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A new classification scheme of European cold-water coral habitats: implications for ecosystem-based management of the deep sea ArchiMer
Davies, J. S.; Guillaumont, Brigitte; Tempera, Fernando; Vertino, A.; Beuck, L.; Olafsdottir, S. H.; Smith, C. J.; Fossa, J. H.; Van Den Beld, Inge; Savini, A.; Rengstorf, A.; Bayle, Christophe; Bourillet, Jean-francois; Arnaud-haond, Sophie; Grehan, A..
Cold-water coral (CWC) habitats can form complex structures which provide refuge, nursery grounds and physical support for a diversity of other living organisms, but despite their ecological significance, CWCs are still vulnerable to human pressures such as fishing, pollution, ocean acidification and global warming Providing coherent and representative conservation of vulnerable marine ecosystems including CWCs is one of the aims of the Marine Protected Areas networks being implemented across European seas and oceans under the EC Habitats Directive, the Marine Strategy Framework Directive and the OSPAR Convention. In order to adequately represent ecosystem diversity these initiatives require a standardised habitat classification that organises the variety...
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Ano: 2017 URL: http://archimer.ifremer.fr/doc/00383/49474/49961.pdf
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A Well-Kept Treasure at Depth: Precious Red Coral Rediscovered in Atlantic Deep Coral Gardens (SW Portugal) after 300 Years ArchiMer
Boavida, Joana; Paulo, Diogo; Aurelle, Didier; Arnaud-haond, Sophie; Marschal, Christian; Reed, John; Goncalves, Jorge M. S.; Serrao, Ester A..
Background The highly valuable red coral Corallium rubrum is listed in several Mediterranean Conventions for species protection and management since the 1980s. Yet, the lack of data about its Atlantic distribution has hindered its protection there. This culminated in the recent discovery of poaching activities harvesting tens of kg of coral per day from deep rocky reefs off SW Portugal. Red coral was irregularly exploited in Portugal between the 1200s and 1700s, until the fishery collapsed. Its occurrence has not been reported for the last 300 years. Results Here we provide the first description of an Atlantic red coral assemblage, recently rediscovered dwelling at 60-100 m depth in southern Portugal. We report a very slow growth rate (0.23 mm year-1),...
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Ano: 2016 URL: https://archimer.ifremer.fr/doc/00314/42498/41877.pdf
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Better off alone? Compared performance of monoclonal and polyclonal stands of a cultivated red alga growth ArchiMer
Usandizaga, Sara; Buschmann, Alejandro H.; Camus, Carolina; Kappes, José Luis; Arnaud-haond, Sophie; Mauger, Stéphane; Valero, Myriam; Guillemin, Marie Laure.
The objective of this study was to test, using a field experiment, the effect of genotypic diversity on productivity of farmed populations (Ancud and Chaica, Chile) of the domesticated red alga Agarophyton chilense (formerly known as Gracilaria chilensis), a species considered as economically important in Chile. Monoclonal and polyclonal (4 and 8 genotypes) subplots were outplanted into the mid intertidal in Metri Bay (Puerto Montt, Chile) during summer, a season in which A. chilense face higher temperatures (>18°C) and low nitrogen availability (<4.00 μmol). Ancud farm genotypes show higher growth rates in the monoclonal rather than the two polyclonal subplots. A similar tendency, yet not significant, was discernible in Chaica. In addition, whatever...
Tipo: Text Palavras-chave: Domestication; General‐purpose genotypes; Genotypic diversity; Productivity; Seaweed.
Ano: 2020 URL: https://archimer.ifremer.fr/doc/00605/71727/70197.pdf
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Biogeographical distribution of Rimicaris exoculata resident gut epibiont communities along the Mid-Atlantic Ridge hydrothermal vent sites ArchiMer
Durand, Lucile; Roumagnac, Marie; Cueff-gauchard, Valerie; Jan, Cyrielle; Guri, Mathieu; Tessier, Claire; Haond, Marine; Crassous, Philippe; Zbinden, Magali; Arnaud-haond, Sophie; Cambon-bonavita, Marie-anne.
