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Auteur (up) Meynard, C.N.; Kaplan, D.M.; Leroy, B. doi  openurl
  Titre Detecting outliers in species distribution data: Some caveats and clarifications on a virtual species study Type Article scientifique
  Année 2019 Publication Revue Abrégée J. Biogeogr.  
  Volume 46 Numéro 9 Pages 2141-2144  
  Mots-Clés enm; observation errors; outliers; prevalence; probabilistic approach; sample bias; simulations; species distribution models; thresholds; virtual ecology; virtual species  
  Résumé Liu et al. (2018) used a virtual species approach to test the effects of outliers on species distribution models. In their simulations, they applied a threshold value over the simulated suitabilities to generate the species distributions, suggesting that using a probabilistic simulation approach would have been more complex and yield the same results. Here, we argue that using a probabilistic approach is not necessarily more complex and may significantly change results. Although the threshold approach may be justified under limited circumstances, the probabilistic approach has multiple advantages. First, it is in line with ecological theory, which largely assumes non-threshold responses. Second, it is more general, as it includes the threshold as a limiting case. Third, it allows a better separation of the relevant intervening factors that influence model performance. Therefore, we argue that the probabilistic simulation approach should be used as a general standard in virtual species studies.  
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  ISSN 0305-0270 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2640  
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Auteur (up) Meynard, C.N.; Leroy, B.; Kaplan, D.M. url  doi
openurl 
  Titre Testing methods in species distribution modelling using virtual species: what have we learnt and what are we missing? Type Article scientifique
  Année 2019 Publication Revue Abrégée Ecography  
  Volume 42 Numéro 12 Pages 2021-2036  
  Mots-Clés artificial species; environmental niche models; niche; simulations; species distribution modelling; virtual ecologist  
  Résumé Species distribution models (SDMs) have become one of the major predictive tools in ecology. However, multiple methodological choices are required during the modelling process, some of which may have a large impact on forecasting results. In this context, virtual species, i.e. the use of simulations involving a fictitious species for which we have perfect knowledge of its occurrence–environment relationships and other relevant characteristics, have become increasingly popular to test SDMs. This approach provides for a simple virtual ecologist framework under which to test model properties, as well as the effects of the different methodological choices, and allows teasing out the effects of targeted factors with great certainty. This simplification is therefore very useful in setting up modelling standards and best practice principles. As a result, numerous virtual species studies have been published over the last decade. The topics covered include differences in performance between statistical models, effects of sample size, choice of threshold values, methods to generate pseudo-absences for presence-only data, among many others. These simulations have therefore already made a great contribution to setting best modelling practices in SDMs. Recent software developments have greatly facilitated the simulation of virtual species, with at least three different packages published to that effect. However, the simulation procedure has not been homogeneous, which introduces some subtleties in the interpretation of results, as well as differences across simulation packages. Here we 1) review the main contributions of the virtual species approach in the SDM literature; 2) compare the major virtual species simulation approaches and software packages; and 3) propose a set of recommendations for best simulation practices in future virtual species studies in the context of SDMs.  
