|   | 
Détails
   web
Enregistrements
Auteur Authier, M.; Saraux, C.; Péron, C.
Titre Variable selection and accurate predictions in habitat modelling: a shrinkage approach Type Article scientifique
Année 2017 Publication Revue Abrégée Ecography
Volume (down) 40 Numéro 4 Pages 549-560
Mots-Clés account; distributional data; Ecology; indian-ocean; inference; Mediterranean Sea; regression methods; small pelagic fish; spatial autocorrelation; species distribution models
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.
Adresse
Auteur institutionnel Thèse
Editeur Lieu de Publication Éditeur
Langue English Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 0906-7590 ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ alain.herve @ collection 2130
Lien permanent pour cet enregistrement
 

 
Auteur Cazelles, K.; Mouquet, N.; Mouillot, D.; Gravel, D.
Titre On the integration of biotic interaction and environmental constraints at the biogeographical scale Type Article scientifique
Année 2016 Publication Revue Abrégée Ecography
Volume (down) 39 Numéro 10 Pages 921-931
Mots-Clés biodiversity; climate-change; cooccurrence; distributions; ecological communities; evolutionary; food webs; networks; niche; species distribution models
Résumé Biogeography is primarily concerned with the spatial distribution of biodiversity, including performing scenarios in a changing environment. The efforts deployed to develop species distribution models have resulted in predictive tools, but have mostly remained correlative and have largely ignored biotic interactions. Here we build upon the theory of island biogeography as a first approximation to the assembly dynamics of local communities embedded within a metacommunity context. We include all types of interactions and introduce environmental constraints on colonization and extinction dynamics. We develop a probabilistic framework based on Markov chains and derive probabilities for the realization of species assemblages, rather than single species occurrences. We consider the expected distribution of species richness under different types of ecological interactions. We also illustrate the potential of our framework by studying the interplay between different ecological requirements, interactions and the distribution of biodiversity along an environmental gradient. Our framework supports the idea that the future research in biogeography requires a coherent integration of several ecological concepts into a single theory in order to perform conceptual and methodological innovations, such as the switch from single-species distribution to community distribution.
Adresse
Auteur institutionnel Thèse
Editeur Lieu de Publication Éditeur
Langue English Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 0906-7590 ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ alain.herve @ collection 1683
Lien permanent pour cet enregistrement
 

 
Auteur Yates, K.L.; Bouchet, P.J.; Caley, M.J.; Mengersen, K.; Randin, C.F.; Parnell, S.; Fielding, A.H.; Bamford, A.J.; Ban, S.; Marcia Barbosa, A.; Dormann, C.F.; Elith, J.; Embling, C.B.; Ervin, G.N.; Fisher, R.; Gould, S.; Graf, R.F.; Gregr, E.J.; Halpin, P.N.; Heikkinen, R.K.; Heinanen, S.; Jones, A.R.; Krishnakumar, P.K.; Lauria, V.; Lozano-Montes, H.; Mannocci, L.; Mellin, C.; Mesgaran, M.B.; Moreno-Amat, E.; Mormede, S.; Novaczek, E.; Oppel, S.; Crespo, G.O.; Peterson, A.T.; Rapacciuolo, G.; Roberts, J.J.; Ross, R.E.; Scales, K.L.; Schoeman, D.; Snelgrove, P.; Sundblad, G.; Thuiller, W.; Torres, L.G.; Verbruggen, H.; Wang, L.; Wenger, S.; Whittingham, M.J.; Zharikov, Y.; Zurell, D.; Sequeira, A.M.M.
Titre Outstanding Challenges in the Transferability of Ecological Models Type Article scientifique
Année 2018 Publication Revue Abrégée Trends Ecol. Evol.
Volume (down) 33 Numéro 10 Pages 790-802
Mots-Clés abundance; biotic interactions; climate-change; decision-making; distributions; habitat selection; niche; predictive models; species distribution models; temporal transferability
Résumé Predictive models are central to many scientific disciplines and vital for informing management in a rapidly changing world. However, limited understanding of the accuracy and precision of models transferred to novel conditions (their 'transferability') undermines confidence in their predictions. Here, 50 experts identified priority knowledge gaps which, if filled, will most improve model transfers. These are summarized into six technical and six fundamental challenges, which underlie the combined need to intensify research on the determinants of ecological predictability, including species traits and data quality, and develop best practices for transferring models. Of high importance is the identification of a widely applicable set of transferability metrics, with appropriate tools to quantify the sources and impacts of prediction uncertainty under novel conditions.
Adresse
Auteur institutionnel Thèse
Editeur Lieu de Publication Éditeur
Langue English Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 0169-5347 ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ alain.herve @ collection 2447
Lien permanent pour cet enregistrement
 

