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Auteur Matthews, T.J.; Triantis, K.A.; Whittaker, R.J.; Guilhaumon, F.
Titre sars: an R package for fitting, evaluating and comparing species-area relationship models Type Article scientifique
Année 2019 Publication Revue Abrégée Ecography
Volume 42 Numéro 8 Pages 1446-1455
Mots-Clés (up) accumulation; curves; diversity; diversity-area relationship; island biogeography; islands; richness; species-area relationship
Résumé The species-area relationship (SAR) constitutes one of the most general ecological patterns globally. A number of different SAR models have been proposed. Recent work has shown that no single model universally provides the best fit to empirical SAR datasets: multiple models may be of practical and theoretical interest. However, there are no software packages available that a) allow users to fit the full range of published SAR models, or b) provide functions to undertake a range of additional SAR-related analyses. To address these needs, we have developed the R package 'sars' that provides a wide variety of SAR-related functionality. The package provides functions to: a) fit 20 SAR models using non-linear and linear regression, b) calculate multi-model averaged curves using various information criteria, and c) generate confidence intervals using bootstrapping. Plotting functions allow users to depict and scrutinize the fits of individual models and multi-model averaged curves. The package also provides additional SAR functionality, including functions to fit, plot and evaluate the random placement model using a species-sites abundance matrix, and to fit the general dynamic model of oceanic island biogeography. The 'sars' R package will aid future SAR research by providing a comprehensive set of simple to use tools that enable in-depth exploration of SARs and SAR-related patterns. The package has been designed to allow other researchers to add new functions and models in the future and thus the package represents a resource for future SAR work that can be built on and expanded by workers in the field.
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ISSN 0906-7590 ISBN Médium
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Notes WOS:000477975800010 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2625
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Auteur Leroy, B.; Dias, M.S.; Giraud, E.; Hugueny, B.; Jezequel, C.; Leprieur, F.; Oberdorff, T.; Tedesco, P.A.
Titre Global biogeographical regions of freshwater fish species Type Article scientifique
Année 2019 Publication Revue Abrégée J. Biogeogr.
Volume Numéro Pages
Mots-Clés (up) actinopterygians; biogeographical regions; biogeography; bioregionalization; bioregions; connectivity; dispersal; diversity; evolution; freshwater fish; history; homogenization; network; patterns; richness; transition zones; vicariance; world; zoogeographical regions
Résumé Aim To define the major biogeographical regions and transition zones for freshwater fish species. Taxon Strictly freshwater species of actinopterygian fish (i.e. excluding marine and amphidromous fish families). Methods We based our bioregionalization on a global database of freshwater fish species occurrences in drainage basins, which, after filtering, includes 11,295 species in 2,581 basins. On the basis of this dataset, we generated a bipartite (basin-species) network upon which we applied a hierarchical clustering algorithm (the Map Equation) to detect regions. We tested the robustness of regions with a sensitivity analysis. We identified transition zones between major regions with the participation coefficient, indicating the degree to which a basin has species from multiple regions. Results Our bioregionalization scheme showed two major supercontinental regions (Old World and New World, 50% species of the world and 99.96% endemics each). Nested within these two supercontinental regions lie six major regions (Nearctic, Neotropical, Palearctic, Ethiopian, Sino-Oriental and Australian) with extremely high degrees of endemism (above 96% except for the Palearctic). Transition zones between regions were of limited extent compared to other groups of organisms. We identified numerous subregions with high diversity and endemism in tropical areas (e.g. Neotropical), and a few large subregions with low diversity and endemism at high latitudes (e.g. Palearctic). Main conclusions Our results suggest that regions of freshwater fish species were shaped by events of vicariance and geodispersal which were similar to other groups, but with freshwater-specific processes of isolation that led to extremely high degrees of endemism (far exceeding endemism rates of other continental vertebrates), specific boundary locations and limited extents of transition zones. The identified bioregions and transition zones of freshwater fish species reflect the strong isolation of freshwater fish faunas for the past 10-20 million years. The extremely high endemism and diversity of freshwater fish fauna raises many questions about the biogeographical consequences of current introductions and extinctions.
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Volume de collection Numéro de collection Edition
ISSN 0305-0270 ISBN Médium
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Notes WOS:000484392300001 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2637
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Auteur Hill, S.L.; Hinke, J.; Bertrand, S.; Fritz, L.; Furness, R.W.; Ianelli, J.N.; Murphy, M.; Oliveros‐Ramos, R.; Pichegru, L.; Sharp, R.; Stillman, R.A.; Wright, P.J.; Ratcliffe, N.
