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2. Temporal variability of larval drift of tropical amphidromous gobies along a watershed in reunion island

Author

Lagarde, Raphael, Teichert, Nils, Grondin, Henri, Magalon, Helene, Pirog, Agathe, and Ponton, Dominique

Subjects
Réunion -- Environmental aspects, Mortality -- Analysis -- France, Gobiidae -- Natural history, Earth sciences
Abstract

Freshwater gobies of tropical islands are amphidromous: adults reproduce in rivers and larvae passively drift down to the sea immediately after hatching. Describing the phenology of this larval drift is essential to understanding the population dynamics of amphidromous gobies and to developing ecologically based recommendations for managing the watersheds. The larval drift patterns of two amphidromous gobies of Reunion Island, Sicyopterus lagocephalus and Cotylopus acutipinnis, were studied on a monthly basis for 1 year using plankton nets at two sites on the Mat River, located 20 km and 7 km from the river mouth. Genetic analyses showed that larval assemblages were dominated at 90% by S. lagocephalus, although the proportion of C. acutipinnis increased during early summer. Our findings highlighted a marked larval drift peak in full austral summer. The diel larval drift dynamic was described using periodic linear models. A diel pattern was only observed downstream, peaking a few hours after sunset. Finally, this study presents a new approach that improves standard methods for sampling and analyzing larval drift of amphidromous species. Les gobies dulcaquicoles des iles tropicales sont amphidromes : les adultes se reproduisent dans les rivieres et, immediatement apres l'eclosion, les larves derivent passivement jusqu'a la mer. La description de la phenologie de la derive des larves en eau douce est indispensable a la comprehension de la dynamique des populations de ces gobies amphidromes et pour preconiser des mesures de gestion des bassins versants adaptees a leur ecologie. Les patrons de derive des larves de deux especes de gobies amphidromes de l'ile de La Reunion, Sicyopterus lagocephalus et Cotylopus acutipinnis, ont ete decrits mensuellement pendant une annee a l'aide de filets planctoniques au niveau de deux sites de la riviere du Mat, situes respectivement a 20 km et 7 kmde l'embouchure. Les analyses genetiques ont montre que les assemblages larvaires etaient domines a 90% par S. lagocephalus. Cependant, la proportion de C. acutipinnis etait plus importante en debut d'ete. Nos resultats ont mis en evidence que la derive des larves avait lieu principalement pendant l'ete austral. La dynamique journaliere de derive des larves a ete decrite a l'aide de modeles periodiques lineaires. Un patron journalier n'a ete observe qu'en aval avec un pic quelques heures apres la tombee de la nuit. Enfin, cette etude presente une approche originale, basee sur l'amelioration des methodes standards d'echantillonnage et d'analyse des donnees de derive des larves des especes amphidromes., Introduction Diadromy is a life history strategy involving migrations between freshwater and marine biomes (Myers 1949). Within diadromy, amphidromy is a subcategory in which the longest part of the individual's [...]

Published
2017
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5. Rapport de campagne de nourriceries côtières : Campagnes Nurse 2020

Author

Brind'Amour, Anik, Droual, Gabin, Crampon, Alexis, Pirog, Agathe, Berthele, Olivier, Delaunay, Damien, and Régimbart, Amélie

Subjects
dynamique temporelle, Fonctionnement des nourriceries côtières, DCSMM, suivi, communautés bentho-démersales
Abstract

Dans le cadre de la mise en œuvre du programme de surveillance de la directive cadre stratégie pour le milieu marin (DCSMM), le suivi des poissons et céphalopodes démersaux des milieux meubles côtiers a été jugé prioritaire. Pour ce faire, une série de campagnes halieutiques récurrentes a été déployée dans les nourriceries côtières, constituant des habitats essentiels pour de nombreuses espèces marines. La caractérisation de l’état écologique des peuplements et l’étude de la fonctionnalité des habitats de nourriceries s’avèrent nécessaires au calcul des indicateurs du Bon Etat Ecologique requis par la DCSMM et primordiales pour la mise en place de mesures de gestion écosystémique garantissant des usages durables. La campagne Nurse conduite dans le golfe de Gascogne s'inscrit donc dans le programme de surveillance des « Poissons-céphalopodes », le présent rapport présente les principaux résultats acquis en 2020.

