Cefas Laboratory

Lowestoft, United Kingdom

Cefas Laboratory

Lowestoft, United Kingdom
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Santos A.R.,University College Cork | Santos A.R.,CEFAS Laboratory | Trueman C.,University of Southampton | Connolly P.,Marine Institute of Ireland | Rogan E.,University College Cork
Deep-Sea Research Part I: Oceanographic Research Papers | Year: 2013

The black scabbardfish is a deep water species of high commercial interest in the NE Atlantic. Specimens were collected from commercial trawls to the west of the British Isles and from longliners operating near Madeira between September 2008 and May 2010. Stomach content analysis was confined to samples from the northern area, because of a high number of empty stomachs from Madeira. Stable isotope analyses identified that black scabbardfish feeds on species with epipelagic and benthopelagic affinities. For the west of British Isles, the δN values were significantly different between seasons suggesting a change in the diet throughout the year. Black scabbardfish have higher δN and δC values compared with other co-occurring benthopelagic feeders and lower nitrogen values than the true benthic predators and/or scavengers. Comparison with stable isotope analysis in samples from Madeira indicated that black scabbardfish feed at a similar trophic level and has the same trophic niche width in both areas, assuming similar baseline isotope compositions. The diet in the northern area comprised fish (68% N), crustaceans (22% N) and cephalopods (15% N) with blue whiting (Micromesistius poutassou) constituting 40% of the prey. Seasonal shift in diet was observed, with a predominance of blue whiting (70%) in the first quarter of the year, shifting to a more diverse diet in the remainder of the year. These results indicate that the diet of black scabbardfish is closely linked with the seasonal migration of blue whiting and that they likely select prey in proportion to availability. This study demonstrates that the combined used of both methods can elucidate the trophic ecology of black scabbardfish, in situations where conventional methods alone provide insufficient data. © 2013.

Spencer M.,University of Liverpool | Mieszkowska N.,Marine Biological Association of The United Kingdom | Robinson L.A.,University of Liverpool | Simpson S.D.,University of Bristol | And 18 more authors.
Global Change Biology | Year: 2012

Regime shifts are sudden changes in ecosystem structure that can be detected across several ecosystem components. The concept that regime shifts are common in marine ecosystems has gained popularity in recent years. Many studies have searched for the step-like changes in ecosystem state expected under a simple interpretation of this idea. However, other kinds of change, such as pervasive trends, have often been ignored. We assembled over 300 ecological time series from seven UK marine regions, covering two to three decades. We developed state-space models for the first principal component of the time series in each region, a common measure of ecosystem state. Our models allowed both trends and step changes, possibly in combination. We found trends in three of seven regions and step changes in two of seven regions. Gradual and sudden changes are therefore important trajectories to consider in marine ecosystems. © 2011 Blackwell Publishing Ltd.

Spencer M.,University of Liverpool | Birchenough S.N.R.,Cefas Laboratory | Mieszkowska N.,Marine Biological Association of The United Kingdom | Robinson L.A.,University of Liverpool | And 18 more authors.
Marine Ecology | Year: 2011

A regime shift is a large, sudden, and long-lasting change in the dynamics of an ecosystem, affecting multiple trophic levels. There are a growing number of papers that report regime shifts in marine ecosystems. However, the evidence for regime shifts is equivocal, because the methods used to detect them are not yet well developed. We have collated over 300 biological time series from seven marine regions around the UK, covering the ecosystem from phytoplankton to marine mammals. Each time series consists of annual measures of abundance for a single group of organisms over several decades. We summarised the data for each region using the first principal component, weighting either each time series or each biological component (e.g. plankton, fish, benthos) equally. We then searched for regime shifts using Rodionov's regime shift detection (RSD) method, which found regime shifts in the first principal component for all seven marine regions. However, there are consistent temporal trends in the data for six of the seven regions. Such trends violate the assumptions of RSD. Thus, the regime shifts detected by RSD in six of the seven regions are likely to be artefacts caused by temporal trends. We are therefore developing more appropriate time series models for both single populations and whole communities that will explicitly model temporal trends and should increase our ability to detect true regime shift events. © 2010 Blackwell Verlag GmbH.