Titre Reference points for predators will progress ecosystem-based management of fisheries Type Article scientifique
Année 2020 Publication Revue Abrégée Fish and Fisheries
Volume 21 Numéro 2 Pages 368-378
Mots-Clés (up) adaptive management; Aichi Biodiversity Targets; ecosystem interactions; indirect impacts; management strategy; precautionary approach
Résumé Ecosystem-based management of fisheries aims to allow sustainable use of fished stocks while keeping impacts upon ecosystems within safe ecological limits. Both the FAO Code of Conduct for Responsible Fisheries and the Aichi Biodiversity Targets promote these aims. We evaluate implementation of ecosystem-based management in six case-study fisheries in which potential indirect impacts upon bird or mammal predators of fished stocks are well publicized and well studied. In particular, we consider the components needed to enable management strategies to respond to information from predator monitoring. Although such information is available in all case-studies, only one has a reference point defining safe ecological limits for predators and none has a method to adjust fishing activities in response to estimates of the state of the predator population. Reference points for predators have been developed outside the fisheries management context, but adoption by fisheries managers is hindered a lack of clarity about management objectives and uncertainty about how fishing affects predator dynamics. This also hinders the development of adjustment methods because these generally require information on the state of ecosystem variables relative to reference points. Nonetheless, most of the case-studies include precautionary measures to limit impacts on predators. These measures are not used tactically and therefore risk excessive restrictions on sustainable use. Adoption of predator reference points to inform tactical adjustment of precautionary measures would be an appropriate next step towards ecosystem-based management.
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Volume de collection Numéro de collection Edition
ISSN 1467-2979 ISBN Médium
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Notes WOS:000505754400001 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2684
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Auteur Jousset, A.; Eisenhauer, N.; Merker, M.; Mouquet, N.; Scheu, S.
Titre High functional diversity stimulates diversification in experimental microbial communities Type Article scientifique
Année 2016 Publication Revue Abrégée Sci. Adv.
Volume 2 Numéro 6 Pages e1600124
Mots-Clés (up) adaptive radiation; biodiversity; competition; evolution; phase variation; pseudomonas-fluorescens; recombination; root colonization; selection; soil
Résumé There is a growing awareness that biodiversity not only drives ecosystem services but also affects evolutionary dynamics. However, different theories predict contrasting outcomes on when do evolutionary processes occur within a context of competition. We tested whether functional diversity can explain diversification patterns. We tracked the survival and diversification of a focal bacterial species (Pseudomonas fluorescens) growing in bacterial communities of variable diversity and composition. We found that high functional diversity reduced the fitness of the focal species and, at the same time, fostered its diversification. This pattern was linked to resource competition: High diversity increased competition on a portion of the resources while leaving most underexploited. The evolved phenotypes of the focal species showed a better use of underexploited resources, albeit at a cost of lower overall growth rates. As a result, diversification alleviated the impact of competition on the fitness of the focal species. We conclude that biodiversity can stimulate evolutionary diversification, provided that sufficient alternative niches are available.
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Volume de collection Numéro de collection Edition
ISSN 2375-2548 ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 1649
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Auteur Calcagno, V.; Jarne, P.; Loreau, M.; Mouquet, N.; David, P.
Titre Diversity spurs diversification in ecological communities Type Article scientifique
Année 2017 Publication Revue Abrégée Nat. Commun.
Volume 8 Numéro Pages 15810
Mots-Clés (up) adaptive radiations; biodiversity; colonization; competition; drive speciation; evolutionary emergence; limiting similarity; stability; sympatric speciation; trade-off
Résumé Diversity is a fundamental, yet threatened, property of ecological systems. The idea that diversity can itself favour diversification, in an autocatalytic process, is very appealing but remains controversial. Here, we study a generalized model of ecological communities and investigate how the level of initial diversity influences the possibility of evolutionary diversification. We show that even simple models of intra- and inter-specific ecological interactions can predict a positive effect of diversity on diversification: adaptive radiations may require a threshold number of species before kicking-off. We call this phenomenon DDAR (diversity-dependent adaptive radiations) and identify mathematically two distinct pathways connecting diversity to diversification, involving character displacement and the positive diversity-productivity relationship. Our results may explain observed delays in adaptive radiations at the macroscale and diversification patterns reported in experimental microbial communities, and shed new light on the dynamics of ecological diversity, the diversity-dependence of diversification rates, and the consequences of biodiversity loss.
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Volume de collection Numéro de collection Edition
ISSN 2041-1723 ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 2148
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