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Auteur Mante, C.; Kide, S.O.; Yao-Lafourcade, A.-F.; Mérigot, B. doi  openurl
  Titre Fitting the truncated negative binomial distribution to count data A comparison of estimators, with an application to groundfishes from the Mauritanian Exclusive Economic Zone Type Article scientifique
  Année 2016 Publication Revue Abrégée Environ. Ecol. Stat.  
  Volume 23 Numéro 3 Pages (down) 359-385  
  Mots-Clés Birth-and-dead models; classification; curves; diversity; habitat; Log-series; Minimum Hellinger distance; Negative binomial; parametric models; population; series; Species abundance; species abundance distributions; zeros  
  Résumé Modeling empirical distributions of repeated counts with parametric probability distributions is a frequent problem when studying species abundance. One must choose a family of distributions which is flexible enough to take into account very diverse patterns and possess parameters with clear biological/ecological interpretations. The negative binomial distribution fulfills these criteria and was selected for modeling counts of marine fish and invertebrates. This distribution depends on a vector of parameters, and ranges from the Poisson distribution (when ) to Fisher's log-series, when . Moreover, these parameters have biological/ecological interpretations which are detailed in the literature and in this study. We compared three estimators of K, and the parameter of Fisher's log-series, following the work of Rao CR (Statistical ecology. Pennsylvania State University Press, University Park, 1971) on a three-parameter unstandardized variant of the negative binomial distribution. We further investigated the coherence underlying parameter values resulting from the different estimators, using both real count data collected in the Mauritanian Exclusive Economic Zone (MEEZ) during the period 1987-2010 and realistic simulations of these data. In the case of the MEEZ, we first built homogeneous lists of counts (replicates), by gathering observations of each species with respect to “typical environments” obtained by clustering the sampled stations. The best estimation of was generally obtained by penalized minimum Hellinger distance estimation. Interestingly, the parameters of most of the correctly sampled species seem compatible with the classical birth-and-dead model of population growth with immigration by Kendall (Biometrika 35:6-15, 1948).  
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  Volume de collection Numéro de collection Edition  
  ISSN 1352-8505 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2067  
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Auteur Benedetti, F.; Guilhaumon, F.; Adloff, F.; Ayata, S.-D. doi  openurl
  Titre Investigating uncertainties in zooplankton composition shifts under climate change scenarios in the Mediterranean Sea Type Article scientifique
  Année 2018 Publication Revue Abrégée Ecography  
  Volume 41 Numéro 2 Pages (down) 345-360  
  Mots-Clés marine biodiversity; species distribution models; north-atlantic; beta diversity; calanoid copepods; ecological-niche; envelope models; habitat-suitability; mass mortality; pseudo-absence data  
  Résumé Ensemble niche modelling has become a common framework to predict changes in assemblages composition under climate change scenarios. The amount of uncertainty generated by the different components of this framework has rarely been assessed. In the marine realm forecasts have usually focused on taxa representing the top of the marine food-web, thus overlooking their basal component: the plankton. Calibrating environmental niche models at the global scale, we modelled the habitat suitability of 106 copepod species and estimated the dissimilarity between present and future zooplanktonic assemblages in the surface Mediterranean Sea. We identified the patterns (species replacement versus nestedness) driving the predicted dissimilarity, and quantified the relative contributions of different uncertainty sources: environmental niche models, greenhouse gas emission scenarios, circulation model configurations and species prevalence. Our results confirm that the choice of the niche modelling method is the greatest source of uncertainty in habitat suitability projections. Presence-only and presence-absence methods provided different visions of the niches, which subsequently lead to different future scenarios of biodiversity changes. Nestedness with decline in species richness is the pattern driving dissimilarity between present and future copepod assemblages. Our projections contrast with those reported for higher trophic levels, suggesting that different components of the pelagic food-web may respond discordantly to future climatic changes.  