Published
2021

6. Genetic population structure and demography of an apex predator, the tiger shark Galeocerdo cuvier

Author

Pirog, Agathe, Jaquemet, Sébastien, Ravigné, Virginie, Cliff, Geremy, Clua, Eric, Holmes, Bonnie, Hussey, Nigel, Nevill, John E. G., Temple, Andrew, Berggren, Per, Vigliola, Laurent, Magalon, Hélène, Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Institut de Recherche pour le Développement (IRD), Laboratoire d'Ecologie Marine (ECOMAR), Université de La Réunion (UR), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de La Réunion (UR)-Institut National de la Recherche Agronomique (INRA), Biomedical Resource Unit, University of KwaZulu-Natal (UKZN), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD), Centre for Marine Science, School of Biological Sciences, University of Queensland, University of Queensland [Brisbane], University of Windsor [Ca], School of Natural and Environmental Sciences, Newcastle University [Newcastle], School of Marine Science and Technology, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Ecologie marine tropicale des océans Pacifique et Indien (ENTROPIE [Nouvelle-Calédonie]), Ifremer - Nouvelle-Calédonie, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Université de la Nouvelle-Calédonie (UNC), Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), University of KwaZulu-Natal [Durban, Afrique du Sud] (UKZN), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Ifremer - Nouvelle-Calédonie, and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Nouvelle-Calédonie (UNC)

Subjects
bottleneck, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], tiger shark, mitochondrial DNA, L10 - Génétique et amélioration des animaux, Requin, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, approximate Bayesian computation, Variation génétique, lcsh:QH540-549.5, Dynamique des populations, microsatellite DNA, lcsh:Ecology, L20 - Écologie animale, Galeocerdo cuvier, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, effective population size, Original Research
Abstract

International audience; Population genetics has been increasingly applied to study large sharks over the last decade. Whilst large shark species are often difficult to study with direct methods, improved knowledge is needed for both population management and conservation, especially for species vulnerable to anthropogenic and climatic impacts. The tiger shark, Galeocerdo cuvier, is an apex predator known to play important direct and indirect roles in tropical and subtropical marine ecosystems. While the global and Indo‐West Pacific population genetic structure of this species has recently been investigated, questions remain over population structure and demographic history within the western Indian (WIO) and within the western Pacific Oceans (WPO). To address the knowledge gap in tiger shark regional population structures, the genetic diversity of 286 individuals sampled in seven localities was investigated using 27 microsatellite loci and three mitochondrial genes (CR, COI, and cytb). A weak genetic differentiation was observed between the WIO and the WPO, suggesting high genetic connectivity. This result agrees with previous studies and highlights the importance of the pelagic behavior of this species to ensure gene flow. Using approximate Bayesian computation to couple information from both nuclear and mitochondrial markers, evidence of a recent bottleneck in the Holocene (2,000–3,000 years ago) was found, which is the most probable cause for the low genetic diversity observed. A contemporary effective population size as low as 111 [43,369] was estimated during the bottleneck. Together, these results indicate low genetic diversity that may reflect a vulnerable population sensitive to regional pressures. Conservation measures are thus needed to protect a species that is classified as Near Threatened.

Published
2019

7. Evaluation de l’état écologique de l’ichtyofaune des eaux côtières françaises

Author

Pirog, Agathe, Barille, Anne-laure, Delaunay, Damien, Le Bris, Hervé, Lepage, Mario, Vaz, Sandrine, Vogel, Camille, Brind'Amour, Anik, Pirog, Agathe, Barille, Anne-laure, Delaunay, Damien, Le Bris, Hervé, Lepage, Mario, Vaz, Sandrine, Vogel, Camille, and Brind'Amour, Anik