Hintzen N.T.,Institute for Marine Resources and Ecosystem Studies | Roel B.,Cefas Laboratory | Benden D.,Institute for Marine Resources and Ecosystem Studies | Clarke M.,Marine Institute of Ireland | And 4 more authors.
ICES Journal of Marine Science | Year: 2014

Natural resource managers aim to manage fish stocks at sustainable levels. Often, management of these stocks is based on the results of analytical stock assessments. Accurate catch data, which can be attributed to a specific population unit and reflects the population structure, are needed for these approaches. Often though, the quality of the catch data is compromised when dealing with a complex population structure where fish of different population units mix in a fishery. The herring population units west of the British Isles are prone to mixing. Here, the inability to perfectly allocate the fish caught to the population unit they originate from, due to classification problems, poses problems for management. These mixing proportions are often unknown; therefore, we use simulation modelling combined with management strategy evaluation to evaluate the role fisheries-independent surveys can play in an assessment to provide unbiased results, irrespective of population unit mixing and classification success. We show that failure to account for mixing is one of the major drivers of biased estimates of population abundance, affecting biomass reference points and MSY targets. When mixing of population units occurs, the role a survey can play to provide unbiased assessment results is limited. Either different assessment models should be employed or stock status should be considered from the survey data alone. In addition, correctly classifying the origin of fish is especially important for those population units that are markedly smaller in size than other units in the population complex. Without high classification success rates, smaller population units are extremely vulnerable to overexploitation. © 2014 International Council for the Exploration of the Sea.

PubMed | James Cook University, University of Western Australia, Deakin University, Natural Environment Research Council and 26 more.
Type: Journal Article | Journal: Trends in ecology & evolution | Year: 2016

It is a golden age for animal movement studies and so an opportune time to assess priorities for future work. We assembled 40 experts to identify key questions in this field, focussing on marine megafauna, which include a broad range of birds, mammals, reptiles, and fish. Research on these taxa has both underpinned many of the recent technical developments and led to fundamental discoveries in the field. We show that the questions have broad applicability to other taxa, including terrestrial animals, flying insects, and swimming invertebrates, and, as such, this exercise provides a useful roadmap for targeted deployments and data syntheses that should advance the field of movement ecology.

Mapp J.,University of East Anglia | Fisher M.,University of East Anglia | Bagnall A.,University of East Anglia | Lines J.,University of East Anglia | And 2 more authors.
ICPRAM 2013 - Proceedings of the 2nd International Conference on Pattern Recognition Applications and Methods | Year: 2013

We present a study comparing Curvature Scale Space (CSS) representation with Shapelet transformed data with a view to discriminating between sagittal otoliths of North-Sea and Thames Herring using otolith boundary and boundary metrics. CSS transformed boundaries combined with measures of their circularity, eccentricity and aspect-ratio are used to classify using nearest-neighbour selections with distance being computed using CSS matching methods. Shapelet transformed data are classified using a number of techniques (Nearest-Neighbour, Naive-Bayes, C4.5, Support Vector Machines, Random and Rotation Forest) and compared to CSS classification results. Both methods use Leave One Out Cross Validation (LOOCV). We describe the method of encoding and the matching algorithm used during CSS classification and give an overview of Shapelet transforms and the classifiers that are used on the data. It is shown that whilst CSS forms part of the MPEG-7 standard and performs better than random selection, it can be significantly out-performed by recent additions to machine-learning methods in this application. Shapelets also show that with regard to intra-species distinction, the discriminatory features of otolith boundaries may lie not in the major inflection points, but the boundary points between them.

Wahlberg M.,University of Southern Denmark | Westerberg H.,Institute of Freshwater Research | Aarestrup K.,Technical University of Denmark | Feunteun E.,French National Center for Scientific Research | And 2 more authors.
Deep-Sea Research Part I: Oceanographic Research Papers | Year: 2014

