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Authier, M., Saraux, C., & Péron, C. (2017). Variable selection and accurate predictions in habitat modelling: a shrinkage approach. Ecography, 40(4), 549–560.
Résumé: Habitat modelling is increasingly relevant in biodiversity and conservation studies. A typical application is to predict potential zones of specific conservation interest. With many environmental covariates, a large number of models can he investigated but multi-model inference may become impractical. Shrinkage regression overcomes this issue by dealing with the identification and accurate estimation of effect size for prediction. In a Bayesian framework we investigated the use of a shrinkage prior, the Horseshoe, for variable selection in spatial generalized linear models (GLM). As study cases, we considered 5 datasets on small pelagic fish abundance in the Gulf of Lion (Mediterranean Sea, France) and 9 environmental inputs. We compared the predictive performances of a simple kriging model, a full spatial GLM model with independent normal priors for regression coefficients, a full spatial GLM model with a Horseshoe prior for regression coefficients and 2 zero-inflated models (spatial and non-spatial) with a Horseshoe prior. Predictive performances were evaluated by cross validation on a hold-out subset of the data: models with a Horseshoe prior performed best, and the full model with independent normal priors worst. With an increasing number of inputs, extrapolation quickly became pervasive as we tried to predict from novel combinations of covariate values. By shrinking regression coefficients with a Horseshoe prior, only one model needed to be fitted to the data in order to obtain reasonable and accurate predictions, including extrapolations.
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Dortel, E., Pecquerie, L., & Chassot, E. (2020). A Dynamic Energy Budget simulation approach to investigate the eco-physiological factors behind the two-stanza growth of yellowfin tuna (Thunnus albacares). Ecol. Model., 437, 109297.
Résumé: The growth of yellowfin tuna has been the subject of considerable research efforts since the early 1960s. Most studies support a complex two-stanza growth pattern with a sharp acceleration departing from the von Bertalanffy growth curve used for most fish populations. This growth pattern has been assumed to result from a combination of physiological, ecological and behavioral factors but the role and contribution of each of them have not been addressed yet. We developed a bioenergetic model for yellowfin tuna in the context of Dynamic Energy Budget theory to mechanistically represent the processes governing yellowfin tuna growth. Most parameters of the model were inferred from Pacific bluefin tuna using body-size scaling relationships while some essential parameters were estimated from biological data sets collected in the Indian Ocean. The model proved particularly suitable for reproducing the data collected during the Pacific yellowfin tuna farming experience conducted by the Inter-American Tropical Tuna Commission at the Achotines Laboratory in Panama. In addition, model predictions appeared in agreement with knowledge of the biology and ecology of wild yellowfin tuna. We used our model to explore through simulations two major assumptions that might explain the existence of growth stanzas observed in wild yellowfin tuna: (i) a lower food supply during juvenile stage in relation with high infra- and inter-species competition and (ii) ontogenetic changes in food diet. Our results show that both assumptions are plausible although none of them is self-sufficient to explain the intensity of growth acceleration observed in wild Indian Ocean yellowfin tuna, suggesting that the two factors may act in concert. Our study shows that the yellowfin growth pattern is likely due to behavioral changes triggered by the acquisition of physiological abilities and anatomical traits through ontogeny that result in a major change in intensity of schooling and in a shift in the biotic habitat and trophic ecology of this commercially important tuna species.
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Draredja, M. A., Frihi, H., Boualleg, C., Abadie, E., & Laabir, M. (2020). Distribution of dinoflagellate cyst assemblages in recent sediments from a southern Mediterranean lagoon (Mellah, Algeria) with emphasis on toxic species. Environ. Sci. Pollut. Res., .
Résumé: This is the first study on the dinoflagellate cysts in Algerian waters and in Mellah Lagoon (South Western Mediterranean), located within a protected reserve. In total, 42 species of dinocysts belonging to 7 orders, 12 families and 23 genera, were identified in the 26 superficial sediment samples from Mellah Lagoon. The distribution of dinocysts in the sediment of this lagoon is heterogeneous. Indeed, their abundance oscillates between 1 and 315 cysts g(-1) dry sediment (DS). Cyst morphotype assemblages were dominated by a few numbers of species: Alexandrium minutum (15.87%), Gonyaulax verior (9.81%), Protoperidinium spp. (7.74%), Alexandrium affine (7.05%), Scrippsiella trochoidea (6.67%), and Alexandrium pseudogonyaulax (6.19%). There is a positive correlation between the density of cysts and the depth (r = 0.61; p < 0.05), organic matter (r = 0.70; p < 0.05), water content (r = 0.71; p < 0.05), and the fine fraction of sediment (r = 0.74; p < 0.05). Surprisingly, although the Mellah Lagoon is almost semi-closed, it holds an important specific richness in dinocysts (42 species) higher than others observed in Mediterranean lagoons. However, cyst abundances are low compared to other lagoons in the Mediterranean Sea. Finally, the presence of dinocysts of Alexandrium catenella/tamarense, A. minutum, and Gymnodinium catenatum associated to paralytic shellfish toxins, A. pseudogonyaulax which produces goniodomin A, also Protoceratium reticulatum and Gonyaulax spinifera complex which produce yessotoxins, needs to implement a monitoring program to prevent a potential human intoxication due to the consumption of contaminated sea products by these potent neurotoxins.