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  ISSN 1600-0587 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2687  
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Auteur (up) Miller, M.J.; Bonhommeau, S.; Munk, P.; Castonguay, M.; Hanel, R.; McCleave, J.D. url  openurl
  Titre A century of research on the larval distributions of the Atlantic eels: a re-examination of the data Type Article scientifique
  Année 2014 Publication Revue Abrégée Biological Reviews  
  Volume Numéro Pages  
  Mots-Clés anguilla; freshwater eels; larval distribution; oceanic fronts.; Sargasso Sea; spawning area  
  Résumé The spawning areas of the Atlantic freshwater eels were discovered about a century ago by the Danish scientistJohannes Schmidt who after years of searching found newly hatched larvae of the European eel, Anguillaanguilla, and the American eel, Anguilla rostrata, in the southern Sargasso Sea. The discovery showed thatanguillid eels migrate thousands of kilometers to offshore spawning areas for reproduction, and that theirlarvae, called leptocephali, are transported equally long distances by ocean currents to their continentalrecruitment areas. The spawning sites were found to be related to oceanographic conditions several decadeslater by German and American surveys from 1979 to 1989 and by a Danish survey in 2007 and a Germansurvey in 2011. All these later surveys showed that spawning occurred within a restricted latitudinal range,between temperature fronts within the Subtropical Convergence Zone of the Sargasso Sea. New data andre-examinations of Schmidt’s data confirmed his original conclusions about the two species having someoverlap in spawning areas. Although there have been additional collections of leptocephali in various parts ofthe North Atlantic, and both otolith research and transport modelling studies have subsequently been carriedout, there is still a range of unresolved questions about the routes of larval transport and durations of migration.This paper reviews the history and basic findings of surveys for anguillid leptocephali in the North Atlantic andanalyses a new comprehensive database that includes 22612 A. anguilla and 9634 A. rostrata leptocephali, whichprovides a detailed view of the spatial and temporal distributions and size of the larvae across the Atlantic basinand in the Mediterranean Sea. The differences in distributions, maximum sizes, and growth rates of the twospecies of larvae are likely linked to the contrasting migration distances to their recruitment areas on eachside of the basin. Anguilla rostrata leptocephali originate from a more western spawning area, grow faster, andmetamorphose at smaller sizes of <70mm than the larvae of A. anguilla, which mostly are spawned further eastand can reach sizes of almost 90 mm. The larvae of A. rostrata spread west and northwest from the spawningarea as they grow larger, with some being present in the western Caribbean and eastern Gulf of Mexico. Larvaeof A. anguilla appear to be able to reach Europe by entering the Gulf Stream system or by being entrainedinto frontal countercurrents that transport them directly northeastward. The larval duration of A. anguillais suggested to be quite variable, but gaps in sampling effort prevent firm conclusions. Although knowledgeabout larval behaviour is lacking, some influences of directional swimming are implicated by the temporaldistributions of the largest larvae. Ocean–atmosphere changes have been hypothesized to affect the survivalof the larvae and cause reduced recruitment, so even after about a century following the discovery of theirspawning areas, mysteries still remain about the marine life histories of the Atlantic eels.  
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  ISSN 1464-7931 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1125  
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Auteur (up) Morato, T.; Gonzalez-Irusta, J.-M.; Dominguez-Carrio, C.; Wei, C.-L.; Davies, A.; Sweetman, A.K.; Taranto, G.H.; Beazley, L.; Garcia-Alegre, A.; Grehan, A.; Laffargue, P.; Murillo, F.J.; Sacau, M.; Vaz, S.; Kenchington, E.; Arnaud-Haond, S.; Callery, O.; Chimienti, G.; Cordes, E.; Egilsdottir, H.; Freiwald, A.; Gasbarro, R.; Gutierrez-Zarate, C.; Gianni, M.; Gilkinson, K.; Wareham Hayes, V.E.; Hebbeln, D.; Hedges, K.; Henry, L.-A.; Johnson, D.; Koen-Alonso, M.; Lirette, C.; Mastrototaro, F.; Menot, L.; Molodtsova, T.; Duran Munoz, P.; Orejas, C.; Pennino, M.G.; Puerta, P.; Ragnarsson, S. a; Ramiro-Sanchez, B.; Rice, J.; Rivera, J.; Roberts, J.M.; Ross, S.W.; Rueda, J.L.; Sampaio, I.; Snelgrove, P.; Stirling, D.; Treble, M.A.; Urra, J.; Vad, J.; van Oevelen, D.; Watling, L.; Walkusz, W.; Wienberg, C.; Woillez, M.; Levin, L.A.; Carreiro-Silva, M. doi  openurl
  Titre Climate-induced changes in the suitable habitat of cold-water corals and commercially important deep-sea fishes in the North Atlantic Type Article scientifique
  Année 2020 Publication Revue Abrégée Glob. Change Biol.  