Rimicaris exoculata is a deep-sea hydrothermal vent shrimp which enlarged gill chamber houses a complex trophic epibiotic community. Its gut harbours an autochthonous and distinct microbial community. This species dominates hydrothermal ecosystems megafauna along the Mid-Atlantic Ridge, regardless of contrasted geochemical conditions prevailing in them. Here, the resident gut epibiont community at four contrasted hydrothermal vent sites (Rainbow/TAG/Logatchev/Ashadze) was analysed and compiled with previous data to evaluate the possible influence of site location, using 16S rRNA surveys and microscopic observations (TEM, SEM and FISH analyses). Filamentous epibionts inserted between the epithelial cells microvilli were observed on all examined samples....
Tipo: Text Palavras-chave: Epibiont; Extreme environments; Network analyses; Phylogeography.
Ano: 2015 URL: http://archimer.ifremer.fr/doc/00288/39890/38443.pdf
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Biogeography Revisited with Network Theory: Retracing the History of Hydrothermal Vent Communities ArchiMer
Moalic, Yann; Desbruyeres, Daniel; Duarte, Carlos M.; Rozenfeld, Alejandro F.; Bachraty, Charleyne; Arnaud-haond, Sophie.
Defining biogeographic provinces to understand the history and evolution of communities associated with a given kind of ecosystem is challenging and usually requires a priori assumptions to be made. We applied network theory, a holistic and exploratory method, to the most complete database of faunal distribution available on oceanic hydrothermal vents, environments which support fragmented and unstable ecosystems, to infer the processes driving their worldwide biogeography. Besides the identification of robust provinces, the network topology allowed us to identify preferential pathways that had hitherto been overlooked. These pathways are consistent with the previously proposed hypothesis of a role of plate tectonics in the biogeographical history of...
Tipo: Text Palavras-chave: Biogeography; Deep sea ecology; Hydrothermal vents; Network analysis; Systems biology.
Ano: 2012 URL: http://archimer.ifremer.fr/doc/00063/17400/15164.pdf
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Climate‐induced changes in the suitable habitat of cold‐water corals and commercially important deep‐sea fishes in the North Atlantic ArchiMer
Morato, Telmo; González‐irusta, José‐manuel; Dominguez‐carrió, Carlos; Wei, Chih‐lin; Davies, Andrew; Sweetman, Andrew K.; Taranto, Gerald H.; Beazley, Lindsay; García‐alegre, Ana; Grehan, Anthony; Laffargue, Pascal; Murillo, Francisco Javier; Sacau, Mar; Vaz, Sandrine; Kenchington, Ellen; Arnaud-haond, Sophie; Callery, Oisín; Chimienti, Giovanni; Cordes, Erik; Egilsdottir, Hronn; Freiwald, André; Gasbarro, Ryan; Gutiérrez‐zárate, Cristina; Gianni, Matthew; Gilkinson, Kent; Wareham Hayes, Vonda E.; Hebbeln, Dierk; Hedges, Kevin; Henry, Lea‐anne; Johnson, David; Koen‐alonso, Mariano; Lirette, Cam; Mastrototaro, Francesco; Menot, Lenaick; Molodtsova, Tina; Durán Muñoz, Pablo; Orejas, Covadonga; Pennino, Maria Grazia; Puerta, Patricia; Ragnarsson, Stefán Á.; Ramiro‐sánchez, Berta; Rice, Jake; Rivera, Jesús; Roberts, J. Murray; Ross, Steve W.; Rueda, José L.; Sampaio, Íris; Snelgrove, Paul; Stirling, David; Treble, Margaret A.; Urra, Javier; Vad, Johanne; Oevelen, Dick; Watling, Les; Walkusz, Wojciech; Wienberg, Claudia; Woillez, Mathieu; Levin, Lisa A.; Carreiro‐silva, Marina.
The deep sea plays a critical role in global climate regulation through uptake and storage of heat and carbon dioxide. However, this regulating service causes warming, acidification and deoxygenation of deep waters, leading to decreased food availability at the seafloor. These changes and their projections are likely to affect productivity, biodiversity and distributions of deep‐sea fauna, thereby compromising key ecosystem services. Understanding how climate change can lead to shifts in deep‐sea species distributions is critically important in developing management measures. We used environmental niche modelling along with the best available species occurrence data and environmental parameters to model habitat suitability for key cold‐water coral and...
Tipo: Text Palavras-chave: Climate change; Cold-water corals; Deep-sea; Fisheries; Fishes; Habitat suitability modelling; Octocorals; Scleractinians; Species distribution models; Vulnerable marine ecosystems.