Mots-Clés: alexandrium-catenella; bizerte lagoon; coastal waters; cochlodinium-polykrikoides; Dinoflagellate cysts; Diversity; Environmental factors; genus alexandrium; harmful algal blooms; Mellah lagoon; northwestern indian-ocean; resting cysts; Spatial distribution; spatial-distribution; surface sediments; Toxic species
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Grande, M., Murua, H., Zudaire, I., Arsenault-Pernet, E. J., Pernet, F., & Bodin, N. (2016). Energy allocation strategy of skipjack tuna Katsuwonus pelamis during their reproductive cycle. J. Fish Biol., 89(5), 2434–2448.
Résumé: The lipid composition of somatic and reproductive tissues was determined for female skipjack tuna Katsuwonus pelamis caught in the western Indian Ocean between latitude 10 degrees N and 20 degrees S and longitude 40 degrees and 70 degrees E. The highest total lipid (TL) contents were in the liver and gonads, with white muscle levels approximately three-fold lower. Three lipid classes dominated: triacylglycerols (TAG), sterol esters and wax esters (SE-WE) and phospholipids (PL). Collectively, these accounted for between 70 and 80% of TLs. Changes in lipid concentrations were evaluated over the maturation cycle. Immature fish had the lowest gonad and liver TL levels; concentrations of TL, TAG, SE-WE and PL accumulated from immature to mature (spawning-capable) phase, reflecting sustained vitellogenic activity of the liver and a transfer of lipids to developing oocytes from the onset of vitellogenesis. Gonado-somatic and hepato-somatic indices were positively correlated with each other and positively related to TL in the gonads and liver. Fulton's condition index and lipid concentrations in muscle did not vary significantly over the maturation cycle; fat content in the main storage tissues was undepleted as the ovary developed. Hence, K. pelamis apparently supports reproduction directly from food intake over the breeding season. In the gonads, reserve lipids (SE-WE and TAG) and sterols were related to batch fecundity but this was not the case for somatic and hepatic tissues. These results suggest that K. pelamis utilizes an income breeding strategy.
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Lopez, J., Moreno, G., Lennert-Cody, C., Maunder, M., Sancristobal, I., Caballero, A., et al. (2017). Environmental preferences of tuna and non-tuna species associated with drifting fish aggregating devices (DFADs) in the Atlantic Ocean, ascertained through fishers' echo-sounder buoys. Deep-Sea Res. Part II-Top. Stud. Oceanogr., 140, 127–138.
Résumé: Understanding the relationship between environmental variables and pelagic species concentrations and dynamics is helpful to improve fishery management, especially in a changing environment. Drifting fish aggregating device (DFAD)-associated tuna and non-tuna biomass data from the fishers' echo-sounder buoys operating in the Atlantic Ocean have been modelled as functions of oceanographic (Sea Surface Temperature, Chlorophyll-a, Salinity, Sea Level Anomaly, Thermocline depth and gradient, Geostrophic current, Total Current, Depth) and DFAD variables (DFAD speed, bearing and soak time) using Generalized Additive Mixed Models (GAMMs). Biological interaction (presence of non-tuna species at DFADs) was also included in the tuna model, and found to be significant at this time scale. All variables were included in the analyses but only some of them were highly significant, and variable significance differed among fish groups. In general, most of the fish biomass distribution was explained by the ocean productivity and DFAD-variables. Indeed, this study revealed different environmental preferences for tunas and non-tuna species and suggested the existence of active habitat selection. This improved assessment of environmental and DFAD effects on tuna and non-tuna catchability in the purse seine tuna fishery will contribute to transfer of better scientific advice to regional tuna commissions for the management and conservation of exploited resources.
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