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  Volume de collection Numéro de collection Edition  
  ISSN 0906-7590 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2282  
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Auteur Virgili, A.; Authier, M.; Boisseau, O.; Cañadas, A.; Claridge, D.; Cole, T.; Corkeron, P.; Dorémus, G.; David, L.; Di‐Méglio, N.; Dunn, C.; Dunn, T.E.; García‐Barón, I.; Laran, S.; Lauriano, G.; Lewis, M.; Louzao, M.; Mannocci, L.; Martínez‐Cedeira, J.; Palka, D.; Panigada, S.; Pettex, E.; Roberts, J.J.; Ruiz, L.; Saavedra, C.; Santos, M.B.; Canneyt, O.V.; Bonales, J.A.V.; Monestiez, P.; Ridoux, V. url  doi
openurl 
  Titre Combining multiple visual surveys to model the habitat of deep-diving cetaceans at the basin scale Type Article scientifique
  Année 2019 Publication Revue Abrégée Global Ecology and Biogeography  
  Volume 28 Numéro 3 Pages (down) 300-314  
  Mots-Clés beaked whales; data-assembling; deep-diving cetaceans; habitat modelling; kogiids; sperm whales  
  Résumé Aim Deep-diving cetaceans are oceanic species exposed to multiple anthropogenic pressures including high intensity underwater noise, and knowledge of their distribution is crucial to manage their conservation. Due to intrinsic low densities, wide distribution ranges and limited presence at the sea surface, these species are rarely sighted. Pooling data from multiple visual surveys sharing a common line-transect methodology can increase sightings but requires accounting for heterogeneity in protocols and platforms. Location North Atlantic Ocean and Mediterranean Sea. Time period 1998 to 2015. Major taxa Ziphiidae; Physeteriidae; Kogiidae. Methods About 1,240,000 km of pooled effort provided 630 sightings of ziphiids, 836 of physeteriids and 106 of kogiids. For each taxon, we built a hierarchical model to estimate the effective strip width depending on observation conditions and survey types. We then modelled relative densities in a generalized additive modelling framework. Geographical predictions were limited to interpolations identified with a gap analysis of environmental space coverage. Results Deeper areas of the North Atlantic gyre were mostly environmental extrapolation in the predictions, thereby highlighting gaps in sampling across the different surveys. For the three species groups, the highest relative densities were predicted along continental slopes, particularly in the western North Atlantic Ocean where the Gulf Stream creates dynamic frontal zones and eddies. Main conclusions Pooling a large number of surveys provided the first basin-wide models of distribution for deep-diving cetaceans, including several data-deficient taxa, across the North Atlantic Ocean and the Mediterranean Sea. These models can help the conservation of elusive and poorly known marine megafauna.  
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  ISSN 1466-8238 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2756  
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Auteur Cox, S.L.; Embling, C.B.; Hosegood, P.J.; Votier, S.C.; Ingram, S.N. doi  openurl
  Titre Oceanographic drivers of marine mammal and seabird habitat-use across shelf-seas: A guide to key features and recommendations for future research and conservation management Type Article scientifique
  Année 2018 Publication Revue Abrégée Estuar. Coast. Shelf Sci.  