Ano: 2020 URL: https://archimer.ifremer.fr/doc/00610/72211/71007.pdf
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ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps ArchiMer
Becheler, Ronan; Masson, Jean-pierre; Arnaud-haond, Sophie; Halkett, Fabien; Mariette, Stephanie; Guillemin, Marie-laure; Valero, Myriam; Destombe, Christophe; Stoeckel, Solenn.
Partial clonality is commonly used in Eukaryotes and has large consequences for their evolution and ecology. Assessing accurately the relative importance of clonal versus sexual reproduction matters for studying and managing such species. Here, we proposed a Bayesian approach, ClonEstiMate, to infer rates of clonality c from populations sampled twice over a short time interval, ideally one generation time. The method relies on the likelihood of the transitions between genotype frequencies of ancestral and descendent populations, using an extended Wright-Fisher model explicitly integrating reproductive modes. Our model provides posterior probability distribution of inferred c, given the assumed rates of mutation, as well as inbreeding and selfing when...
Tipo: Text Palavras-chave: Inbreeding; Instantaneous inference; Population genetics model; Rate of asexuality; Selfing.
Ano: 2017 URL: https://archimer.ifremer.fr/doc/00390/50187/50810.pdf
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Cold-water coral habitats in submarine canyons of the Bay of Biscay ArchiMer
Van Den Beld, Inge; Bourillet, Jean-francois; Arnaud-haond, Sophie; De Chambure, Laurent; Davies, Jaime S; Guillaumont, Brigitte; Olu, Karine; Menot, Lenaick.
The topographical and hydrological complexity of submarine canyons, coupled with high substratum heterogeneity, make them ideal environments for cold-water coral (CWC) habitats. These habitats, including reefs, are thought to provide important functions for many organisms. The canyons incising the continental slope of the Bay of Biscay have distinct morphological differences from the north to the south. CWCs have been reported from this basin in the late 19th century; however, little is known about their present-day distribution, diversity and environmental drivers in the canyons. In this study, the characteristics and distribution of CWC habitats in the submarine canyons of the Bay of Biscay are investigated. Twenty-four canyons and three locations...
Tipo: Text Palavras-chave: Cold-water corals; Habitats; Submarine canyons; Bay of Biscay; NE Atlantic; ROV; Towed camera; Distribution.
Ano: 2017 URL: https://archimer.ifremer.fr/doc/00382/49343/49733.pdf
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Comparative Analysis of Stability-Genetic Diversity in Seagrass (Posidonia oceanica) Meadows Yields Unexpected Results ArchiMer
Arnaud-haond, Sophie; Marba, Nuria; Diaz-almela, Elena; Serrao, Ester A.; Duarte, Carlos M..
The diversity-stability relationship is the subject of a long-standing debate in ecology, but the genetic component of diversity has seldom been explored. In this study, we analyzed the interplay between genetic diversity and demographic responses to environmental pressures. This analysis included 30 meadows formed by the Mediterranean endemic seagrass, Posidonia oceanica, showing a wide range of population dynamics ranging from a near equilibrium state to steep decline due to strong environmental pressures close to aquaculture installations. Our results show that sedimentation rates are much better predictors of mortality than clonal or genetic components. An unexpected positive trend was observed between genotypic diversity and mortality, along with a...
Tipo: Text Palavras-chave: Seagrass; Demography; Clonality; Genetic richness; Diversity-stability; Posidonia oceanica.
Ano: 2010 URL: http://archimer.ifremer.fr/doc/00006/11693/8498.pdf
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Comprendre et inférer la connectivité marine pour mieux gérer les ressources ArchiMer
Bierne, Nicolas; Arnaud-haond, Sophie.
Tipo: Text
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00487/59820/62963.pdf
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Connecting MPAs - eight challenges for science and management ArchiMer
Lagabrielle, Erwann; Crochelet, Estelle; Andrello, Marco; Schill, Steven R.; Arnaud-haond, Sophie; Alloncle, Neil; Ponge, Benjamin.
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;...
Tipo: Text Palavras-chave: Ocean; Coastal; Conservation evaluation; Marine protected areas; Spatial modelling; Fishing.
Ano: 2014 URL: http://archimer.ifremer.fr/doc/00226/33742/33891.pdf
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Dedicated population genomics for the silent world: the specific questions of marine population genetics ArchiMer
Bierne, Nicolas; Bonhomme, Francois; Arnaud-haond, Sophie.