Temperature and depth logging tags were implanted into adult eels released on Atlantic west coasts of France and Ireland to study their oceanic migration behavior. For three of the tags, 25 to 256 days after release there was a dramatic rise in temperature from 10. °C to 36. °C and the dive profile changed from depths of 300-1000. m to repeated ascents to the surface. This indicated that the eels carrying the tags had been eaten by a mammalian predator. Two of the tags had sufficient sampling rate to resolve the dives in detail. They recorded a total of 91 dives to maximum depths of 250-860. m lasting 11-12. min and with surface intervals of 5-7. min. More than two thirds of the dives included a rapid descent from approximately 500. m to 600-700. m. From this we infer that the predator was most likely a deep-diving toothed whale. The dives logged while the tags were inside the predator revealed that the temperature usually decreased during dives, and increased again during surface periods. The temperature drops during dives were probably caused by the ingestion of prey or water. These observations provide insights into the behavior of toothed whales foraging in the mesopelagic zone. © 2014 Elsevier Ltd.

Laptikhovsky V.,Cefas Laboratory | Salman A.,Ege University | Onsoy B.,Mugla Sitki Kocman Universites | Akalin M.,Ege University | Ceylan B.,Mugla Sitki Kocman Universites
Deep-Sea Research Part I: Oceanographic Research Papers | Year: 2014

Reproductive patterns of two benthic bathyal octopods, Pteroctopus tetracirrhus and Scaeurgus unicirrhus have been studied in extremely nutrient-poor environment of the deep-sea Eastern Mediterranean. Both species were found to exhibit a reproductive tactics of producing eggs much larger than in the western part of the sea which likely results in larger hatchlings with higher viability. P. tetracirrhus exhibited a typical "deep-sea" spawning strategy of simultaneous maturation of a single batch of large eggs with atresia of excessive oocytes, whereas reproductive strategy of S. unicirrhus is particular for shelf octopodids: asynchronous maturation of numerous batches of small eggs with no obvious regulatory atresia. Existence of these two types of ovary development and utilisation of fecundity are closely related to two types of evolutionary stable reproductive strategies based on existence of either very large or very small eggs with a few species occupying the "intermediate" position. © 2014 Elsevier Ltd.

Collins C.M.,Marine Scotland - Marine Laboratory | Kerr R.,CEFAS Laboratory | Mcintosh R.,Marine Scotland - Marine Laboratory | Snow M.,Marine Scotland - Marine Laboratory
Diseases of Aquatic Organisms | Year: 2010

Gyrodactylus salaris is a monogenean freshwater parasite that causes high mortality in wild Atlantic salmon, and a number of countries employ monitoring programmes for its presence. A TaqMan®-MGB (minor groove binding) probe real-time multiplex assay targeting the internal transcribed spacer ribosomal DNA (ITS rDNA) was developed to simultaneously identify G. salaris/G. thymalli and 2 other commonly occurring Gyrodactylus species infecting salmonids in northern Europe: G. derjavinoides and G. truttae. In addition, a Gyrodactylus genus-level assay was developed to assess parasite DNA quality. The species-specific real-time PCR method correctly identified target species from a wide geographical range and from a number of salmonid hosts. It did not amplify G. lucii or G. teuchis. These species were successfully amplified using the Gyrodactylus genus real-time assay. The species-specific real-time assay proved to be significantly faster than the currently employed molecular screening method of ITS rDNA PCR amplification followed by restriction fragment length polymorphism analyses (RFLP). However, as with ITS RFLP, the real-time method did not distinguish between G. salaris and the non-pathogenic G. thymalli, its principle advantage being a significant reduction in time to achieve an initial diagnostic screen before the employment of more in-depth analyses for those specimens giving a positive G. salaris/G. thymalli real-time result.

Sparrevohn C.R.,Technical University of Denmark | Aarestrup K.,Technical University of Denmark | Stenberg C.,Technical University of Denmark | Righton D.,Cefas Laboratory
Journal of Fish Biology | Year: 2014

A radio frequency identification (RFID) antenna system, build into a sledge that can be towed behind a vessel like a trawl and thereby has the potential to detect the position of a passive inductor technology (PIT)-tagged fish in a wide variety of habitats, is presented. By scanning for hatchery-reared PIT-tagged turbot Psetta maxima released into a natural habitat, the performance of the system was compared to a standard juvenile trawl and results suggested that the efficiency of the sledge was five times that of the trawl, which in absolute values corresponds to 75% of P. maxima lying in the pathway of the sledge. © 2014 The Fisheries Society of the British Isles.

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