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Auteur 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 Ecol. Inform.
Volume 59 Numéro Pages 101130
Mots-Clés Automated modelling framework; Bioclimatic envelope models; biodiversity; climate-change; ecosystems; english-channel; fishes; Future projections; Habitat models; impacts; patterns; platform; Pseudo-absences; suitability; Vertical gradient; web
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 userfriendly 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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Langue English Langue du Résumé Titre Original
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Volume de collection Numéro de collection Edition
ISSN 1574-9541 ISBN Médium
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Notes WOS:000564618700007 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection (down) 2869
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Auteur Arnaud-Haond, S.; Stoeckel, S.; Bailleul, D.
Titre New insights into the population genetics of partially clonal organisms: When seagrass data meet theoretical expectations Type Article scientifique
Année 2020 Publication Revue Abrégée Mol. Ecol.
Volume 29 Numéro 17 Pages 3248-3260
Mots-Clés asexual reproduction; climate-change; clonal growth; differentiation; dispersal; diversity; efficiency; growth; larval dispersal; marine meadows; mating system; migration; ria formosa; seagrass; zostera-marina
Résumé Seagrass meadows are among the most important coastal ecosystems in terms of both spatial extent and ecosystem services, but they are also declining worldwide. Understanding the drivers of seagrass meadow dynamics is essential for designing sound management, conservation and restoration strategies. However, poor knowledge of the effect of clonality on the population genetics of natural populations severely limits our understanding of the dynamics and connectivity of meadows. Recent modelling approaches have described the expected distributions of genotypic and genetic descriptors under increasing clonal rates, which may help us better understand and interpret population genetics data obtained for partial asexuals. Here, in the light of these recent theoretical developments, we revisited population genetics data for 165 meadows of four seagrass species. Contrasting shoot lifespan and rhizome turnover led to the prediction that the influence of asexual reproduction would increase along a gradient fromZostera noltiitoZostera marina, Cymodocea nodosaandPosidonia oceanica, with increasing departure from Hardy-Weinberg equilibrium (F-is), mostly towards heterozygote excess, and decreasing genotypic richness (R). This meta-analysis provides a nested validation of this hypothesis at both the species and meadow scales through a significant relationship betweenF(is)andRwithin each species. By empirically demonstrating the theoretical expectations derived from recent modelling approaches, this work calls for the use of Hardy-Weinberg equilibrium (F-is) rather than only the strongly sampling-sensitiveRto assess the importance of clonal reproduction (c), at least when the impact of selfing onF(is)can be neglected. The results also emphasize the need to revise our appraisal of the extent of clonality and its influence on the dynamics, connectivity and evolutionary trajectory of partial asexuals in general, including in seagrass meadows, to develop the most accurate management strategies.
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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 0962-1083 ISBN Médium
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Notes WOS:000563628600001 Approuvé pas de
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Auteur Albouy, C.; Delattre, V.; Donati, G.; Frolicher, T.L.; Albouy-Boyer, S.; Rufino, M.; Pellissier, L.; Mouillot, D.; Leprieur, F.
Titre Global vulnerability of marine mammals to global warming Type Article scientifique
Année 2020 Publication Revue Abrégée Sci Rep
Volume 10 Numéro 1 Pages 548
Mots-Clés biodiversity; climate-change; conservation; eubalaena-japonica; extinction risk; functional diversity; gray whales; life-history traits; range changes; right whales
Résumé Although extinctions due to climate change are still uncommon, they might surpass those caused by habitat loss or overexploitation over the next few decades. Among marine megafauna, mammals fulfill key and irreplaceable ecological roles in the ocean, and the collapse of their populations may therefore have irreversible consequences for ecosystem functioning and services. Using a trait-based approach, we assessed the vulnerability of all marine mammals to global warming under high and low greenhouse gas emission scenarios for the middle and the end of the 21st century. We showed that the North Pacific Ocean, the Greenland Sea and the Barents Sea host the species that are most vulnerable to global warming. Future conservation plans should therefore focus on these regions, where there are long histories of overexploitation and there are high levels of current threats to marine mammals. Among the most vulnerable marine mammals were several threatened species, such as the North Pacific right whale (Eubalaena japonica) and the dugong (Dugong dugon), that displayed unique combinations of functional traits. Beyond species loss, we showed that the potential extinctions of the marine mammals that were most vulnerable to global warming might induce a disproportionate loss of functional diversity, which may have profound impacts on the future functioning of marine ecosystems worldwide.
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Langue English Langue du Résumé Titre Original
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Volume de collection Numéro de collection Edition
ISSN 2045-2322 ISBN Médium
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Notes WOS:000562813800014 Approuvé pas de
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Auteur Villon, S.; Mouillot, D.; Chaumont, M.; Subsol, G.; Claverie, T.; Villeger, S.
Titre A new method to control error rates in automated species identification with deep learning algorithms Type Article scientifique
Année 2020 Publication Revue Abrégée Sci Rep
Volume 10 Numéro 1 Pages 10972
Mots-Clés aerial vehicles; biodiversity; reject
Résumé Processing data from surveys using photos or videos remains a major bottleneck in ecology. Deep Learning Algorithms (DLAs) have been increasingly used to automatically identify organisms on images. However, despite recent advances, it remains difficult to control the error rate of such methods. Here, we proposed a new framework to control the error rate of DLAs. More precisely, for each species, a confidence threshold was automatically computed using a training dataset independent from the one used to train the DLAs. These species-specific thresholds were then used to post-process the outputs of the DLAs, assigning classification scores to each class for a given image including a new class called “unsure”. We applied this framework to a study case identifying 20 fish species from 13,232 underwater images on coral reefs. The overall rate of species misclassification decreased from 22% with the raw DLAs to 2.98% after post-processing using the thresholds defined to minimize the risk of misclassification. This new framework has the potential to unclog the bottleneck of information extraction from massive digital data while ensuring a high level of accuracy in biodiversity assessment.
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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 WOS:000546533700003 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection (down) 2861
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Auteur 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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Editeur Lieu de Publication Éditeur
Langue English Langue du Résumé Titre Original
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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 (down) 2849
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