Tipo: Text
Ano: 2016 URL: https://archimer.ifremer.fr/doc/00374/48545/48841.pdf
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Deep-sea genetic resources ArchiMer
Desbruyere, D; Arnaud-haond, Sophie; Fabri, Marie-claire; Guezennec, Jean; Querellou, Joel.
Two third of our Planet are covered by oceans more than 3,000m deep (~ 307 millions km2) and the mean depth of the sea is approximately 3,800m. The volume of the deep ocean (aphotic) is about 1,280 Millions of km3 while the volume of terrestrial ecosystems is only 125 Millions of km3. Therefore, the deep-sea ecosystem is by far the largest complex biome on the Earth. However, it suffers from a general disinterest of the public and decision makers due to its remoteness and inaccessibility. Edward Forbes "azoic theory" is still deeply rooted in most people brains and during public conferences, a large part of the audience being still amazed to hear that macroscopic life does exist in the deepest part of the sea floor (11,000m depth).
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Ano: 2007 URL: http://archimer.ifremer.fr/doc/00153/26452/24558.pdf
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Discriminating Micropathogen Lineages and Their Reticulate Evolution through Graph Theory-Based Network Analysis: The Case of Trypanosoma cruzi, the Agent of Chagas Disease ArchiMer
Arnaud-haond, Sophie; Moalic, Yann; Barnabe, Christian; Ayala, Francisco Jose; Tibayrenc, Michel.
Micropathogens (viruses, bacteria, fungi, parasitic protozoa) share a common trait, which is partial clonality, with wide variance in the respective influence of clonality and sexual recombination on the dynamics and evolution of taxa. The discrimination of distinct lineages and the reconstruction of their phylogenetic history are key information to infer their biomedical properties. However, the phylogenetic picture is often clouded by occasional events of recombination across divergent lineages, limiting the relevance of classical phylogenetic analysis and dichotomic trees. We have applied a network analysis based on graph theory to illustrate the relationships among genotypes of Trypanosoma cruzi, the parasitic protozoan responsible for Chagas disease,...
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Ano: 2014 URL: http://archimer.ifremer.fr/doc/00212/32374/30837.pdf
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Disentangling the Influence of Mutation and Migration in Clonal Seagrasses Using the Genetic Diversity Spectrum for Microsatellites ArchiMer
Arnaud-haond, Sophie; Moalic, Yann; Hernandez-garcia, Emilio; Eguiluz, Victor M.; Alberto, Filipe; Serrao, Ester A.; Duarte, Carlos M..
The recurrent lack of isolation by distance reported at regional scale in seagrass species was recently suggested to stem from stochastic events of large-scale dispersal. We explored the usefulness of phylogenetic information contained in microsatellite loci to test this hypothesis by using the Genetic Diversity Spectrum (GDS) on databases containing, respectively, 7 and 9 microsatellites genotypes for 1541 sampling units of Posidonia oceanica and 1647 of Cymodocea nodosa. The simultaneous increase of microsatellite and geographic distances that emerges reveals a coherent pattern of isolation by distance in contrast to the chaotic pattern previously described using allele frequencies, in particular, for the long-lived P. oceanica. These results suggest...
Tipo: Text Palavras-chave: Clonality; Genetic Diversity Spectrum; Genetic divergence; Microsatellites; Seagrass; Stepwise mutation.
Ano: 2014 URL: http://archimer.ifremer.fr/doc/00182/29292/27733.pdf
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Ecological Restoration in the Deep Sea: Desiderata ArchiMer
Van Dover, C. L.; Aronson, J.; Pendleton, L.; Smith, S.; Arnaud-haond, Sophie; Moreno-mateos, D.; Barbier, E.; Billett, D.; Bowers, K.; Danovaro, R.; Edwards, A.; Kellert, S.; Morato, T.; Pollard, E.; Rogers, A.; Warner, R..
An era of expanding deep-ocean industrialization is before us, with policy makers establishing governance frameworks for sustainable management of deep-sea resources while scientists learn more about the ecological structure and functioning of the largest biome on the planet. Missing from discussion of the stewardship of the deep ocean is ecological restoration. If existing activities in the deep sea continue or are expanded and new deep-ocean industries are developed, there is need to consider what is required to minimize or repair resulting damages to the deep-sea environment. In addition, thought should be given as to how any past damage can be rectified. This paper develops the discourse on deep-sea restoration and offers guidance on planning and...
