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Aim: Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio-economic factors. Location: Tropical, temperate and polar coastal areas. Time period: Present day. Major taxa studied: Marine fishes. Methods: We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio-economic factors on alpha-and beta-diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic alpha-and beta-diversity measured from our barcodes, and phylogenetic but also functional diversity. Results: We show that fish eDNA MOTU and sequence alpha-and beta-diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity. Main conclusions: Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions., Global Ecology and Biogeography, ISSN:1466-822X, ISSN:1466-8238

Supplementary Methods

Statistical sensitivity analyses

International audience

Place: Dordrecht Publisher: Springer WOS:000523583200002; Figure 1 has been published incorrectly in the original article. The correct version of Figure 1 is provided in this correction.

International audience

International audience

Studying demographic and genetic connectivity can help assessing marine meta-population structure. Rays and skates have no larval phase hence population connectivity can only result from active movement of individuals. Using thornback ray (Raja clavata) in European waters as a case study, demographic and genetic connectivity were studied for 11 putative populations for unequal population abundances and two hypotheses of dispersal rates. Genetic simulation results highlighted three large meta-populations: in the Mediterranean, around the Azores and on the Northeast Atlantic shelf. Demographic results highlighted a finer population structure indicating that several pairs of putative populations might be demographically linked. Results were highly sensitive to dispersal assumptions and relative population abundances, which provided insights into the potential magnitude of genetic and demographic connectivity differences. Accounting for demographic connectivity appears to be crucial for managing and conserving rays and skates while genetic connectivity provides a longer term perspective and less subtle spatial structures. Moreover, accounting for heterogeneity in population abundances is a key factor for determining or interpreting meta-population connectivity.

Effective population size Ne is a central parameter in evolutionary and conservation biology and can be estimated with demographic- and genetic-based methods. The objective of this thesis was to analyze the effects of life-history on Ne in species with overlapping generations using demographic models. One demographic and two genetic estimators were used to derive Ne in the endangered perennial plant Eryngium alpinum. The three methods gave considerably different estimates. The differences could be attributed to the difficulty in obtaining al the necessary data needed in the demographic model, but also to the reduced precision of genetic estimators when dealing with small genetic sample sizes. Demographic models nonetheless permitted identifying the effect of lifehistory on Ne through elasticity and sensitivity analyses. Numerical elasticity was employed to study the effect of stage-specific vital rates on Ne in E. alpinum and the endangered perennial plant Dracocephalum austriacum. The derived elasticity patterns were often, but not always, similar in populations with comparable demography. One demographic model was then analysed in detail to derive analytically an expression for the sensitivity of Ne/N to age-specific vital rates. This expression was used to study Ne/N in three species differing in their survivorship curves (humans, sparrows and barnacles). In this way, the differences in the sensitivity patterns among the three species could be attributed to specific components of the life-cycle. This thesis demonstrates that demographic models are powerful methods to understand the effects of the life-history on Ne and could be useful tools to complement genetic estimators when sufficient ecological and demographic data are available. The next step will be to generalize the observed elasticity and sensitivity patterns using a comparative approach on a large number of populations, which will be possible thanks to the quick accumulation of large amounts of demographic and genetic data on a great number of species., La taille efficace des populations, Ne, est un paramètre central en biologie de la conservation et en biologie évolutive et peut être estimée avec des méthodes démographiques et génétiques. L'objectif de cette thèse a été l'analyse des effets de l'histoire de vie sur Ne dans des espèces à générations chevauchantes en utilisant des modèles démographiques. Un modèle démographique et deux estimateurs génétiques ont été utilisés pour dériver Ne dans des population d' Eryngium alpinum, une plante pérenne et menacée. Les trois méthodes ont donné des estimations considérablement différentes. Les différences ont pu être attribuées à la difficulté d'obtenir toutes les données nécessaires au modèle démographique, mais aussi à la faible précision des estimateurs génétiques quand ils sont appliqués à des jeux de données limités. Les modèles démographiques ont cependant permis l'identification des effets de l'histoire de vie sur Ne à travers des analyses de sensibilité et d'élasticité. L'élasticité numérique a été utilisée pour étudier les effets sur Ne de taux vitaux stadespécifiques dans E. alpinum et dans Dracocephalum austriacum, une plante alpine pérenne et menacée. Les patrons d'élasticité dérivés étaient souvent, mais pas toujours, similaires dans des populations à démographie comparable. Ensuite, un modèle démographique a été analysé en détail pour dériver analytiquement une expression pour la sensibilité de Ne/N aux taux vitaux âgespécifiques. Cette expression a été utilisée pour étudier Ne/N dans trois espèces qui diffèrent dans leur patron de courbe de survie (humains, bruants et balanes). Les différences des patrons de sensibilité entre ces trois espèces ont pu être ainsi attribuées à des composantes spécifiques du cycle de vie. Cette thèse montre que les modèles démographiques sont des méthodes utiles pour comprendre les effets de l'histoire de vie sur Ne et qu'ils pourraient être des outils puissants pour complémenter les estimateurs génétiques quand des données écologiques et démographiques sont disponibles en quantité suffisante. L'étape suivante sera la généralisation des patrons de sensibilité et d'élasticité observés en utilisant une approche comparative sur un grande nombre de populations, ce qui sera possible grâce à la rapide accumulation de grandes quantités des données démographiques et génétiques sur un grand nombre d'espèces.