Abstract

La mise en œuvre de la Directive Cadre Stratégie Milieu Marin prévoit, dans le cadre de la thématique « Poissons et Céphalopodes », de développer des indicateurs en vue de l’évaluation du Bon Etat Ecologique (BEE) prévue en 2022. Un indicateur doit notamment être développé pour renseigner le descripteur D1 (Biodiversité) sur le groupe des poissons démersaux des milieux meubles côtiers. Des séries historiques de données sont disponibles pour ces milieux, notamment dans le golfe de Gascogne. Ces données ont été utilisées pour mettre au point un indicateur côtier, après avoir vérifié que la stratégie d’échantillonnage était suffisamment robuste et standardisée pour ne pas introduire de biais. La méthodologie développée pour construire l’indicateur s’est rapprochée de celle mise en place pour calculer l’indicateur poisson utilisé dans le cadre de la Directive Cadre sur l’Eau en zone estuarienne (indicateur ELFI). Ceci a été possible grâce à la similarité des protocoles d’échantillonnage en zone côtière et en zone estuarienne. Ce rapport présente donc, dans un premier temps, les résultats des tests pour vérifier l’absence de biais lié aux modifications (date d’échantillonnage, marée, …) du protocole d’échantillonnage sur la série historique 2000 – 2020. Ensuite, l’indicateur ELFI a été calculé (sans modification) sur les données disponibles en zone côtière afin d’évaluer l’applicabilité de cet indicateur sur cette zone dont les communautés ichtyologiques sont proches de celles présentes en zone estuarienne. Néanmoins certaines métriques poissons utilisées pour l’ELFI se révélant peu adaptées aux communautés côtières (densité des espèces diadromes, peu présentes en zone côtière), de nouvelles métriques et de nouveaux seuils ont été ensuite définis pour construire un nouvel indicateur côtier (ELFI-C). Une comparaison entre l’évaluation du BEE avec ce nouvel indicateur et avec l’ELFI a ensuite été effectuée.

Published
2021
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8. Population structure, connectivity, and demographic history of an apex marine predator, the bull shark Carcharhinus leucas

Author

Pirog, Agathe, Ravigné, Virginie, Fontaine, Michael C., Rieux, Adrien, Gilabert, Aude, Cliff, Geremy, Clua, Eric, Daly, Ryan, Heithaus, Michael, Kiszka, Jérémy, Matich, Philip, Nevill, John, Smoothey, Amy, Temple, Andrew, Berggren, Per, Jaquemet, Sébastien, Magalon, Hélène, Fontaine lab, Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Institut de Recherche pour le Développement (IRD), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Diversity, ecology, evolution & Adaptation of arthropod vectors (MIVEGEC-DEEVA), Evolution des Systèmes Vectoriels (ESV), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Groningen Institute for Evolutionary Life Sciences [Groningen] (GELIFES), University of Groningen [Groningen], Biomedical Resource Unit, University of KwaZulu-Natal (UKZN), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Oceanographic research institute (ORI), South African Institute for Aquatic Biodiversity, Department of Biological Sciences [Miami], Florida International University [Miami] (FIU), Marine Sciences Program, Newcastle University [Newcastle], School of Marine Science and Technology, Western Indian Ocean Marine Science Association-Funded BYCAM Project : MASMA/CP/2014/01, Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), University of KwaZulu-Natal [Durban, Afrique du Sud] (UKZN), and Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE)

Subjects
mitochondrial DNA, Variation génétique, lcsh:QH540-549.5, Dynamique des populations, Marqueur génétique, Structure de la population, mito‐nuclear discordance, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], L60 - Taxonomie et géographie animales, Microsatellite, population genetics, ABC-RF, mito-nuclear discordance, ABC‐RF, Carcharhinus leucas, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, M40 - Écologie aquatique, microsatellite DNA, Écologie animale, lcsh:Ecology, L20 - Écologie animale, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; Knowledge of population structure, connectivity, and effective population size remains limited for many marine apex predators, including the bull shark Carcharhinus leucas. This large-bodied coastal shark is distributed worldwide in warm temperate and tropical waters, and uses estuaries and rivers as nurseries. As an apex predator, the bull shark likely plays a vital ecological role within marine food webs, but is at risk due to inshore habitat degradation and various fishing pressures. We investigated the bull shark's global population structure and demographic history by analyzing the genetic diversity of 370 individuals from 11 different locations using 25 microsatellite loci and three mitochondrial genes (CR, nd4, and cytb). Both types of markers revealed clustering between sharks from the Western Atlantic and those from the Western Pacific and the Western Indian Ocean, with no contemporary gene flow. Microsatellite data suggested low differentiation between the Western Indian Ocean and the Western Pacific, but substantial differentiation was found using mitochondrial DNA. Integrating information from both types of markers and using Bayesian computation with a random forest procedure (ABC-RF), this discordance was found to be due to a complete lack of contemporary gene flow. High genetic connectivity was found both within the Western Indian Ocean and within the Western Pacific. In conclusion, these results suggest important structuring of bull shark populations globally with important gene flow occurring along coastlines, highlighting the need for management and conservation plans on regional scales rather than oceanic basin scale.