  Volume 212 Numéro Pages (down) 294-310  
  Mots-Clés Bio-physical coupling; bottle-nosed dolphins; california current system; coastal upwelling system; Conservation management; ecosystem-based management; Foraging ecology; Habitat selection; Marine mammals; Oceanography; porpoise phocoena-phocoena; predator-prey interactions; Seabirds; southeastern bering-sea; st-george island; thin zooplankton layers; tidal-stream environments  
  Résumé Mid-latitude (similar to 30-60 degrees) seasonally stratifying shelf-seas support a high abundance and diversity of marine predators such as marine mammals and seabirds. However, anthropogenic activities and climate change impacts are driving changes in the distributions and population dynamics of these animals, with negative consequences for ecosystem functioning. Across mid-latitude shelf-seas marine mammals and seabirds are known to forage across a number of oceanographic habitats that structure the spatio-temporal distributions of prey fields. Knowledge of these and the bio-physical mechanisms driving such associations are needed to improve marine management and policy. Here, we provide a concise and easily accessible guide for both researchers and managers of marine systems on the predominant oceanographic habitats that are favoured for foraging by marine mammals and seabirds across mid-latitude shelf-seas. We (1) identify and describe key discrete physical features present across the continental shelf, working inshore from the shelf-edge to the shore line, (2) provide an overview of findings relating to associations between these habitats and marine mammals and seabirds, (3) identify areas for future research and (4) discuss the relevance of such information to conservation management. We show that oceanographic features preferentially foraged at by marine mammals and seabirds include shelf edge fronts, upwelling and tidal-mixing fronts, offshore banks and internal waves, regions of stratification, and topographically complex coastal areas subject to strong tidal flow. Whilst associations were variable across taxa and through space and time, in the majority of cases interactions between bathymetry and tidal currents appear to play a dominant role, alongside patterns in seasonal stratification and shelf-edge upwelling. We suggest that the ecological significance of these bio-physical structures stems from a capacity to alter the densities, distributions (both horizontally and vertically) and/or behaviours of prey in a persistent and/or predictable manner that increases accessibility for predators, and likely enhances foraging efficiency. Future conservation management should aim to preserve and protect these habitats. This will require adaptive and holistic strategies that are specifically tailored to the characteristics of an oceanographic feature, and where necessary, evolve through space and time in response to spatio-temporal variability. Improved monitoring of animal movements and biophysical conditions across shelf-seas would aid in this. Areas for future research include multi-disciplinary/ trophic studies of the mechanisms linking bio-physical processes, prey and marine mammals and seabirds (which may elucidate the importance of lesser studied features such as bottom fronts and Langmuir circulation cells), alongside a better understanding of how predators perceive their environment and develop foraging strategies during immature/juvenile stages. Estimates of the importance of oceanographic habitat features at a population level should also be obtained. Such information is vital to ensuring the future health of these complex ecosystems, and can be used to assess how anthropogenic activities and future environmental changes will impact the functioning and spatio-temporal dynamics of these bio-physical features and their use by marine predators.  
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  Langue English Langue du Résumé Titre Original  
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  Volume de collection Numéro de collection Edition  
  ISSN 0272-7714 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2428  
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Auteur Machu, E.; Ettahiri, O.; Kifani, S.; Benazzouz, A.; Makaoui, A.; Demarcq, H. url  doi
openurl 
  Titre Environmental control of the recruitment of sardines (Sardina pilchardus) over the western Saharan shelf between 1995 and 2002 : a coupled physical/biogeochemical modelling experiment Type Article scientifique
  Année 2009 Publication Revue Abrégée Fisheries Oceanography  
  Volume 18 Numéro 5 Pages (down) 287-300  
  Mots-Clés biomass; Canary upwelling; hydrodynamic and biogeochemical modelling; plankton; potential spawning habitat; recruitment; Sardina pilchardus  
  Résumé Fisheries constitute an important economic sector for Morocco, where the species Sardina pilchardus represents the main landings. In acoustic evaluations conducted along the Moroccan coast since 1995, the absence of juveniles in 1996 and 1998 and the collapse of the sardine stock between 1996 and 1997 represent the main events until 2002. Sardines are known to be microphageous planktivores and thus are sensitive to environmental variability. A biogeochemical model coupled to a hydrodynamic model (ROMS) was run over the Canary Current System (1991-2002) to investigate the environmental factors that could have played a role in the variability of the sardine spawning. A grid refinement (1/12 degrees) centred on the Saharan Bank (SB) region was built to study the main spawning ground of sardines off northwest Africa. The volume of the potential spawning habitat (PSH) of sardines was defined as a function of depth, temperature and salinity, which are included in the ranges 0-200 m, 15-21 degrees C and 35.8-36.8, respectively. Our modelling frame was able to reproduce the seasonal cycle of temperature, phytoplankton concentration and PSH over the SB. It also captured the warming associated with the negative index of the North Atlantic Oscillation of 1995-1997 and allowed a description of the inter-annual variability of the PSH. Our experiment shows that the volume of PSH was much reduced in 1996 compared to the other years. The results suggest that the delay between high abundance of plankton and favourable spawning conditions is a good proxy for determining the recruitment failure of sardine in this oceanic region.  
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  ISSN 1054-6006 ISBN Médium  
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  Numéro d'Appel LL @ pixluser @ collection 43  
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