International audience; * Connectivity is a crucial process underpinning the persistence, recovery, and productivity of marine ecosystems. The Convention on Biological Diversity, through the Aichi Target 11, has set the ambitious objective of implementing a ‘well connected system of protected areas’ by 2020. * This paper identifies eight challenges toward the integration of connectivity into MPA network management and planning. A summary table lists the main recommendations in terms of method, tool, advice, or action to address each of these challenges. Authors belong to a science–management continuum including researchers, international NGO officers, and national MPA agency members. * Three knowledge challenges are addressed: selecting and integrating connectivity measurement metrics; assessing the accuracy and uncertainty of connectivity measurements; and communicating and visualizing connectivity measurements. * Three management challenges are described: integrating connectivity into the planning and management of MPA networks; setting quantitative connectivity targets; and implementing connectivity-based management across scales and marine jurisdictions. * Finally, two paths toward a better integration of connectivity science with MPA management are proposed: setting management-driven priorities for connectivity research, bridging connectivity science, and MPA network management. * There is no single method to integrate connectivity into marine spatial planning. Rather, an array of methods can be assembled according to the MPA network objectives, budget, available skills, data, and timeframe. * Overall, setting up ‘boundary organizations’ should be promoted to organize complex cross-disciplinary, cross-sectoral and cross-jurisdiction interactions that are needed between scientists, managers, stakeholders and decision-makers to make informed decision regarding connectivity-based MPA planning and management. Copyright © 2014 John Wiley & Sons, Ltd.

International audience; Marine protected areas (MPAs) are major tools to protect biodiversity and sustain fisheries. For species with a sedentary adult phase and a dispersive larval phase, the effectiveness of MPA networks for population persistence depends on connectivity through larval dispersal. However, connectivity patterns between MPAs remain largely unknown at large spatial scales. Here, we used a biophysical model to evaluate connectivity between MPAs in the Mediterranean Sea, a region of extremely rich biodiversity that is currently protected by a system of approximately a hundred MPAs. The model was parameterized according to the dispersal capacity of the dusky grouper Epinephelus marginatus, an archetypal conservation-dependent species, with high economic importance and emblematic in the Mediterranean. Using various connectivity metrics and graph theory, we showed that Mediterranean MPAs are far from constituting a true, well-connected network. On average, each MPA was directly connected to four others and MPAs were clustered into several groups. Two MPAs (one in the Balearic Islands and one in Sardinia) emerged as crucial nodes for ensuring multi-generational connectivity. The high heterogeneity of MPA distribution, with low density in the SouthEastern Mediterranean, coupled with a mean dispersal distance of 120 km, leaves about 20% of the continental shelf without any larval supply. This low connectivity, here demonstrated for a major Mediterranean species, poses new challenges for the creation of a future Mediterranean network of well-connected MPAs providing recruitment to the whole continental shelf. This issue is even more critical given that the expected reduction of pelagic larval duration following sea temperature rise will likely decrease connectivity even more.

International audience; The evolutionary enlightened management of species with complex life cycles often requires the development of mathematical models integrating demographic and genetic data. The genetic structure of the endangered European eel (Anguilla anguilla L.) has been thoroughly analyzed in several studies in the past years. However, the interpretation of the key demographic and biologic processes that determine the observed spatio-temporal genetic structure has been very challenging owing to the complex life cycle of this catadromous species. Here, we present the first integrated demographic-genetic model applied to the European eel that explicitly accounts for different levels of larval and adult mixing during oceanic migrations and allows us to explore alternative hypotheses on genetic differentiation. Our analyses show that (i) very low levels of mixing occurring during larval dispersal or adult migration are sufficient to erase entirely any genetic differences among sub-populations; (ii) small-scale temporal differentiation in recruitment can arise if the spawning stock is subdivided in distinct reproductive groups; and (iii) the geographic differentiation component might be overestimated if a limited number of temporal recruits are analyzed. Our study can inspire the scientific debate on the interpretation of genetic structure in other species characterized by complex life cycle and long-range migrations.

Marine reserves are viewed as flagship tools to protect exploited species and to contribute to the effective management of coastal fisheries. Yet, the extent to which marine reserves are globally interconnected and able to effectively seed areas, where fisheries are most critical for food and livelihood security is largely unknown. Using a hydrodynamic model of larval dispersal, we predict that most marine reserves are not interconnected by currents and that their potential benefits to fishing areas are presently limited, since countries with high dependency on coastal fisheries receive very little larval supply from marine reserves. This global mismatch could be reversed, however, by placing new marine reserves in areas sufficiently remote to minimize social and economic costs but sufficiently connected through sea currents to seed the most exploited fisheries and endangered ecosystems., Nature Communications, 8, ISSN:2041-1723