Published
2019

10. Structure génétique des populations et biologie de la reproduction chez le requin bouledogue Carcharhinus leucas et le requin tigre Galeocerdo cuvier

Author

Pirog, Agathe, Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Université de la Réunion, Sébastien Jaquemet, Hélène Magalon, Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Institut de Recherche pour le Développement (IRD), and STAR, ABES

Subjects
[SDV.EE]Life Sciences [q-bio]/Ecology, environment, Requin bouledogue, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.BDLR.RS] Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, Philopatrie, Polyandrie, Philopatry, [SDV.GEN] Life Sciences [q-bio]/Genetics, Structure des populations, Population structure, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, Bull shark, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, Effective population size, Taille efficace, Polyandry, Requin tigre, Cycles de reproduction, Reproductive cycles, Tiger shark
Abstract

This PhD thesis focuses on two large shark species, the bull shark Carcharhinus leucas and the tiger shark Galeocerdo cuvier. The aims are to study the genetic structuring of their populations, the effective population size of the delimited populations and the reproductive modes of both species. A strong genetic differentiation was highlighted between bull shark populations from the Western Indian Ocean and the Western Pacific, due to either an absence of contemporary gene flow or to an absence of female gene flow only. On the opposite, tiger shark populations seem genetically homogenous, with important genetic connectivity between both regions. Within each region, no genetic differentiation among localities was highlighted for both species. A weaker genetic diversity was identified for the tiger shark, probably linked to the occurrence of a recent bottleneck occurring less than 3,000 years ago. Around Reunion Island, bull and tiger shark populations present different dynamics, linked to their reproductive modes. Bull shark individuals from both sexes seem to exhibit some fidelity to specific coastal sites (philopatry) to mate and/or deliver embryos, and litters are frequently issued from several fathers (polyandry). On the opposite, mating and pupping areas of the tiger shark remain poorly known, and this species seems exclusively monoandrous, probably linked to its semi-oceanic nature.This work highlights the high dispersal abilities of both species. Their populations present different dynamics, leading to different sensitivities to anthropogenic pressures. These results point out the need to adopt management plans specific to each species, Cette thèse porte sur deux espèces de grands requins, le requin bouledogue Carcharhinus leucas et le requin tigre Galeocerdo cuvier. Les objectifs sont d'étudier la structure génétique de leurs populations, la taille efficace des populations identifiées et les modes de reproduction de ces deux espèces. Une différenciation génétique importante a été identifiée entre les populations de requin bouledogue de l'Ouest de l'océan Indien et de l'Ouest du Pacifique, reflétant soit une absence de flux de gènes contemporains, soit des flux de gènes uniquement assurés par les mâles. À l'inverse, les populations de requin tigre de ces deux régions sont homogènes génétiquement. Une plus faible diversité génétique a été identifiée chez le requin tigre que chez le requin bouledogue, peut-être liée à une diminution forte des effectifs datant de moins de 3 000 ans. Autour de La Réunion, les populations des requins bouledogue et tigre suivent des dynamiques différentes, liées à leurs modes de reproduction. Chez le requin bouledogue, les individus semblent fidèles à des zones côtières particulières (philopatrie) pour s'accoupler et/ou mettre bas, et les portées sont fréquemment issues de plusieurs pères (polyandrie). À l'inverse, les zones d'accouplement et de mise bas du requin tigre restent mal connues, et cette espèce semble exclusivement monoandre, caractéristiques liées à sa nature semi-océanique. Ces travaux montrent les capacités de dispersion importantes de ces deux espèces. Leurs populations présentent des dynamiques différentes induisant une vulnérabilité différente aux pressions anthropiques.

Published
2018

12. Identification of ciguatoxins in a shark involved in a fatal food poisoning in the Indian Ocean

Author

European Commission, Diogène, Jorge, Reverté, Laia, Rambla-Alegre, Maria, Del Rió, Vanessa, De La Iglesia, Pablo, Campàs, Mònica, Palacios, Óscar, Flores, Cintia, Caixach, Josep, Ralijaona, Christian, Razanajatovo, Iony Manitra, Pirog, Agathe, Magalon, Hélène, Arnich, Nathalie, Turquet, Jean, European Commission, Diogène, Jorge, Reverté, Laia, Rambla-Alegre, Maria, Del Rió, Vanessa, De La Iglesia, Pablo, Campàs, Mònica, Palacios, Óscar, Flores, Cintia, Caixach, Josep, Ralijaona, Christian, Razanajatovo, Iony Manitra, Pirog, Agathe, Magalon, Hélène, Arnich, Nathalie, and Turquet, Jean

