45 Works

Journal de bord de la campagne PUFFAlis, 18 mars - 02 avril 2017

V. Allain, Philippe Borsa, Anne Lebourges-Dhaussy, Christophe Menkès , Martine Rodier, David Varillon & Mina Vilayleck
Du 18 mars au 02 avril 2017 s'est déroulée la mission PUFFAlis à bord du navire océanographique Alis de l'IRD. Cette campagne s'inscrit dans la continuité d'expéditions océanographiques centrées sur les zones d'alimentation des oiseaux marins, effectuées précédemment en mer (MOMAlis) comme à terre sur la colonie de puffins de Gouaro Deva. Elle est aussi la prolongation des campagnes NECTAlis destinées à étudier la chaîne trophique océanique qui conduit aux thons. Six scientifiques ont embarqué...

Data from: Body reserves mediate trade-offs between life history traits: new insights from small pelagic fish reproduction

Pablo Brosset, Josep Lloret, Marta Muñoz, Christian Fauvel, Elisabeth Van Beveren, Virginie Marques, Jean-Marc Fromentin, Frédéric Ménard & Claire Saraux
Limited resources in the environment prevent individuals from simultaneously maximizing all life-history traits, resulting in trade-offs. In particular, the cost of reproduction is well known to negatively affect energy investment in growth and maintenance. Here, we investigated these trade-offs during contrasting periods of high versus low fish size and body condition (before/after 2008) in the Gulf of Lions. Female reproductive allocation and performance in anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) were examined based on...

Data from: An experimental comparison of three Towed Underwater Video Systems using species metrics, benthic impact and performance

Emma V. Sheehan, Sandrine Vaz, Erin Pettifer, Nicola L. Foster, Sarah J. Nancollas, Sophie Cousens, Luke Holmes, Jean-Valery Facq, Gregory Germain & Martin J. Attrill
1. Managing ecological systems, which operate over large spatial scales is inherently difficult and often requires sourcing data from different countries and organizations. The assumption might be made that data collected using similar methodologies are comparable but this is rarely tested. Here, benthic video data recorded using different towed underwater video systems (TUVSs) were experimentally compared. 2. Three technically different TUVSs were compared on different seabed types (rocky, mixed ground and sandy) in Kingmere Marine...

European North West Shelf/Iberia Biscay Irish Seas – High Resolution ODYSSEA L4 Sea Surface Temperature Analys

EU Copernicus Marine Service European North West Shelf/Iberia Biscay Irish Seas – High Resolution ODYSSEA L4 Sea Surface Temperature Analysis Produ

Changes in key traits versus depth and latitude suggest energy-efficient locomotion, opportunistic feeding and light lead to adaptive morphologies of marine fishes.

Elisabeth Myers, Marti Anderson, David Eme, Libby Liggins & Clive Roberts
1. Understanding patterns and processes governing biodiversity along broad-scale environmental gradients, such as depth or latitude, requires an assessment of not just taxonomic richness, but also morphological and functional traits of organisms. Studies of traits can help to identify major selective forces acting on morphology. Currently, little is known regarding patterns of variation in the traits of fishes at broad spatial scales. 2. The aims of this study were: (i) to identify a suite of...

Data from: Phylogenetic measures reveal eco-evolutionary drivers of biodiversity along a depth gradient

David Eme, Marti Anderson, Elisabeth Myers, Clive Roberts & Libby Liggins
Energy and environmental stability are positively correlated with species richness along broad-scale spatial gradients in terrestrial ecosystems, so their relative importance in generating and preserving diversity cannot be readily disentangled. This study seeks to exploit the negative correlation between energy and stability along the oceanic depth gradient to better understand their relative contribution in shaping broadscale biodiversity patterns. We develop a conceptual framework by simulating speciation and extinction along energy and stability gradients to generate...

