|   | 
Détails
   web
Enregistrements
Auteur Meynard, C.N.; Mouillot, D.; Mouquet, N.; Douzery, E.J.P.
Titre (down) A Phylogenetic Perspective on the Evolution of Mediterranean Teleost Fishes Type Article scientifique
Année 2012 Publication Revue Abrégée PLoS One
Volume 7 Numéro 5 Pages
Mots-Clés cytochrome-b; divergence time; diversification; dna sequences; missing data; mitochondrial genome sequences; molecular phylogeny; nuclear; ray-finned fishes; tetraodontiform fishes
Résumé The Mediterranean Sea is a highly diverse, highly studied, and highly impacted biogeographic region, yet no phylogenetic reconstruction of fish diversity in this area has been published to date. Here, we infer the timing and geographic origins of Mediterranean teleost species diversity using nucleotide sequences collected from GenBank. We assembled a DNA supermatrix composed of four mitochondrial genes (12S ribosomal DNA, 16S ribosomal DNA, cytochrome c oxidase subunit I and cytochrome b) and two nuclear genes (rhodopsin and recombination activating gene I), including 62% of Mediterranean teleost species plus 9 outgroups. Maximum likelihood and Bayesian phylogenetic and dating analyses were calibrated using 20 fossil constraints. An additional 124 species were grafted onto the chronogram according to their taxonomic affinity, checking for the effects of taxonomic coverage in subsequent diversification analyses. We then interpreted the time-line of teleost diversification in light of Mediterranean historical biogeography, distinguishing non-endemic natives, endemics and exotic species. Results show that the major Mediterranean orders are of Cretaceous origin, specifically similar to 100-80 Mya, and most Perciformes families originated 80-50 Mya. Two important clade origin events were detected. The first at 100-80 Mya, affected native and exotic species, and reflects a global diversification period at a time when the Mediterranean Sea did not yet exist. The second occurred during the last 50 Mya, and is noticeable among endemic and native species, but not among exotic species. This period corresponds to isolation of the Mediterranean from Indo-Pacific waters before the Messinian salinity crisis. The Mediterranean fish fauna illustrates well the assembly of regional faunas through origination and immigration, where dispersal and isolation have shaped the emergence of a biodiversity hotspot.
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 1932-6203 ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 408
Lien permanent pour cet enregistrement
 

 
Auteur Rogers, N.J.; UrbinaLt, M.A.; Reardon, E.E.; McKenzie, D.J.; Wilsonl, R.W.
Titre (down) A new analysis of hypoxia tolerance in fishes using a database of critical oxygen level (P-crit) Type Article scientifique
Année 2016 Publication Revue Abrégée Conserv. Physiol.
Volume 4 Numéro Pages cow012
Mots-Clés Carbon dioxide; carp cyprinus-carpio; critical oxygen tension; eel anguilla-anguilla; environmental hypoxia; fresh-water fishes; goldfish carassius-auratus; inanga galaxias-maculatus; intermittent-flow respirometry; metabolic rate; oxygen and capacity limitation of thermal tolerance; physiological trait; postprandial metabolic-response; snapper pagrus-auratus; trout oncorhynchus-mykiss
Résumé Hypoxia is a common occurrence in aquatic habitats, and it is becoming an increasingly frequent and widespread environmental perturbation, primarily as the result of anthropogenic nutrient enrichment and climate change. An in-depth understanding of the hypoxia tolerance of fishes, and how this varies among individuals and species, is required to make accurate predictions of future ecological impacts and to provide better information for conservation and fisheries management. The critical oxygen level (P-crit)m has been widely used as a quantifiable trait of hypoxia tolerance. It is defined as the oxygen level below which the animal can no longer maintain a stable rate of oxygen uptake (oxyregulate) and uptake becomes dependent on ambient oxygen availability (the animal transitions to oxyconforming). A comprehensive database of P-crit values, comprising 331 measurements from 96 published studies, covering 151 fish species from 58 families, provides the most extensive and up-to-date analysis of hypoxia tolerance in teleosts. Methodologies for determining Pcrit are critically examined to evaluate its usefulness as an indicator of hypoxia tolerance in fishes. Various abiotic and biotic factors that interact with hypoxia are analysed for their effect on P, including temperature, CO,, acidification, toxic metals and feeding. Salinity, temperature, body mass and routine metabolic rate were strongly correlated with P-crit; 20% of variation in the P-crit, data set was explained by these four variables. An important methodological issue not previously considered is the inconsistent increase in partial pressure of CO, within a closed respirometer during the measurement of P-crit. Modelling suggests that the final partial pressure of CO, reached can vary from 650 to 3500 mu atm depending on the ambient pH and salinity, with potentially major effects on blood acid-base balance and P it itself. This database will form part of a widely accessible repository of physiological trait data that will serve as a resource to facilitate future studies of fish ecology, conservation and management.
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 2051-1434 ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ alain.herve @ collection 1656
Lien permanent pour cet enregistrement
 