Abstract

Severe food poisoning events after the consumption of sharks have been reported since the 1940s; however, there has been no clear understanding of their cause. Herein, we report for the first time the presence of ciguatoxins (CTXs) in sharks. The identification by mass spectrometry of CTXs, including two new analogues, in a bull shark (Carcharhinus leucas) that was consumed by humans, causing the poisoning and death of 11 people in Madagascar in 2013 is described. Typical neurotoxic ciguatera symptoms were recorded in patients, and toxicological assays on extracts of the shark demonstrated CTX-like activity. These results confirm this episode as a ciguatera poisoning event and expand the range of pelagic fish species that are involved in ciguatera in the Indian Ocean. Additionally, gambieric acid D, a molecule originally described in CTX-producing microalgae, was identified for the first time in fish. This finding can contribute to a better understanding of trophic relations within food webs. The present work confirms that consumption of sharks from the Indian Ocean should be considered a ciguatera risk, and actions should be taken to evaluate its magnitude and risk in order to manage shark fisheries. © 2017 The Author(s).

Published
2017

14. Identification of ciguatoxins in a shark involved in a fatal food poisoning in the Indian Ocean

Author

Diogène, Jorge, primary, Reverté, Laia, additional, Rambla-Alegre, Maria, additional, del Río, Vanessa, additional, de la Iglesia, Pablo, additional, Campàs, Mònica, additional, Palacios, Oscar, additional, Flores, Cintia, additional, Caixach, Josep, additional, Ralijaona, Christian, additional, Razanajatovo, Iony, additional, Pirog, Agathe, additional, Magalon, Hélène, additional, Arnich, Nathalie, additional, and Turquet, Jean, additional

Published
2017
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17. Isolation and characterization of eight microsatellite loci from Galeocerdo cuvier (tiger shark) and cross-amplification in Carcharhinus leucas, Carcharhinus brevipinna, Carcharhinus plumbeus and Sphyrna lewini

Author

Pirog, Agathe, Jaquemet, Sebastien, Blaison, Antonin, Soria, Marc, Magalon, Helene, Pirog, Agathe, Jaquemet, Sebastien, Blaison, Antonin, Soria, Marc, and Magalon, Helene

Abstract

The tiger shark Galeocerdo cuvier (Carcharhinidae) is a large elasmobranch suspected to have, as other apex predators, a keystone function in marine ecosystems and is currently considered Near Threatened (Red list IUCN). Knowledge on its ecology, which is crucial to design proper conservation and management plans, is very scarce. Here we describe the isolation of eight polymorphic microsatellite loci using 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Their characteristics were tested on a population of tiger shark (n = 101) from Reunion Island (South-Western Indian Ocean). All loci were polymorphic with a number of alleles ranging from two to eight. No null alleles were detected and no linkage disequilibrium was detected after Bonferroni correction. Observed and expected heterozygosities ranged from 0.03 to 0.76 and from 0.03 to 0.77, respectively. No locus deviated from Hardy-Weinberg equilibrium and the global F-IS of the population was of 0.04(NS). Some of the eight loci developed here successfully cross-amplified in the bull shark Carcharhinus leucas (one locus), the spinner shark Carcharhinus brevi pi n n a (four loci), the sandbar shark Carcharhinus plumbeus (five loci) and the scalloped hammerhead shark Sphyrna lewini (two loci). We also designed primers to amplify and sequence a mitochondrial marker, the control region. We sequenced 862 bp and found a low genetic diversity, with four polymorphic sites, a haplotype diversity of 0.15 and a nucleotide diversity of 2 x 10(-4).

Published
2016
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19. Artificial daily fluctuations of river discharge affect the larval drift and survival of a tropical amphidromous goby.

Author

Lagarde, Raphaël, Teichert, Nils, Faivre, Laëtitia, Grondin, Henri, Magalon, Hélène, Pirog, Agathe, Valade, Pierre, and Ponton, Dominique

Subjects
RIVER ecology, GOBIIDAE, FISH larvae, TROPICAL fish, HATCHABILITY of eggs, FISH locomotion
Abstract