High temperature induces transcriptomic changes in Crassostrea gigas that hinder progress of ostreid herpes virus (OsHV-1) and promote survival

Lizenn Delisle, Marianna Pauletto, Jeremie Vidal-Dupiol, Bruno Petton, Luca Bargelloni, Caroline Montagnani, Fabrice Pernet, Charlotte Corporeau & Elodie Fleury
Of all environmental factors, seawater temperature plays a decisive role in triggering marine diseases. Like fever in vertebrates, high seawater temperature could modulate the host response to pathogens in ectothermic animals. In France, massive mortality of Pacific oysters, Crassostrea gigas, caused by the ostreid herpesvirus 1 (OsHV-1) is markedly reduced when temperatures exceed 24°C in the field. In the present study we assess how high temperature influences the host response to the pathogen by comparing...

Gene expression plasticity, genetic variation and fatty acid remodelling in divergent populations of a tropical bivalve species: lipid profiles

Jérémy Le Luyer
Ocean warming challenges marine organisms’ resilience, especially for species experiencing temperatures close to their upper thermal limits. A potential increase in thermal tolerance might significantly reduce the risk of population decline, which is intrinsically linked to variability in local habitat temperatures. Our goal was to assess the plastic and genetic potential of response to elevated temperatures in a tropical bivalve model, Pinctada margaritifera. We benefit from two ecotypes for which local environmental conditions are characterized...

Data from: Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system

Mehdi Adjeroud, Aurélie Guérécheau, Jeremie Vidal-Dupiol, Jean-François Flot, Sophie Arnaud-Haond & François Bonhomme
Clonality and genetic structure of the coral Pocillopora damicornis sensu lato were assessed using five microsatellites in 12 populations from four islands of the Society Archipelago (French Polynesia) sampled in June 2008. The 427 analysed specimens fell into 132 multilocus genotypes (MLGs), suggesting that asexual reproduction plays an important role in the maintenance of these populations. A haploweb analysis of ITS2 sequences of each MLG was consistent with all of them being conspecific. Genetic differentiation...

European North West Shelf/Iberia Biscay Irish Seas - High Resolution L4 Sea Surface Temperature Reprocessed

EU Copernicus Marine Service European North West Shelf/Iberia Biscay Irish Seas - High Resolution L4 Sea Surface Temperature Reprocessed Product

Data from: RClone: a package to identify MultiLocus Clonal Lineages and handle clonal datasets in R

Diane Bailleul, Solenn Stoeckel & Sophie Arnaud-Haond
Partially clonal species are common in the Tree of Life. And yet, population genetics models still mostly focus on the extremes: strictly sexual versus purely asexual reproduction. Here we present an R package built upon GenClone software including new functions and several improvements. The RClone package includes functions to handle clonal datasets, allowing (i) checking for dataset reliability to discriminate multi-locus genotypes (MLG), (ii) ascertainment of MLG and semi-automatic determination of clonal lineages (MLL), (iii)...

Data from: Restriction to large-scale gene flow versus regional panmixia among cold seep Escarpia spp. (Polychaeta, Siboglinidae)

Dominique A. Cowart, Chunya Huang, Sophie Arnaud-Haond, Susan L. Carney, Charles R. Fisher & Stephen W. Schaeffer
The history of colonization and dispersal in fauna distributed among deep-sea chemosynthetic ecosystems remains enigmatic and poorly understood because of an inability to mark and track individuals. A combination of molecular, morphological and environmental data improves understanding of spatial and temporal scales at which panmixia, disruption of gene flow or even speciation may occur. Vestimentiferan tubeworms of the genus Escarpia are important components of deep -sea cold seep ecosystems, as they provide long-term habitat for...

Data from: Evolution without standing genetic variation: change in transgenerational plastic response under persistent predation pressure

Arnaud Sentis, Raphaël Bertram, Nathalie Dardenne, Felipe Ramon-Portugal, Gilles Espinasse, Ines Louit, Lucie Negri, Elena Haeler, Thomas Ashkar, Théo Pannetier, James Cunningham, Christoph Grunau, Gaël Le Trionnaire, Jean-Christophe Simon, Alexandra Margo, Benoit Pujol, Jean-Louis Hemptinne & Etienne Danchin
Transgenerational phenotypic plasticity is a fast nongenetic response to environmental modifications that can buffer the effects of environmental stresses on populations. However, little is known about the evolution of plasticity in the absence of standing genetic variation although several nongenetic inheritance mechanisms have now been identified. Here, we monitored the pea aphid transgenerational phenotypic response to ladybird predators (production of winged offspring) during 27 generations of experimental evolution in the absence of initial genetic variation...