 
Auteur Cahill, A.E.; De Jode, A.; Dubois, S.; Bouzaza, Z.; Aurelle, D.; Boissin, E.; Chabrol, O.; David, R.; Egea, E.; Ledoux, J.-B.; Mérigot, B.; Weber, A.A.-T.; Chenuil, A.
Titre (down) A multispecies approach reveals hot spots and cold spots of diversity and connectivity in invertebrate species with contrasting dispersal modes Type Article scientifique
Année 2017 Publication Revue Abrégée Mol. Ecol.
Volume 26 Numéro 23 Pages 6563-6577
Mots-Clés genetic diversity; dispersal; life-history traits; reef fishes; marine connectivity; pelagic larval duration; mediterranean sea; amphipholis-squamata; brooding brittle star; coralligenous assemblages; larvae; marine invertebrates; phylogeographical breaks; population structure; population genetic-structure; species genetic diversity correlation
Résumé Genetic diversity is crucial for species' maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes via dispersal of gametes and larvae. Species with a larval period are expected to have more connected populations than those without larval dispersal. We assessed the relationship between measures of species and genetic diversity, and between dispersal ability and connectivity. We compiled data on genetic patterns and life history traits in nine species across five phyla. Sampling sites spanned 600km in the northwest Mediterranean Sea and focused on a 50-km area near Marseilles, France. Comparative population genetic approaches yielded three main results. (i) Species without larvae showed higher levels of genetic structure than species with free-living larvae, but the role of larval type (lecithotrophic or planktotrophic) was negligible. (ii) A narrow area around Marseilles, subject to offshore advection, limited genetic connectivity in most species. (iii) We identified sites with significant positive contributions to overall genetic diversity across all species, corresponding with areas near low human population densities. In contrast, high levels of human activity corresponded with a negative contribution to overall genetic diversity. Genetic diversity within species was positively and significantly linearly related to local species diversity. Our study suggests that local contribution to overall genetic diversity should be taken into account for future conservation strategies.
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 0962-1083 ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ alain.herve @ collection 2262
Lien permanent pour cet enregistrement
 

 
Auteur Villon, S.; Mouillot, D.; Chaumont, M.; Darling, E.S.; Subsol, G.; Claverie, T.; Villeger, S.
Titre (down) A Deep learning method for accurate and fast identification of coral reef fishes in underwater images Type Article scientifique
Année 2018 Publication Revue Abrégée Ecol. Inform.
Volume 48 Numéro Pages 238-244
Mots-Clés Automated identification; Convolutional neural network; density; Machine learning; Marine fishes; neural-networks; system; temperate; Underwater pictures; video stations; visual census; vulnerability
Résumé Identifying and counting fish individuals on photos and videos is a crucial task to cost-effectively monitor marine biodiversity, yet it remains difficult and time-consuming. In this paper, we present a method to assist the identification of fish species on underwater images, and we compare our model performances to human ability in terms of speed and accuracy. We first tested the performance of a convolutional neural network (CNN) trained with different photographic databases while accounting for different post-processing decision rules to identify 20 fish species. Finally, we compared the performance of species identification of our best CNN model with that of humans on a test database of 1197 fish images representing nine species. The best CNN was the one trained with 900,000 images including (i) whole fish bodies, (ii) partial fish bodies and (iii) the environment (e.g. reef bottom or water). The rate of correct identification was 94.9%, greater than the rate of correct identification by humans (89.3%). The CNN was also able to identify fish individuals partially hidden behind corals or behind other fish and was more effective than humans to identify fish on smallest or blurry images while humans were better to identify fish individuals in unusual positions (e.g. twisted body). On average, each identification by our best CNN using a common hardware took 0.06 s. Deep Learning methods can thus perform efficient fish identification on underwater images and offer promises to build-up new video-based protocols for monitoring fish biodiversity cheaply and effectively.
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 1574-9541 ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2475
Lien permanent pour cet enregistrement
 

 
Auteur Hattab, T.; Albouy, C.; Lasram, F.B.; Le Loc'h, F.; Guilhaumon, F.; Leprieur, F.
Titre (down) A biogeographical regionalization of coastal Mediterranean fishes Type Article scientifique
Année 2015 Publication Revue Abrégée Journal of Biogeography
Volume 42 Numéro 7 Pages 1336-1348
Mots-Clés Beta diversity; Biogeography; bioregionalization; coastal fishes; compositional turnover; environmental gradient; historical processes; Mediterranean Sea; phylogenetic turnover; species composition
Résumé AimTo delineate the biogeographical regions of the continental shelf of the Mediterranean Sea based on the spatial distributions of coastal marine fishes and their evolutionary relationships, with a view to furthering our capacity to answer basic and applied biogeographical, ecological and evolutionary questions. LocationMediterranean Sea. MethodsWe used a dataset summarizing the occurrences of 203 coastal Mediterranean fishes (0.1 degrees resolution grid system) and a molecular phylogenetic tree to quantify both compositional and phylogenetic dissimilarity (or beta diversity) between cells. We then applied multivariate analyses to delineate biogeographical regions and to evaluate how they related to broad-scale environmental gradients. We also assessed the differences between the biogeographical regions identified using phylogenetic beta diversity versus those obtained using compositional beta diversity. ResultsThe bioregionalization schemes based on phylogenetic and compositional beta diversity identified broadly similar regions, each consisting of six distinct pools of coastal fishes. Clear separations between northern and southern regions were observed, as well as a disjunct between inshore and offshore areas. These beta diversity patterns were mainly related to a north-south gradient in sea-surface temperature and bathymetric constraints. Main conclusionsIncorporating phylogenetic information into the measurement of beta diversity did not offer further insights to the bioregionalization scheme based solely on compositional beta diversity. This suggests that evolutionary and historical processes played only a minor role in shaping the contemporary patterns of beta diversity in the Mediterranean coastal fish fauna. However, our results support the view that contemporary environmental conditions play a major role in determining the distribution of these species.
Adresse
Auteur institutionnel Thèse
Editeur Lieu de Publication Éditeur
Langue Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 0305-0270 ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1331
Lien permanent pour cet enregistrement