Abstract: Amphidromous fish species reproduce in rivers, and their larvae immediately drift to the sea after hatching. Most of these larvae survive in freshwater for a few days only, rapidly reaching sea water is thus essential. Being of small size, especially among species of the Sicydiinae subfamily, the larvae possess poor swimming abilities; their drift dynamics is considered to be mainly passive and influenced by flow conditions. The influence of daily fluctuations in flow regime on Sicyopterus lagocephalus (Sicydiinae) larval drift patterns was studied using drift nets at three sites along the dammed Langevin River in Reunion Island. The river flow was stable at the upstream site when frequent anthropogenic river flow fluctuations were observed at the two sites downstream to the dam. Weak diel larval drift dynamics were detected at the upstream site and the first site under anthropogenic river flow conditions. In contrast, larval drift dynamics at the most downstream site was strongly influenced by anthropogenic daily fluctuations of discharge: the abundance of drifting larvae increased with peaks of discharge, regardless of the time. As higher mortality rates of drifting larvae were observed during discharge peaks, the benefit of a more rapid travel to the ocean associated with these peaks should be lower than expected. It is concluded that peaks of discharge increase the number of larvae drifting to the sea probably due to higher physical constraints on the egg clutches, but also decrease the chance of survival for larvae that may be nonfully developed. [ABSTRACT FROM AUTHOR]

Published
2018
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21. Population structure, connectivity, and demographic history of an apex marine predator, the bull shark Carcharhinus leucas .

Author

Pirog A, Ravigné V, Fontaine MC, Rieux A, Gilabert A, Cliff G, Clua E, Daly R, Heithaus MR, Kiszka JJ, Matich P, Nevill JEG, Smoothey AF, Temple AJ, Berggren P, Jaquemet S, and Magalon H

Abstract

Knowledge of population structure, connectivity, and effective population size remains limited for many marine apex predators, including the bull shark Carcharhinus leucas . This large-bodied coastal shark is distributed worldwide in warm temperate and tropical waters, and uses estuaries and rivers as nurseries. As an apex predator, the bull shark likely plays a vital ecological role within marine food webs, but is at risk due to inshore habitat degradation and various fishing pressures. We investigated the bull shark's global population structure and demographic history by analyzing the genetic diversity of 370 individuals from 11 different locations using 25 microsatellite loci and three mitochondrial genes ( CR , nd4 , and cytb ). Both types of markers revealed clustering between sharks from the Western Atlantic and those from the Western Pacific and the Western Indian Ocean, with no contemporary gene flow. Microsatellite data suggested low differentiation between the Western Indian Ocean and the Western Pacific, but substantial differentiation was found using mitochondrial DNA. Integrating information from both types of markers and using Bayesian computation with a random forest procedure (ABC-RF), this discordance was found to be due to a complete lack of contemporary gene flow. High genetic connectivity was found both within the Western Indian Ocean and within the Western Pacific. In conclusion, these results suggest important structuring of bull shark populations globally with important gene flow occurring along coastlines, highlighting the need for management and conservation plans on regional scales rather than oceanic basin scale., Competing Interests: None declared., (© 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Published
2019
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22. Isolation and characterization of eight microsatellite loci from Galeocerdo cuvier (tiger shark) and cross-amplification in Carcharhinus leucas, Carcharhinus brevipinna, Carcharhinus plumbeus and Sphyrna lewini.

Author

Pirog A, Jaquemet S, Blaison A, Soria M, and Magalon H

Abstract

The tiger shark Galeocerdo cuvier (Carcharhinidae) is a large elasmobranch suspected to have, as other apex predators, a keystone function in marine ecosystems and is currently considered Near Threatened (Red list IUCN). Knowledge on its ecology, which is crucial to design proper conservation and management plans, is very scarce. Here we describe the isolation of eight polymorphic microsatellite loci using 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Their characteristics were tested on a population of tiger shark (n = 101) from Reunion Island (South-Western Indian Ocean). All loci were polymorphic with a number of alleles ranging from two to eight. No null alleles were detected and no linkage disequilibrium was detected after Bonferroni correction. Observed and expected heterozygosities ranged from 0.03 to 0.76 and from 0.03 to 0.77, respectively. No locus deviated from Hardy-Weinberg equilibrium and the global F IS of the population was of 0.04 (NS) . Some of the eight loci developed here successfully cross-amplified in the bull shark Carcharhinus leucas (one locus), the spinner shark Carcharhinus brevipinna (four loci), the sandbar shark Carcharhinus plumbeus (five loci) and the scalloped hammerhead shark Sphyrna lewini (two loci). We also designed primers to amplify and sequence a mitochondrial marker, the control region. We sequenced 862 bp and found a low genetic diversity, with four polymorphic sites, a haplotype diversity of 0.15 and a nucleotide diversity of 2 × 10(-4).

Published
2016
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