A fisheries acoustic multi-frequency indicator to inform on large scale spatial patterns of aquatic pelagic ecosystems

Fisheries acoustic instruments provide information on four major groups in aquatic ecosystems: fish with and without swim bladder (tertiary and quaternary consumers), fluidlike zooplankton (secondary consumers) and small gas bearing organisms such as larval fish and phytoplankton (predominantly primary producers). We entertain that this information is useable to describe the spatial structure of organism groups in pelagic ecosystems. The proposal we make is based on a multi-frequency indicator that synthesises in a single metric the shape of the acoustic frequency response of different organism groups, i.e. the dependence of received acoustic backscattered energy on emitting echosounder frequency. We demonstrate the development and interpretation of the multi-frequency indicator using simulated data. We then calculate the indicator for acoustic water-column survey data from the Bay of Biscay and use it to create reference maps for the spatial structure of the four scattering groups as well as their small scale spatial variability. These maps provide baselines for monitoring future changes in the structure of the pelagic ecosystem

Precision and accuracy of fish length measurements obtained with two visual underwater methods

During the VITAL cruise in the Bay of Biscay in summer 2002, two devices for measuring the length of swimming fish were tested: 1) a mechanical crown that emitted a pair of parallel laser beams and that was mounted on the main camera and 2) an underwater auto-focus video camera. The precision and accuracy of these devices were compared and the various sources of measurement errors were estimated by repeatedly measuring fixed and mobile objects and live fish. It was found that fish mobility is the main source of error for these devices because they require that the objects to be measured are perpendicular to the field of vision. The best performance was obtained with the laser method where a video-replay of laser spots (projected on fish bodies) carrying real-time size information was used. The auto-focus system performed poorly because of a delay in obtaining focus and because of some technical problems

Development of management models and assessment methods for red deer on the open hill in Scotland

Models to assist the management of red deer on the open hill in Scotland and methods for estimating red deer abundance were studied in this thesis. Currently red deer abundance is assessed by census methods with no estimate of precision. A coefficient of variation of 11-13% was estimated as the precision of repeated census counts on Rum. Misclassification in census counts was studied. Mean relative differences between two simultaneous independent counts were -0.9% (0.16) for stags, -0.5% (0.10) for hinds and 4.4% (0.61) for calves. Numbers in brackets are standard errors. Aerial line transect methodology for estimating deer numbers was tested. Mean estimates were comparable to a census count. In a case study comparison between line transects and census counts the former were shown to be quicker and cheaper for large areas. Past numbers of red deer on the open hill in Scotland estimated by Markov chain Monte Carlo methods, suggested a 30% increase between 1970 and 1992, followed by a small decrease since. Convergence problems lead to reservations about the results. A postal questionnaire survey provided information about current management practices and data availability. An age and sex structured stochastic population dynamics model for red deer was developed incorporating age, sex and density dependent survival rates and weight dependent fertility rates. An updating algorithm was proposed for calibrating the model parameters for any population using only count and cull information for that population. Prior parameter values were obtained from well studied populations. The updating algorithm was based on approximate sequential Bayesian estimation carried out by simulation. Additional features were linear filtering of population estimates and a smoothed bootstrap to generate model parameter estimates. The linear filtering reduced one step ahead prediction errors. The smoothed bootstrap allowed substantial reduction in the number of simulations. For an example red deer population posterior parameter values produced smaller variances of predicted numbers compared to prior parameter values. The calibrated model was used to investigate the effects of alternative culling strategies for a red deer population

A new compilation of stomach content data for commercially-important pelagic fish species in the Northeast Atlantic

There is increasing demand for information on predator–prey interactions in the ocean as a result of legislative commitments aimed at achieving sustainable exploitation. However, comprehensive data sets are lacking for many fish species and this has hampered development of multispecies fisheries models and the formulation of effective food-web indicators. This work describes a new compilation of stomach content data for five pelagic fish species (herring, blue whiting, mackerel, albacore and bluefin tuna) sampled across the northeast Atlantic and submitted to the PANGAEA open-access data portal (www.pangaea.de). We provide detailed descriptions of sample origin and of the corresponding database structures. We describe the main results in terms of diet composition and predator–prey relationships. The feeding preferences of small pelagic fish (herring, blue whiting, mackerel) were sampled over a very broad geographic area within the North Atlantic basin, from Greenland in the west, to the Lofoten Islands in the east and from the Bay of Biscay northwards to the Arctic. This analysis revealed significant differences in the prey items selected in different parts of the region at different times of year. Tunas (albacore and bluefin) were sampled in the Bay of Biscay and Celtic Sea. Dominant prey items for these species varied by location, year and season. This data compilation exercise represents one of the largest and most wide-ranging ever attempted for pelagic fish in the North Atlantic. The earliest data included in the database were collected in 1864, whereas the most recent were collected in 2012. Data sets are available at doi:10.1594/PANGAEA.820041 and doi:10.1594/PANGAEA.826992

Effects of Ignoring Survey Design Information for Data Reuse

Data are currently being used, and reused, in ecological research at an unprecedented rate. To ensure appropriate reuse however, we need to ask the question: "Are aggregated databases currently providing the right information to enable effective and unbiased reuse?" We investigate this question, with a focus on designs that purposefully favor the selection of sampling locations (upweighting the probability of selection of some locations). These designs are common and examples are those designs that have uneven inclusion probabilities or are stratified. We perform a simulation experiment by creating data sets with progressively more uneven inclusion probabilities and examine the resulting estimates of the average number of individuals per unit area (density). The effect of ignoring the survey design can be profound, with biases of up to 250% in density estimates when naive analytical methods are used. This density estimation bias is not reduced by adding more data. Fortunately, the estimation bias can be mitigated by using an appropriate estimator or an appropriate model that incorporates the design information. These are only available however, when essential information about the survey design is available: the sample location selection process (e.g., inclusion probabilities), and/or covariates used in their specification. The results suggest that such information must be stored and served with the data to support meaningful inference and data reuse.Peer reviewe

Marine Strategy Framework Directive - Task Group 4 Report Food Webs

The Marine Strategy Framework Directive (2008/56/EC) (MSFD) requires that the European Commission (by 15 July 2010) should lay down criteria and methodological standards to allow consistency in approach in evaluating the extent to which Good Environmental Status (GES) is being achieved. ICES and JRC were contracted to provide scientific support for the Commission in meeting this obligation. A total of 10 reports have been prepared relating to the descriptors of GES listed in Annex I of the Directive. Eight reports have been prepared by groups of independent experts coordinated by JRC and ICES in response to this contract. In addition, reports for two descriptors (Contaminants in fish and other seafood and Marine Litter) were written by expert groups coordinated by DG SANCO and IFREMER respectively. A Task Group was established for each of the qualitative Descriptors. Each Task Group consisted of selected experts providing experience related to the four marine regions (the Baltic Sea, the North-east Atlantic, the Mediterranean Sea and the Black Sea) and an appropriate scope of relevant scientific expertise. Observers from the Regional Seas Conventions were also invited to each Task Group to help ensure the inclusion of relevant work by those Conventions. This is the report of Task Group 4 Food Webs.JRC.DDG.H.5-Rural, water and ecosystem resource