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Auteur Arnaud-Haond, S.; Aires, T.; Candeias, R.; Teixeira, S.J.L.; Duarte, C.M.; Valero, M.; Serrao, E.A. doi  openurl
  Titre Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia Type Article scientifique
  Année 2017 Publication Revue Abrégée Mol. Ecol.  
  Volume 26 Numéro 8 Pages (down) 2379-2391  
  Mots-Clés Algae; australia; Caulerpa; Chlorophyta; clonal diversity; dna; endophytic communities; genetic diversity; holobiont; invasion paradox; marine invasion; Mediterranean Sea; microsatellite markers; parasites; plant invasions; polymorphism  
  Résumé 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 alpha and beta 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 invasion, bacterial communities exhibit metabolic functions that can potentially enhance adaptability and competitiveness of the consortium they form with their host. We thus hypothesize that low genetic diversities of both host and symbiont communities may contribute to the recent regression in the Mediterranean, in contrast with the persistence of highly diverse assemblages in southern Australia. This study supports the importance of scaling up from the host to the holobiont for a comprehensive understanding of invasions.  
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  ISSN 0962-1083 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2143  
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Auteur Albouy, C.; Lasram, F.B.R.; Velez, L.; Guilhaumon, F.; Meynard, C.N.; Boyer, S.; Benestan, L.; Mouquet, N.; Douzery, E.; Aznar, R.; Troussellier, M.; Somot, S.; Leprieur, F.; Le Loc'h, F.; Mouillot, D. url  doi
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  Titre FishMed: traits, phylogeny, current and projected species distribution of Mediterranean fishes, and environmental data Type Article scientifique
  Année 2015 Publication Revue Abrégée Ecology  
  Volume 96 Numéro 8 Pages (down) 2312-2313  
  Mots-Clés climate change; coastal fishes; functional diversity; Mediterranean fish species; Mediterranean Sea; Nemomed8; phylogenetic diversity; species distribution models; taxonomic diversity  
  Résumé The FishMed database provides traits, phylogeny, current and projected species distribution of Mediterranean fishes, and associated sea surface temperature (SST) from the regional oceanic model NEMOMED8. Data for the current geographical distributions of 635 Mediterranean fish species were compiled from a published expert knowledge atlas of fishes of the northern Atlantic and the Mediterranean (FNAM) edited between 1984 and 1986 and from an updated exotic fish species list. Two future sets of projected species distributions were obtained for the middle and end of the 21st century by using an ensemble forecasting approach for 288 coastal Mediterranean fish species based on SST according to the IPPC/SRES A2 scenario implemented with the Mediterranean climatic model NEMOMED8. The functional part of the database encompasses 12 biological and ecological traits (maximal and common lengths, vertical distribution, habitat, migration type, mode of reproduction, sex shift, semelparity, diet type (larvae and adults), social behavior, species origin, and depth) for the 635 fish species. To build the phylogeny we inferred the timing and geographic origins of Mediterranean teleost species diversity using nucleotide sequences collected from GenBank including 62% of Mediterranean teleost species plus nine outgroups. Maximum likelihood Bayesian phylogenetic and dating analyses were calibrated using 20 fossil species. An additional 124 fish species were grafted onto the chronogram according to their taxonomic affinity to obtain a phylogenetic tree including 498 species. Finally we also present the associated SST data for the observed period (1961–1980) and for the middle (2040–2059) and the end of the 21st century (2080–2099) obtained from NEMOMED8 according to the IPCC A2 scenario. The FishMed database might be of interest in the context of global anthropogenic changes as coastal Mediterranean ecosystems are currently recognized as one of the most impacted ecosystems on earth.  
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  ISSN 1939-9170 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 1471  
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Auteur Mouillot, D.; De Bortoli, J.; Leprieur, F.; Parravicini, V.; Kulbicki, M.; Bellwood, D.R. url  doi
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  Titre The challenge of delineating biogeographical regions: nestedness matters for Indo-Pacific coral reef fishes Type Article scientifique
  Année 2013 Publication Revue Abrégée Journal of Biogeography  
  Volume 40 Numéro 12 Pages (down) 2228-2237  
  Mots-Clés -diversity; Archipelago; Coral Triangle; Indo-Australian; Pae; beta-diversity; biodiversity hotspots; conservation; delineation; dissimilarity; dung beetles; endemicity; evolutionary history; global; historical biogeography; nestedness; parsimony analysis; partitioning; patterns; reef fish assemblages; spatial-patterns; turnover  
  Résumé AimThe delineation of regions is a critical procedure in biogeography, but there is still no consensus about the best approach. Traditionally, a compositional dissimilarity index and a clustering algorithm are used to partition locations into regions. However, the choice of index and algorithm may have a profound impact on the final result, particularly when locations display different levels of species richness and when they are nested within each other. Our objective was to estimate the influence of species nestedness among locations on the delineation of biogeographical regions. LocationAs a case study, we used coral reef fishes (families Chaetodontidae, Pomacentridae and Labridae) from the Indo-Pacific, where a large richness gradient extends, often as a series of nested assemblages, from the species-rich Indo-Australian Archipelago (Coral Triangle) to species-poor peripheral locations. MethodsWe used the turnover and nestedness components of the SOrensen and Jaccard dissimilarity indices to estimate the effect of nestedness on the delineation of biogeographical regions. In addition, we compared the results with those obtained using a parsimony analysis of endemicity (PAE). ResultsLow Mantel correlation values revealed that the PAE method assembled locations in a very different way than methods based on dissimilarity indices for Indo-Pacific coral reef fishes. We also found that nestedness mattered when delineating biogeographical units because, for both the SOrensen and the Jaccard indices, reef fish assemblages were grouped differently depending on whether we used the turnover component of each index or the complete index, including the nestedness component. The turnover component ignored variation in species richness attributable to differences in habitat area between locations, and permitted a delineation based solely on species replacement. Main conclusionsWe demonstrate that the choice of the component used to measure dissimilarity between species assemblages is critical, because it may strongly influence regional delineations, at least for Indo-Pacific coral reef fishes. We conclude that the two components of the dissimilarity indices can reveal complementary insights into the role that history may have played in shaping extant patterns of biodiversity.  