Non-linear forcing of climate on denudation in the Alps over the last 75 ka

Apolline Mariotti , Pierre-Henri Blard , Julien Charreau , Samuel Toucanne , Stephan Jorry , Stéphane Molliex & Team ASTER
Reconstruction of denudation rates through time is an important task to quantify and understand the impact of climate on landscape evolution. Cosmogenic nuclides have been widely used as a tool to infer denudation rates at the watershed scale from both river sediments and past stratigraphic records. Here, we analyze the in-situ 10Be cosmogenic concentration over the last 75 ka in sediments cores that were collected offshore the Var River (Western Mediterranean Sea). We present 26...

EMODnet Phase V Updated guidelines for SeaDataNet ODV production Eutrophication Contaminants

Marina Lipizer, Maria Eugenia Molina Jack, ELISABETH KUBIN, Luminita Buga, Lotta Fyrberg, Julie Gatti, Martin M Larsen, Gwenaëlle Moncoiffé, Ann Kristin Ostrem, Reiner Schlitzer, Karin Wesslander & Alessandra GIORGETTI

Observations of turbulence and the geometry and circulation of windrows in a small bay in the St. Lawrence Estuary.

Seth Zippel, Ted Maksym, Malcolm E. Scully, Peter Sutherland & Dany Dumont
Measurements of ocean turbulence, waves, and the geometry and circulation of windrows were made over 5 days in early March in a small bay in the St. Lawrence Estuary. Measurements were made from a small zodiac and from a SWIFT drifter. Two acoustic doppler velocity profilers (ADCPs) were used from the zodiac to measure water velocity and turbulent kinetic energy (TKE) dissipation rates near the surface. The acoustic backscatter from the ADCPs was used in...

Adiip : amélioration et développement d’indicateurs d’impact et de pression pour le suivi du milieu lagonaire. Synthèse du programme suivie de cinq rapports thématiques, un document préliminaire et un document complémentaire

Jean-Michel Fernandez, Bruno Andral, Ludovic Breau, François Galgani, Jean-Louis Gonzalez, Olivier Grauby, Laurent Haddad, Hélène Kaplan, Shilpa Kumar-Roiné, Hélène Le Grand, Jean-Dominique Meunier, Ben Moreton, Mariana de Oliveira Rasa Bonhsack, Stéphanie Pluchino & Jocelyn Senia
Programme Adiip. Tome Nickel et Environnement

Carbon dioxide flux and isotopic composition from sedimentary rock weathering, Waiapu River catchment, New Zealand

Tobias Roylands, Robert G Hilton, Mark H Garnett & Guillaume Soulet Soulet
These data were collected to study oxidative weathering processes in the Waiapu River catchment, New Zealand, with potential carbon release sourced from the oxidation of petrogenic organic carbon or carbonate dissolution coupled to the oxidation of sulfide minerals. There, in mudstones exposed in a highly erosive gully complex, in situ CO2 emissions were measured with drilled gas accumulation chambers following the design by Soulet et al. (2018, Biogeosciences 15, 4087-4102, https://doi.org/10.5194/bg-15-4087-2018). Temporal and spatial variability...

Primary detection records for aquatic nonindigenous species in global estuarine and marine ecosystems and the Great Lakes

Sarah Bailey, Lyndsay Brown, Marnie Campbell, João Canning-Clode, James Carlton, Nuno Castro, Paula Chainho, Farrah Chan, Joel Creed, Amelia Curd, John Darling, Paul Fofonoff, Bella Galil, Chad Hewitt, Graeme Inglis, Inti Keith, Nicholas Mandrak, Agnese Marchini, Cynthia McKenzie, Anna Occhipinti-Ambrogi, Henn Ojaveer, Larissa Pires-Teixeira, Tamara Robinson, Gregory Ruiz, Kimberley Seaward … & Aibin Zhan
Aim The introduction of aquatic non-indigenous species (ANS) has become a major driver for global changes in species biogeography. We examined spatial patterns and temporal trends of ANS detections since 1965 to inform conservation policy and management. Location Global Methods We assembled an extensive dataset of first records of detection of ANS (1965-2015) across 49 aquatic ecosystems, including the i) year of first collection, ii) population status and iii) potential pathway(s) of introduction. Data were...

