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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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Avadi, A., Freon, P., & Quispe, I. (2014). Environmental assessment of Peruvian anchoveta food products : is less refined better ? International Journal of Life Cycle Assessment, 19(6), 1276–1293.
Résumé: Life cycle assessments (LCAs) of various anchovy (anchoveta) direct human consumption products processed in Peru were carried out, to evaluate their relative environmental performance as alternative products to enhance nutrition of communities with low access to fish products in the country. LCA was carried out for fresh, frozen, canned, salted and cured anchoveta products, both at plant gate and featuring local and national distribution over non-refrigerated, chilled and fully refrigerated distribution chain. The functional unit used was 1 kg of fish in the final product. Results demonstrate that, in environmental terms, more-refined products (cured and canned anchoveta products) represent a much higher burden than less- refined products (fresh, frozen and salted). Although this is a likely result, the magnitude of this difference (4 to 27 times when expressed as an environmental single score) is higher than expected and had not been quantified before for salted and cured products, as far as we know. This difference is mainly due to differences in energy consumption between types of products. Furthermore, cured and salted products feature larger biotic resource use, when calculated based on the whole fish equivalent, due to higher processing losses/discards. The relevance of taking into account the different transportation and storage needs is highlighted. For those products requiring refrigerated transportation and storage, over a national distribution chain, those activities increase the overall environmental impacts of the products by 55 % (fresh chilled) to 67 % (frozen). However, such an increase does not worsen the environmental performance of fresh and frozen products in comparison to the energy-intensive canned and cured products. It is concluded that a more sustainability-oriented analysis, including the social and economic pillars of sustainability, is required towards decision-making involving promotion of either product for addressing nutritional deficiencies in Peru.
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Avarre, J. - C., Guinand, B., Dugué, R., Cosson, J., Legendre, M., Panfili, J., et al. (2014). Plasticity of gene expression according to salinity in the testis of broodstock and F1 black-chinned tilapia, Sarotherodon melanotheron heudelotii. PeerJ, 2.
Résumé: The black-chinned tilapia Sarotherodon melanotheron heudelotii Rüppell 1852 (Teleostei, Cichlidae) displays remarkable acclimation capacities. When exposed to drastic changes of salinity, which can be the case in its natural habitat, it develops quick physiological responses and keeps reproducing. The present study focused on the physiological impact of salinity on male reproductive capacities, using gene expression as a proxy of acclimation process. Two series of experimental fish were investigated: the first one was composed of fish maintained in freshwater for several generations and newly acclimated to salinities of 35 and 70, whereas the second one consisted of the descendants of the latter born and were raised under their native salinity. Expression patterns of 43 candidate genes previously identified from the testes of wild males was investigated in the three salinities and two generations. Twenty of them showed significant expression differences between salinities, and their predicted function revealed that most of them are involved in the osmotic tolerance of sperm cells and/or in the maintenance of sperm motility. A high level of expression variation was evidenced, especially for fish maintained in freshwater. In spite of this, gene expression patterns allowed the differentiation between fish raised in freshwater and those maintained in hypersaline water in both generations. Altogether, the results presented here suggest that this high variability of expression is likely to ensure the reproductive success of this species under varying salinities.
Mots-Clés: Acclimation; fish; Gene expression; Male reproduction; salinity
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Ba, A., Chaboud, C., Schmidt, J., Diouf, M., Fall, M., Deme, M., et al. (2019). The potential impact of marine protected areas on the Senegalese sardinella fishery. Ocean Coastal Manage., 169, 239–246.
Résumé: In the early 2000s, Senegal set up several Marine Protected Areas (MPAs) along its coastal zone with the purpose of biodiversity conservation and to support sustainable management of fisheries. However, the impact of MPAs may vary according to the type of fisheries. In Senegal, the sardinella fishery accounts for 70% of total catches. This fishery is of crucial importance for national food security and employment. Given this importance, it is necessary to evaluate the impact of MPAs, often being considered as a tool for fisheries management. An analytical, dynamic and spatial bio-economic model of sardinella fishery, considering fish and fisher migration, has been developed and scenarios over forty years have been analyzed. The results show that the fishery is economically overexploited and that Senegal could lose about 11.6 billion CFA over forty years of exploitation, i.e. 290 million CFA per year. To achieve an optimal level of exploitation, it would be necessary to halve the current fishing capacity. Implementing MPAs for 10, 20 and 30% of the Senegalese exclusive economic zone lead to slight increases in biomass (1%) and rent (5-11%). In addition, spatio-temporal closures can lead to increased exploitation in unclosed areas, due to the absence of enforcement. Achieving target 11 of the Aichi Convention, i.e., 10% of coastal and marine areas protected per country, will have a reserve effect on the resource but also only lead to weak improvements in economic indicators for the Senegalese fishery. Finally, because the sardinella resource is shared among many countries of the Sub-Regional Fisheries Commission (SRFC), a sub-regional cooperation is necessary for a sustainable management.
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Ba, A., Schmidt, J., Deme, M., Lancker, K., Chaboud, C., Cury, P., et al. (2017). Profitability and economic drivers of small pelagic fisheries in West Africa: A twenty year perspective. Mar. Pol., 76, 152–158.
Résumé: Small pelagics are the main fish resource in North West Africa. In Senegal, these are mainly sardinellas (Sardinella aurita and S. maderensis) and bonga shad (Ethmalosa fimbriata). The fisheries, mainly encircling gillnets and purse seines, are predominantly performed by artisanal fishers and are of great importance for the Senegalese economy and for food security in the region. However, in recent years, the main conditions for these fisheries have changed and recent observations have shown strong declines in profit. An analysis over the last twenty years (1993-2013) show that the fisheries lost profit between 65% and 100% while operating costs increased by 25% and 90%, for encircling gillnet and purse seine, respectively. While the fuel price dominates as determining factor during the survey period, important other drivers during the last five years were a decrease in fish biomass and an increase in fishing effort.
Mots-Clés: Income; management; Senegal; small pelagic fish; Small scale fisheries
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