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Auteur (up) Ben Rais Lasram, F.; Hattab, T.; Nogues, Q.; Beaugrand, G.; Dauvin, J.C.; Halouani, G.; Le Loc'h, F.; Niquil, N.; Leroy, B.
Titre An open-source framework to model present and future marine species distributions at local scale Type Article scientifique
Année 2020 Publication Revue Abrégée Ecological Informatics
Volume 59 Numéro Pages 101130
Mots-Clés Automated modelling framework; Bioclimatic envelope models; Future projections; Habitat models; Pseudo-absences; Vertical gradient
Résumé Species Distribution Models (SDMs) are useful tools to project potential future species distributions under climate change scenarios. Despite the ability to run SDMs in recent and reliable tools, there are some misuses and proxies that are widely practiced and rarely addressed together, particularly when dealing with marine species. In this paper, we propose an open-source framework that includes (i) a procedure for homogenizing occurrence data to reduce the influence of sampling bias, (ii) a procedure for generating pseudo-absences, (iii) a hierarchical-filter approach, (iv) full incorporation of the third dimension by considering climatic variables at multiple depths and (v) building of maps that predict current and potential future ranges of marine species. This framework is available for non-modeller ecologists interested in investigating future species ranges with a user-friendly script. We investigated the robustness of the framework by applying it to marine species of the Eastern English Channel. Projections were built for the middle and the end of this century under RCP2.6 and RCP8.5 scenarios.
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ISSN 1574-9541 ISBN Médium
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Notes WOS:000564618700007 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2811
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Auteur (up) Benedetti, F.; Ayata, S.-D.; Irisson, J.-O.; Adloff, F.; Guilhaumon, F.
Titre Climate change may have minor impact on zooplankton functional diversity in the Mediterranean Sea Type Article scientifique
Année 2019 Publication Revue Abrégée Divers. Distrib.
Volume 25 Numéro 4 Pages 568-581
Mots-Clés biogeography; calanus-helgolandicus; climate change; communities; conservation; fish assemblages; framework; functional diversity; future; marine biodiversity; Mediterranean Sea; niche modelling; null model; ocean; trait; zooplankton
Résumé Aim To assess the impact of climate change on the functional diversity of marine zooplankton communities. Location The Mediterranean Sea. Methods We used the functional traits and geographic distributions of 106 copepod species to estimate the zooplankton functional diversity of Mediterranean surface assemblages for the 1965-1994 and 2069-2098 periods. Multiple environmental niche models were trained at the global scale to project the species habitat suitability in the Mediterranean Sea and assess their sensitivity to climate change predicted by several scenarios. Simultaneously, the species traits were used to compute a functional dendrogram from which we identified seven functional groups and estimated functional diversity through Faith's index. We compared the measured functional diversity to the one originated from null models to test if changes in functional diversity were solely driven by changes in species richness. Results All but three of the 106 species presented range contractions of varying intensity. A relatively low decrease of species richness (-7.42 on average) is predicted for 97% of the basin, with higher losses in the eastern regions. Relative sensitivity to climate change is not clustered in functional space and does not significantly vary across the seven copepod functional groups defined. Changes in functional diversity follow the same pattern and are not different from those that can be expected from changes in richness alone. Main conclusions Climate change is not expected to alter copepod functional traits distribution in the Mediterranean Sea, as the most and the least sensitive species are functionally redundant. Such redundancy should buffer the loss of ecosystem functions in Mediterranean zooplankton assemblages induced by climate change. Because the most negatively impacted species are affiliated to temperate regimes and share Atlantic biogeographic origins, our results are in line with the hypothesis of increasingly more tropical Mediterranean communities.
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Volume de collection Numéro de collection Edition
ISSN 1366-9516 ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2582
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Auteur (up) Bryndum‐Buchholz, A.; Tittensor, D.P.; Blanchard, J.L.; Cheung, W.W.L.; Coll, M.; Galbraith, E.D.; Jennings, S.; Maury, O.; Lotze, H.K.
Titre Twenty-first-century climate change impacts on marine animal biomass and ecosystem structure across ocean basins Type Article scientifique
Année 2019 Publication Revue Abrégée Global Change Biology
Volume 25 Numéro 2 Pages 459-472
Mots-Clés climate change; ensemble modeling; future projection; marine animal biomass; marine ecosystem models; model intercomparison; ocean basins; uncertainty
Résumé Climate change effects on marine ecosystems include impacts on primary production, ocean temperature, species distributions, and abundance at local to global scales. These changes will significantly alter marine ecosystem structure and function with associated socio-economic impacts on ecosystem services, marine fisheries, and fishery-dependent societies. Yet how these changes may play out among ocean basins over the 21st century remains unclear, with most projections coming from single ecosystem models that do not adequately capture the range of model uncertainty. We address this by using six marine ecosystem models within the Fisheries and Marine Ecosystem Model Intercomparison Project (Fish-MIP) to analyze responses of marine animal biomass in all major ocean basins to contrasting climate change scenarios. Under a high emissions scenario (RCP8.5), total marine animal biomass declined by an ensemble mean of 15%–30% (±12%–17%) in the North and South Atlantic and Pacific, and the Indian Ocean by 2100, whereas polar ocean basins experienced a 20%–80% (±35%–200%) increase. Uncertainty and model disagreement were greatest in the Arctic and smallest in the South Pacific Ocean. Projected changes were reduced under a low (RCP2.6) emissions scenario. Under RCP2.6 and RCP8.5, biomass projections were highly correlated with changes in net primary production and negatively correlated with projected sea surface temperature increases across all ocean basins except the polar oceans. Ecosystem structure was projected to shift as animal biomass concentrated in different size-classes across ocean basins and emissions scenarios. We highlight that climate change mitigation measures could moderate the impacts on marine animal biomass by reducing biomass declines in the Pacific, Atlantic, and Indian Ocean basins. The range of individual model projections emphasizes the importance of using an ensemble approach in assessing uncertainty of future change.