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  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 0305-0270 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 879  
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Auteur Ottimofiore, E.; Albouy, C.; Leprieur, F.; Descombes, P.; Kulbicki, M.; Mouillot, D.; Parravicini, V.; Pellissier, L. doi  openurl
  Titre Responses of coral reef fishes to past climate changes are related to life-history traits Type Article scientifique
  Année 2017 Publication Revue Abrégée Ecol. Evol.  
  Volume 7 Numéro 6 Pages (down) 1996-2005  
  Mots-Clés climate change; dispersal; diversity; environmental-change; future; global patterns; Indo-Pacific Ocean; range shifts; refugia; richness; sea-level; species distribution; species distribution models; temperature  
  Résumé Coral reefs and their associated fauna are largely impacted by ongoing climate change. Unravelling species responses to past climatic variations might provide clues on the consequence of ongoing changes. Here, we tested the relationship between changes in sea surface temperature and sea levels during the Quaternary and present-day distributions of coral reef fish species. We investigated whether species-specific responses are associated with life-history traits. We collected a database of coral reef fish distribution together with life-history traits for the Indo-Pacific Ocean. We ran species distribution models (SDMs) on 3,725 tropical reef fish species using contemporary environmental factors together with a variable describing isolation from stable coral reef areas during the Quaternary. We quantified the variance explained independently by isolation from stable areas in the SDMs and related it to a set of species traits including body size and mobility. The variance purely explained by isolation from stable coral reef areas on the distribution of extant coral reef fish species largely varied across species. We observed a triangular relationship between the contribution of isolation from stable areas in the SDMs and body size. Species, whose distribution is more associated with historical changes, occurred predominantly in the Indo-Australian archipelago, where the mean size of fish assemblages is the lowest. Our results suggest that the legacy of habitat changes of the Quaternary is still detectable in the extant distribution of many fish species, especially those with small body size and the most sedentary. Because they were the least able to colonize distant habitats in the past, fish species with smaller body size might have the most pronounced lags in tracking ongoing climate change.  
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  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 2045-7758 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2108  
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Auteur Barberan, A.; Fernandez-Guerra, A.; Auguet, J.C.; Galand, P.E.; Casamayor, E.O. doi  openurl
  Titre Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota Type Article scientifique
  Année 2011 Publication Revue Abrégée Mol Ecol  
  Volume 20 Numéro 9 Pages (down) 1988-1996  
  Mots-Clés 16S/genetics Sequence Analysis; Biodiversity Databases; dna; Genetic *Ecosystem Environment Euryarchaeota/*classification/*genetics Genes; Ribosomal; rRNA/*genetics Phylogeny RNA  
  Résumé Despite its widespread distribution and high levels of phylogenetic diversity, microbes are poorly understood creatures. We applied a phylogenetic ecology approach in the Kingdom Euryarchaeota (Archaea) to gain insight into the environmental distribution and evolutionary history of one of the most ubiquitous and largely unknown microbial groups. We compiled 16S rRNA gene sequences from our own sequence libraries and public genetic databases for two of the most widespread mesophilic Euryarchaeota clades, Lake Dagow Sediment (LDS) and Rice Cluster-V (RC-V). The inferred population history indicated that both groups have undergone specific nonrandom evolution within environments, with several noteworthy habitat transition events. Remarkably, the LDS and RC-V groups had enormous levels of genetic diversity when compared with other microbial groups, and proliferation of sequences within each single clade was accompanied by significant ecological differentiation. Additionally, the freshwater Euryarchaeota counterparts unexpectedly showed high phylogenetic diversity, possibly promoted by their environmental adaptability and the heterogeneous nature of freshwater ecosystems. The temporal phylogenetic diversification pattern of these freshwater Euryarchaeota was concentrated both in early times and recently, similarly to other much less diverse but deeply sampled archaeal groups, further stressing that their genetic diversity is a function of environment plasticity. For the vast majority of living beings on Earth (i.e. the uncultured microorganisms), how they differ in the genetic or physiological traits used to exploit the environmental resources is largely unknown. Inferring population history from 16S rRNA gene-based molecular phylogenies under an ecological perspective may shed light on the intriguing relationships between lineage, environment, evolution and diversity in the microbial world.  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1305  
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