays(Mobula birostris)display significantly higher genetic diversity than reef manta rays(Mobula alfredi)and thatM. birostrispopulations display higher connectivity worldwide. Through reconstructing modes of colonisation, we reveal how both contemporary and historical forces have likely influenced these patterns, with important implications for populatio...
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Research Interests: Geography, Biology, Irish, Population, Genetic Structure, and 5 moreFish Migration, Microsatellite, Fishery, Salmo, and Irish Sea
The management and conservation of anadromous sea trout (Salmo trutta L.) during the marine phase of their life history depends on a better understanding their ecology and migratory behaviour in the sea. To address this knowledge gap, a... more
The management and conservation of anadromous sea trout (Salmo trutta L.) during the marine phase of their life history depends on a better understanding their ecology and migratory behaviour in the sea. To address this knowledge gap, a Genetic Stock Identification (GSI) exercise using Individual Assignment (IA) was undertaken. A panel consisting of 18 microsatellite nuclear DNA loci was used for the construction of a genetic baseline for sea trout from river systems flowing into the Irish and Celtic Seas. Sampling design involved the collection of over 5,000 juvenile fish, from putative sea trout spawning areas in 99 riverine locations. This comprehensive sampling programme of Irish, Manx, Scottish, English and Welsh rivers was designed to include the majority of the larger rivers contributing sea trout to the Irish and Celtic Seas. Genomic DNA extracted from these specimens was genotyped and analysed, to examine patterns of population structure, and produce a genetic baseline for ...
Research Interests: Geography, Biology, Irish, Population, Genetic Structure, and 5 moreFish Migration, Microsatellite, Fishery, Salmo, and Irish Sea
Aquatic species throughout the world are threatened by extinction in many parts of their range, particularly in their most southerly distributions. Arctic charr (Salvelinus alpinus) is a Holarctic species with a distribution that includes... more
Aquatic species throughout the world are threatened by extinction in many parts of their range, particularly in their most southerly distributions. Arctic charr (Salvelinus alpinus) is a Holarctic species with a distribution that includes the glacial lakes of North Wales, towards it southern limit. To date, no genetic studies have been conducted to determine the genetic health of the three remaining native Arctic charr populations in North Wales, despite exposure to stocking and adverse environmental and ecological conditions. We used seven microsatellite loci to determine whether: 1) genetic differentiation existed between native populations; 2) translocated populations from Llyn Peris were genetically similar to the historically connected Llyn Padarn population; and 3) hatchery supplementation negatively impacted genetic diversity in Llyn Padarn. All three native populations retained their genetic integrity, with Llyn Bodlyn showing high levels of divergence (FST= 0.26 ± 0.02SD) a...
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Domestication leads to changes in traits that are under directional selection in breeding programmes, though unintentional changes in nonproduction traits can also arise. In offspring of escaping fish and any hybrid progeny, such... more
Domestication leads to changes in traits that are under directional selection in breeding programmes, though unintentional changes in nonproduction traits can also arise. In offspring of escaping fish and any hybrid progeny, such unintentionally altered traits may reduce fitness in the wild. Atlantic salmon breeding programmes were established in the early 1970s, resulting in genetic changes in multiple traits. However, the impact of domestication on eye size has not been studied. We measured body size corrected eye size in 4000 salmon from six common garden experiments conducted under artificial and natural conditions, in freshwater and saltwater environments, in two countries. Within these common gardens, offspring of domesticated and wild parents were crossed to produce 11 strains, with varying genetic backgrounds (wild, domesticated, F1 hybrids, F2 hybrids and backcrosses). Size‐adjusted eye size was influenced by both genetic and environmental factors. Domesticated fish reared ...