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Volume de collection Numéro de collection Edition
ISSN 1365-2486 ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2457
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Auteur (up) Marques, V.; Guerin, P.-E.; Rocle, M.; Valentini, A.; Manel, S.; Mouillot, D.; Dejean, T.
Titre Blind assessment of vertebrate taxonomic diversity across spatial scales by clustering environmental DNA metabarcoding sequences Type Article scientifique
Année 2020 Publication Revue Abrégée Ecography
Volume Numéro Pages
Mots-Clés 12S primer; alpha-beta-delta-diversity; biodiversity change; clustering; edna; future; identification; marine; metabarcoding; MOTUs; rare biosphere; reference database
Résumé Human activities impact all ecosystems on Earth, which urges scientists to better understand biodiversity changes across temporal and spatial scales. Environmental DNA (eDNA) metabarcoding is a promising non-invasive method to assess species composition in a wide range of ecosystems. Yet, this method requires the completeness of a reference database, i.e. a list of DNA sequences attached to each species of the regional pool, which is rarely met. As an alternative, molecular operational taxonomic units (MOTUs) can be extracted as clusters of sequences. However, the extent to which the diversity of MOTUs can predict the diversity of species across spatial scales is unknown. Here, we used 196 samples along the Rhone river (France) for which the reference database is complete to assess whether a blind eDNA approach can reliably predict the ground-truth number of species at different spatial scales. Using the 12S rDNA teleo primer, we curated and clustered 60 million sequences into MOTUs using a new assembled bioinformatic pipeline. We show that stringent quality filters were necessary to remove artefact noise, notably MOTUs present in a single PCR replicate, which represented 55% of MOTUs (103). Post-clustering cleaning also removed 19 additional erroneous MOTUs and only discarded one truly present species. We then show that the diversity of retained fish MOTUs accurately predicted the local (alpha, r = 0.98) and regional (gamma) ground-truth species diversity (67 MOTUs versus 63 species), but also the species dissimilarity between samples (beta-diversity, r = 0.98). This work paves the way towards extending the use of eDNA metabarcoding in community ecology and biogeography despite major gaps in genetic reference databases.
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Volume de collection Numéro de collection Edition
ISSN 0906-7590 ISBN Médium
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Notes WOS:000555293900001 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2849
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Auteur (up) Oikonomou, A.; Leprieur, F.; Leonardos, I.D.
Titre Ecomorphological diversity of freshwater fishes as a tool for conservation priority setting: a case study from a Balkan hotspot Type Article scientifique
Année 2018 Publication Revue Abrégée Environ. Biol. Fishes
Volume 101 Numéro 7 Pages 1121-1136
Mots-Clés assemblages; Balkan peninsula; communities; Conservation; Ecomorphology; environmental-factors; Freshwater fishes; functional diversity; future challenges; habitat gradients; life-history strategies; Originality; species richness; stream; traits
Résumé Biodiversity studies commonly focus on taxonomic diversity measures such as species richness and abundance. However, alternative measures based on ecomorphological traits are also critical for unveiling the processes shaping biodiversity and community assembly along environmental gradients. Our study presents the first analysis of habitat-trait-community structure in a Balkan biodiversity hotspot (Louros river, NW Greece), through the investigation of the relationships among freshwater fish assemblages' composition, morphological traits and habitat features. In order to provide a hierarchical classification of species' priority to protection measures, we highlight the most ecomorphologically distinct species using originality analysis. Our results suggest that the longitudinal changes of habitat variables (water temperature, depth, substrate, altitude) drive the local fish assemblages' structure highlighting the upstream-downstream gradient. We also present evidence for environmental filtering, establishing fish assemblages according to their ecomorphological traits. The calculation of the seven available indices of ecomorphological originality indicates that Valencia letourneuxi and Cobitis hellenica, which are endemic to Louros and threatened with extinction, exhibited the highest distinctiveness; thus their protection is of great importance. The methodological approach followed and the patterns described herein can contribute further to the application of community ecology theory to conservation, highlighting the need to use ecomorphological traits as a useful 'tool'.
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ISSN 0378-1909 ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 2379
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