 
Auteur Stephenson, F.; Goetz, K.; Sharp, B.R.; Mouton, T.L.; Beets, F.L.; Roberts, J.; MacDiarmid, A.B.; Constantine, R.; Lundquist, C.J.
Titre Modelling the spatial distribution of cetaceans in New Zealand waters Type Article scientifique
Année 2020 Publication Revue Abrégée Diversity and Distributions
Volume (down) 26 Numéro 4 Pages 495-516
Mots-Clés boosted regression tree models; cetacean distribution; New Zealand; relative environmental suitability models; spatial management; species distribution models
Résumé Aim Cetaceans are inherently difficult to study due to their elusive, pelagic and often highly migratory nature. New Zealand waters are home to 50% of the world's cetacean species, but their spatial distributions are poorly known. Here, we model distributions of 30 cetacean taxa using an extensive at-sea sightings dataset (n > 14,000) and high-resolution (1 km2) environmental data layers. Location New Zealand's Exclusive Economic Zone (EEZ). Methods Two models were used to predict probability of species occurrence based on available sightings records. For taxa with <50 sightings (n = 15), Relative Environmental Suitability (RES), and for taxa with ≥50 sightings (n = 15), Boosted Regression Tree (BRT) models were used. Independently collected presence/absence data were used for further model evaluation for a subset of taxa. Results RES models for rarely sighted species showed reasonable fits to available sightings and stranding data based on literature and expert knowledge on the species' autecology. BRT models showed high predictive power for commonly sighted species (AUC: 0.79–0.99). Important variables for predicting the occurrence of cetacean taxa were temperature residuals, bathymetry, distance to the 500 m isobath, mixed layer depth and water turbidity. Cetacean distribution patterns varied from highly localised, nearshore (e.g., Hector's dolphin), to more ubiquitous (e.g., common dolphin) to primarily offshore species (e.g., blue whale). Cetacean richness based on stacked species occurrence layers illustrated patterns of fewer inshore taxa with localised richness hotspots, and higher offshore richness especially in locales of the Macquarie Ridge, Bounty Trough and Chatham Rise. Main conclusions Predicted spatial distributions fill a major knowledge gap towards informing future assessments and conservation planning for cetaceans in New Zealand's extensive EEZ. While sightings datasets were not spatially comprehensive for any taxa, these two best available approaches allow for predictive modelling of both more common, and of rarely sighted, cetacean species with limited available information.
Adresse
Auteur institutionnel Thèse
Editeur Lieu de Publication Éditeur
Langue en Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 1472-4642 ISBN Médium
Région Expédition Conférence
Notes WOS:000510589200001 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2692
Lien permanent pour cet enregistrement
 

 
Auteur Mannocci, L.; Roberts, J.J.; Halpin, P.N.; Authier, M.; Boisseau, O.; Bradai, M.N.; Canadas, A.; Chicote, C.; David, L.; Di-Meglio, N.; Fortuna, C.M.; Frantzis, A.; Gazo, M.; Genov, T.; Hammond, P.S.; Holcer, D.; Kaschner, K.; Kerem, D.; Lauriano, G.; Lewis, T.; di Sciara, G.N.; Panigada, S.; Antonio Raga, J.; Scheinin, A.; Ridoux, V.; Vella, A.; Vella, J.
Titre Assessing cetacean surveys throughout the Mediterranean Sea: a gap analysis in environmental space Type Article scientifique
Année 2018 Publication Revue Abrégée Sci Rep
Volume (down) 8 Numéro Pages 3126
Mots-Clés species distribution models; tursiops-truncatus; population-structure; sperm-whales; bottle-nosed dolphins; fin whales; habitat preference; pelagos sanctuary; seasonal distribution; whales balaenoptera-physalus
Résumé Heterogeneous data collection in the marine environment has led to large gaps in our knowledge of marine species distributions. To fill these gaps, models calibrated on existing data may be used to predict species distributions in unsampled areas, given that available data are sufficiently representative. Our objective was to evaluate the feasibility of mapping cetacean densities across the entire Mediterranean Sea using models calibrated on available survey data and various environmental covariates. We aggregated 302,481 km of line transect survey effort conducted in the Mediterranean Sea within the past 20 years by many organisations. Survey coverage was highly heterogeneous geographically and seasonally: large data gaps were present in the eastern and southern Mediterranean and in non-summer months. We mapped the extent of interpolation versus extrapolation and the proportion of data nearby in environmental space when models calibrated on existing survey data were used for prediction across the entire Mediterranean Sea. Using model predictions to map cetacean densities in the eastern and southern Mediterranean, characterised by warmer, less productive waters, and more intense eddy activity, would lead to potentially unreliable extrapolations. We stress the need for systematic surveys of cetaceans in these environmentally unique Mediterranean waters, particularly in non-summer months.
Adresse
Auteur institutionnel Thèse
Editeur Lieu de Publication Éditeur
Langue English Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 2045-2322 ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ alain.herve @ collection 2312
Lien permanent pour cet enregistrement