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Sea turtle populations are under threat from an epizootic tumor disease (animal epidemic) known as fibropapillomatosis. Fibropapillomatosis continues to spread geographically, with prevalence of the disease also growing at many... more
Sea turtle populations are under threat from an epizootic tumor disease (animal epidemic) known as fibropapillomatosis. Fibropapillomatosis continues to spread geographically, with prevalence of the disease also growing at many longer-affected sites globally. However, we do not yet understand the precise environmental, mutational and viral events driving fibropapillomatosis tumor formation and progression.Here we perform transcriptomic and immunohistochemical profiling of five fibropapillomatosis tumor types: external new, established and postsurgical regrowth tumors, and internal lung and kidney tumors. We reveal that internal tumors are molecularly distinct from the more common external tumors. However, they have a small number of conserved potentially therapeutically targetable molecular vulnerabilities in common, such as the MAPK, Wnt, TGFβ and TNF oncogenic signaling pathways. These conserved oncogenic drivers recapitulate remarkably well the core pan-cancer drivers responsible...
Research Interests: Conservation Biology, Cancer, Biology, Ecology, Immunohistochemistry, and 15 moreCancer Research, Medicine, Signal Transduction, Cancer Genomics, Cancer Models, Ecology and Evolutionary Biology, Animals, Article, Gene Regulatory Networks, Carcinogenesis, Animal Sciences, Cell Proliferation, Medicine and Health Sciences, Gene expression profiling, and Communications biology
Accurately assessing community diversity in time and space, and linking these patterns to ecological theory, is essential for effective environmental monitoring. Freshwater macroinvertebrates are an important group of taxa routinely used... more
Accurately assessing community diversity in time and space, and linking these patterns to ecological theory, is essential for effective environmental monitoring. Freshwater macroinvertebrates are an important group of taxa routinely used for riverine environmental assessments due to their wide biological, functional and phylogenetic diversity and their responses to environmental factors. Recently, eDNA metabarcoding based sampling and identification has been shown to increase the accuracy of biodiversity assessments, while reducing cost and time, compared to traditional methods. Here, we present results from a field comparison of eDNA versus traditional riverine biodiversity techniques to assess freshwater macroinvertebrates. In addition, we investigated the effects of landuse and seasonality on community and functional diversity, to infer the underlying regional ecological temporal and spatial dynamics. Comparison of biodiversity dynamics based on traditional and eDNA survey method...
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Sea turtle populations are directly and indirectly under threat from a range of anthropogenic processes. Perhaps the most visibly apparent of these is the disfiguring tumor disease epizootic (animal epidemic) known as fibropapillomatosis.... more
Sea turtle populations are directly and indirectly under threat from a range of anthropogenic processes. Perhaps the most visibly apparent of these is the disfiguring tumor disease epizootic (animal epidemic) known as fibropapillomatosis. Fibropapillomatosis continues to spread geographically, with prevalence of the disease also growing at a number of affected sites globally. Environmental exposures seem key to inducing tumor development, possibly through weakening host immune systems to the point of enabling pathogen-induced tumor formation. However, we do not yet understand the precise molecular and mutational events driving fibropapillomatosis tumor formation and progression. Similarly, many open questions remain about the role of the herpesvirus (chelonid herpesvirus 5, ChHV5) associated with the disease as a potential co-trigger, and whether its occurrence within tumors is causative or opportunistic. Without improved understanding of the basic biology of this disease epizootic,...
Research Interests: Biology and Lytic Cycle
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Practical biodiversity conservation relies on delineation of biologically meaningful units, particularly with respect to global conventions and regulatory frameworks. Traditional approaches have typically relied on morphological... more
Practical biodiversity conservation relies on delineation of biologically meaningful units, particularly with respect to global conventions and regulatory frameworks. Traditional approaches have typically relied on morphological observation, resulting in artificially broad delineations and non-optimal species units for conservation. More recently, species delimitation methods have been revolutionised with High-Throughput Sequencing approaches, allowing study of diversity within species radiations using genome-wide data. The highly mobile elasmobranchs, manta and devil rays (Mobulaspp.), are threatened globally by targeted and bycatch fishing pressures resulting in recent protection under several global conventions. However, a lack of global data, morphological similarities, a succession of recent taxonomic changes and ineffectual traceability measures combine to impede development and implementation of a coherent and enforceable conservation strategy. Here, we generate genome-wide S...