  Volume Numéro Pages  
  Mots-Clés calcification rates; climate change; cod gadus-morhua; cold-water corals; deep-sea; envelope models; fisheries; fishes; habitat suitability modelling; lophelia-pertusa; ocean acidification; octocorals; protected areas; scleractinian corals; scleractinians; species distribution models; species distribution models; thermal tolerance; vulnerable marine ecosystems  
  Résumé The deep sea plays a critical role in global climate regulation through uptake and storage of heat and carbon dioxide. However, this regulating service causes warming, acidification and deoxygenation of deep waters, leading to decreased food availability at the seafloor. These changes and their projections are likely to affect productivity, biodiversity and distributions of deep-sea fauna, thereby compromising key ecosystem services. Understanding how climate change can lead to shifts in deep-sea species distributions is critically important in developing management measures. We used environmental niche modelling along with the best available species occurrence data and environmental parameters to model habitat suitability for key cold-water coral and commercially important deep-sea fish species under present-day (1951-2000) environmental conditions and to project changes under severe, high emissions future (2081-2100) climate projections (RCP8.5 scenario) for the North Atlantic Ocean. Our models projected a decrease of 28%-100% in suitable habitat for cold-water corals and a shift in suitable habitat for deep-sea fishes of 2.0 degrees-9.9 degrees towards higher latitudes. The largest reductions in suitable habitat were projected for the scleractinian coral Lophelia pertusa and the octocoral Paragorgia arborea, with declines of at least 79% and 99% respectively. We projected the expansion of suitable habitat by 2100 only for the fishes Helicolenus dactylopterus and Sebastes mentella (20%-30%), mostly through northern latitudinal range expansion. Our results projected limited climate refugia locations in the North Atlantic by 2100 for scleractinian corals (30%-42% of present-day suitable habitat), even smaller refugia locations for the octocorals Acanella arbuscula and Acanthogorgia armata (6%-14%), and almost no refugia for P. arborea. Our results emphasize the need to understand how anticipated climate change will affect the distribution of deep-sea species including commercially important fishes and foundation species, and highlight the importance of identifying and preserving climate refugia for a range of area-based planning and management tools.  
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  Volume de collection Numéro de collection Edition  
  ISSN 1354-1013 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2752  
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Auteur (up) Ottimofiore, E.; Albouy, C.; Leprieur, F.; Descombes, P.; Kulbicki, M.; Mouillot, D.; Parravicini, V.; Pellissier, L. doi  openurl
  Titre Responses of coral reef fishes to past climate changes are related to life-history traits Type Article scientifique
  Année 2017 Publication Revue Abrégée Ecol. Evol.  
  Volume 7 Numéro 6 Pages 1996-2005  
  Mots-Clés climate change; dispersal; diversity; environmental-change; future; global patterns; Indo-Pacific Ocean; range shifts; refugia; richness; sea-level; species distribution; species distribution models; temperature  
  Résumé Coral reefs and their associated fauna are largely impacted by ongoing climate change. Unravelling species responses to past climatic variations might provide clues on the consequence of ongoing changes. Here, we tested the relationship between changes in sea surface temperature and sea levels during the Quaternary and present-day distributions of coral reef fish species. We investigated whether species-specific responses are associated with life-history traits. We collected a database of coral reef fish distribution together with life-history traits for the Indo-Pacific Ocean. We ran species distribution models (SDMs) on 3,725 tropical reef fish species using contemporary environmental factors together with a variable describing isolation from stable coral reef areas during the Quaternary. We quantified the variance explained independently by isolation from stable areas in the SDMs and related it to a set of species traits including body size and mobility. The variance purely explained by isolation from stable coral reef areas on the distribution of extant coral reef fish species largely varied across species. We observed a triangular relationship between the contribution of isolation from stable areas in the SDMs and body size. Species, whose distribution is more associated with historical changes, occurred predominantly in the Indo-Australian archipelago, where the mean size of fish assemblages is the lowest. Our results suggest that the legacy of habitat changes of the Quaternary is still detectable in the extant distribution of many fish species, especially those with small body size and the most sedentary. Because they were the least able to colonize distant habitats in the past, fish species with smaller body size might have the most pronounced lags in tracking ongoing climate change.  
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  ISSN 2045-7758 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2108  
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