Data from: Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia

Sophie Arnaud-Haond, Tania Aires, Rui Candeias, Sara J. L. Teixeira, Carlos M. Duarte, Myriam Valero & Ester A. Serrão
Successful prevention and mitigation of biological invasions requires retracing the initial steps of introduction, as well as understanding key elements enhancing the adaptability of invasive species. We studied the genetic diversity of the green alga Caulerpa taxifolia and its associated bacterial communities in several areas around the world. The striking congruence of α and ß diversity of the algal genome and endophytic communities reveals a tight association, supporting the holobiont concept as best describing the...

Data from: Genetic diversity of oilseed rape fields and feral populations in the context of coexistence with GM crops

Diane Bailleul, Sébastien Ollier & Jane Lecomte
Despite growing concern about transgenes escaping from fields, few studies have analysed the genetic diversity of crops in an agroecosystem over several years. Accurate information about the dynamics and relationship of the genetic diversity of crops in an agroecosystem is essential for risk assessment and policies concerning the containment of genetically modified crops and their coexistence with crops grown by conventional practices. Here, we analysed the genetic diversity of oilseed rape plants from fields and...

Functional beta diversity of New Zealand fishes: characterising morphological turnover along depth and latitude gradients, with derivation of functional bioregions

Elisabeth Myers, David Eme, Libby Liggins, Euan Harvey, Clive Roberts & Marti Anderson
Changes in the functional structures of communities are rarely examined along multiple large-scale environmental gradients. Here, we describe patterns in functional beta diversity for New Zealand marine fishes vs depth and latitude, including broad-scale delineation of functional bioregions. We derived eight functional traits related to food acquisition and locomotion and calculated complementary indices of functional beta diversity for 144 species of marine ray-finned fishes occurring along large-scale depth (50 - 1200 m) and latitudinal gradients...

Phylogeny and systematics of Crescentieae (Bignoniaceae), a Neotropical clade of cauliflorous and bat-pollinated trees

Audrey C Ragsac, Susan O Grose & Richard G Olmstead
The tribe Crescentieae includes Amphitecna (21 species), Crescentia (six species), and Parmentiera (10 species), three genera of understory trees with a center of diversity in Central America and a small number of species in the Antilles and northern South America. Species in Crescentieae are united by their fleshy, indehiscent fruit and cauliflorous, bat-pollinated flowers. The large fruits are presumed to have evolved to be mammal dispersed, although water dispersal is known to occur. To lay...

Population abundance data and species range maps

Mathieu Chevalier, Olivier Broennimann & Antoine Guisan
Aim – The abundant-center hypothesis (ACH) predicts a negative relationship between species abundance and the distance to geographic range center. Since its formulation, empirical tests of the ACH have involved different settings (e.g. the distance to the ecological niche or to the geographic range center), but studies found contrasting support for this hypothesis. Here, we evaluate whether these discrepancies might stem from differences regarding the context in which the ACH is tested (geographical or environmental),...

Data from: Age and quality-dependent DNA methylation correlate with melanin-based colouration in a wild bird

Carl D. Soulsbury, Anssi Lipponen, Kristie Wood, Charles A. Mein, Joe I. Hoffman, Christophe Lebigre & Joseph I. Hoffman
Secondary sexual trait expression can be influenced by fixed individual factors (such as genetic quality) but also by dynamic factors (such as age and environmentally induced gene expression) that may be associated with variation in condition or quality. In particular, melanin-based traits are known to relate to condition and there is a well-characterized genetic pathway underpinning their expression. However, the mechanisms linking variable trait expression to genetic quality remain unclear. One plausible mechanism is that...

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