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Research Interests: Genetics, Genomics, Biology, Ecology, Marine biodiversity, and 15 moreBiodiversity, Environmental Change, Genetic Diversity, Protein Structure and Function, Functional diversity, Ecosystem, Ecosystem service, DNA Barcode, Nutrient recycling from waste water, Metabolic pathway, Gene Expression Analysis, Marine ecosystem, Environmental DNA, Ecosystem diversity, and NUtrient recycling
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Abstract An RNA derivative (pSPT 18.15) of Jeffreys' 33.15 human minisatellite core sequence was used to probe DNA from individuals of the peach-potato (Myzus persicae) and grain (Sitobion avenae) aphid. Sufficient and reproducible... more
Abstract An RNA derivative (pSPT 18.15) of Jeffreys' 33.15 human minisatellite core sequence was used to probe DNA from individuals of the peach-potato (Myzus persicae) and grain (Sitobion avenae) aphid. Sufficient and reproducible quantities of DNA (M. ...
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Two molecular techniques which reveal highly variable DNA polymorphisms, RAPD and multilocus DNA fingerprinting, were used to evaluate genetic diversity between six aquacultural strains of Oreochromis niloticus (tilapia) from the... more
Two molecular techniques which reveal highly variable DNA polymorphisms, RAPD and multilocus DNA fingerprinting, were used to evaluate genetic diversity between six aquacultural strains of Oreochromis niloticus (tilapia) from the Philippines. The results using both techniques were in close agreement Within‐strain heterozygosity values were similar and were correlated between the two data sets, but statistical errors associated with the RAPD data set were lower. Although genetic distances between strains were greater using DNA fingerprinting, the distances measured using both methods were significantly correlated. Both methods were useful in estimating variation between strains, but they offered different advantages. RAPD was technically easier to perform and produced results with low statistical error, whereas DNA fingerprinting detected greater genetic differentiation between strains. The theoretical basis for using RAPD and multilocus minisatellite markers for population studies i...
Research Interests: Genetics, Biology, Medicine, Genetic Diversity, Molecular Ecology, and 14 moreBiological Sciences, Molecular, Animals, DNA profiling, DNA fingerprinting, RAPD, Tilapia, Theoretical Models, Genetic Polymorphism, Genetic variation, Oreochromis niloticus, Minisatellite, Genetic Markers, and Oreochromis
Research Interests: Genetics, Zoology, Biology, Ecology, Population structure, and 5 moreFish Migration, Fishery, Herring, Mixed layer, and MEPS
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This paper presents data from the first major survey of the diversity, biology and fisheries of elasmobranchs in the Persian (Arabian) Gulf. Substantial landings of elasmobranchs, usually as gillnet by‐catch, were recorded in Kuwait,... more
This paper presents data from the first major survey of the diversity, biology and fisheries of elasmobranchs in the Persian (Arabian) Gulf. Substantial landings of elasmobranchs, usually as gillnet by‐catch, were recorded in Kuwait, Qatar and the Emirate of Abu Dhabi (part of the United Arab Emirates), although larger elasmobranchs from targeted line fisheries were landed in Abu Dhabi. The elasmobranch fauna recorded was distinctive and included species that are undescribed, rare and have a highly restricted known distribution. Numerical abundance was dominated by sharks (c. 80%), of which carcharhinids were by far the most important. The milk shark Rhizoprionodon acutus and whitecheek shark Carcharhinus dussumieri together comprised just under half of all recorded individuals. Around 90% of recorded sharks were small (50–90 cm total length, LT) individuals, most of which were mature individuals of species with a small maximum size (<100 cm LT), although immature individuals of ...