Tipo: Text Palavras-chave: Deep-sea resource use; Restoration science; Marine policy; Hydrothermal vents; Cold-water corals.
Ano: 2014 URL: http://archimer.ifremer.fr/doc/00153/26421/24521.pdf
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EDENetworks: A user-friendly software to build and analyse networks in biogeography, ecology and population genetics ArchiMer
Kivela, Mikko; Arnaud-haond, Sophie; Saramaki, Jari.
The recent application of graph-based network theory analysis to biogeography, community ecology and population genetics has created a need for user-friendly software, which would allow a wider accessibility to and adaptation of these methods. EDENetworks aims to fill this void by providing an easy-to-use interface for the whole analysis pipeline of ecological and evolutionary networks starting from matrices of species distributions, genotypes, bacterial OTUs or populations characterized genetically. The user can choose between several different ecological distance metrics, such as Bray-Curtis or Sorensen distance, or population genetic metrics such as FST or Goldstein distances, to turn the raw data into a distance/dissimilarity matrix. This matrix is...
Tipo: Text Palavras-chave: Biogeography; Biological communities; Graph theory; Microbial ecology; Network analysis; Population genetics.
Ano: 2015 URL: http://archimer.ifremer.fr/doc/00197/30853/29217.pdf
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Entangled effects of allelic and clonal (genotypic) richness in the resistance and resilience of experimental populations of the seagrass Zostera noltii to diatom invasion ArchiMer
Massa, Sonia I.; Paulino, Cristina M.; Serrao, Ester A.; Duarte, Carlos M.; Arnaud-haond, Sophie.
Background: The relationship between species diversity and components of ecosystem stability has been extensively studied, whilst the influence of the genetic component of biodiversity remains poorly understood. Here we manipulated both genotypic and allelic richness of the seagrass Zostera noltii, in order to explore their respective influences on the resistance of the experimental population to stress. Thus far intra-specific diversity was seldom taken into account in management plans, and restoration actions showed very low success. Information is therefore needed to understand the factors affecting resistance and resilience of populations. Results: Our results show a positive influence of both allelic and genotypic richness on the resistance of...
Tipo: Text Palavras-chave: Allelic richness; Genotypic richness; Resistance; Resilience; Zostera noltii; Biotic stress; Seagrass.
Ano: 2013 URL: http://archimer.ifremer.fr/doc/00166/27748/25946.pdf
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Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia ArchiMer
Arnaud-haond, Sophie; Aires, Tania; Candeias, R.; Teixeira, S. J. L.; Duarte, C. M.; Valero, M.; Serrao, E. A..
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 unit of spreading and invasion. Both genomic compartments support the hypotheses of a unique accidental introduction in the Mediterranean and of multiple invasion events in Southern Australia. In addition to helping with tracing the origin of...
Tipo: Text Palavras-chave: Caulerpa; Clonal diversity; Endophytic communities; Holobiont; Invasion paradox; Marine invasion.
Ano: 2017 URL: https://archimer.ifremer.fr/doc/00369/48058/48145.pdf
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Evolutionary history of the seagrass genus Posidonia ArchiMer
Aires, Tania; Marba, Nuria; Cunha, Regina L.; Kendrick, Gary A.; Walker, Diana I.; Serrao, Ester A.; Duarte, Carlos M.; Arnaud-haond, Sophie.
Seagrasses are the structural species of one of the most important coastal ecosystems worldwide and support high levels of biodiversity and biomass production. Posidonia is one of the most ancient seagrass genera and displays a contrasting disjunct biogeographic pattern. It contains one single species in the Northern Hemisphere, P. oceanica, which is endemic to the Mediterranean Sea, and has up to 8 recognized taxa in the Southern Hemisphere, which in Australia are divided into 2 complexes, P. ostenfeldii and P. australis. A phylogeny based on a nuclear marker (rRNA-ITS) revealed an ancient split between the northern (i.e. Mediterranean) and southern (i.e. Australian) taxa, followed by a separation of the 2 recognized Australian complexes. However, the...
Tipo: Text Palavras-chave: Posidonia; Phylogeny; Low evolutionary rates; Ancient diversification.
Ano: 2011 URL: http://archimer.ifremer.fr/doc/00027/13798/10937.pdf
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