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Auteur Pecoraro, C.; Babbucci, M.; Franch, R.; Rico, C.; Papetti, C.; Chassot, E.; Bodin, N.; Cariani, A.; Bargelloni, L.; Tinti, F. doi  openurl
  Titre The population genomics of yellowfin tuna (Thunnus albacares) at global geographic scale challenges current stock delineation Type Article scientifique
  Année 2018 Publication Revue Abrégée Sci Rep  
  Volume 8 Numéro Pages (down) 13890  
  Mots-Clés archival tag data; atlantic bluefin tuna; connectivity; conservation; divergence; fisheries management; habitat utilization; loci; pacific-ocean; relatedness  
  Résumé Yellowfin tuna, Thunnus albacares, is one of the most important seafood commodities in the world. Despite its great biological and economic importance, conflicting evidence arises from classical genetic and tagging studies concerning the yellowfin tuna population structure at local and global oceanic scales. Access to more powerful and cost effective genetic tools would represent the first step towards resolving the population structure of yellowfin tuna across its distribution range. Using a panel of 939 neutral Single Nucleotide Polymorphisms (SNPs), and the most comprehensive data set of yellowfin samples available so far, we found genetic differentiation among the Atlantic, Indian and Pacific oceans. The genetic stock structure analysis carried out with 33 outlier SNPs, putatively under selection, identified discrete populations within the Pacific Ocean and, for the first time, also within the Atlantic Ocean. Stock assessment approaches that consider genetic differences at neutral and adaptive genomic loci should be routinely implemented to check the status of the yellowfin tuna, prevent illegal trade, and develop more sustainable management measures.  
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  ISSN 2045-2322 ISBN Médium  
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Auteur Toussaint, A.; Charpin, N.; Beauchard, O.; Grenouillet, G.; Oberdorff, T.; Tedesco, P.A.; Brosse, S.; Villeger, S. doi  openurl
  Titre Non-native species led to marked shifts in functional diversity of the world freshwater fish faunas Type Article scientifique
  Année 2018 Publication Revue Abrégée Ecol. Lett.  
  Volume 21 Numéro 11 Pages (down) 1649-1659  
  Mots-Clés assemblages; biodiversity; Biotic exchanges; communities; extinction; extirpations; functional richness; functional divergence; homogenization; hydropower; introduction; invasion; islands; macroecology; patterns; richness  
  Résumé Global spread of non-native species profoundly changed the world biodiversity patterns, but how it translates into functional changes remains unanswered at the world scale. We here show that while in two centuries the number of fish species per river increased on average by 15% in 1569 basins worldwide, the diversity of their functional attributes (i.e. functional richness) increased on average by 150%. The inflation of functional richness was paired with changes in the functional structure of assemblages, with shifts of species position toward the border of the functional space of assemblages (i.e. increased functional divergence). Non-native species moreover caused shifts in functional identity toward higher body sized and less elongated species for most of assemblages throughout the world. Although varying between rivers and biogeographic realms, such changes in the different facets of functional diversity might still increase in the future through increasing species invasion and may further modify ecosystem functioning.  
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  ISSN 1461-023x ISBN Médium  
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Auteur Riquet, F.; Liautard-Haag, C.; Woodall, L.; Bouza, C.; Louisy, P.; Hamer, B.; Otero-Ferrer, F.; Aublanc, P.; Beduneau, V.; Briard, O.; El Ayari, T.; Hochscheid, S.; Belkhir, K.; Arnaud-Haond, S.; Gagnaire, P.-A.; Bierne, N. doi  openurl
  Titre Parallel pattern of differentiation at a genomic island shared between clinal and mosaic hybrid zones in a complex of cryptic seahorse lineages Type Article scientifique
  Année 2019 Publication Revue Abrégée Evolution  
  Volume 73 Numéro 4 Pages (down) 817-835  
  Mots-Clés Clinal hybrid zone; demographic history; divergence; ecological speciation; evolution; gene-flow; house mouse; introgression patterns; local adaptation; mosaic hybrid zone; parallel evolution; r-package; reproductive isolation; speciation  
  Résumé Diverging semi-isolated lineages either meet in narrow clinal hybrid zones, or have a mosaic distribution associated with environmental variation. Intrinsic reproductive isolation is often emphasized in the former and local adaptation in the latter, although both reduce gene flow between groups. Rarely are these two patterns of spatial distribution reported in the same study system. Here, we report that the long-snouted seahorse Hippocampus guttulatus is subdivided into discrete panmictic entities by both types of hybrid zones. Along the European Atlantic coasts, a northern and a southern lineage meet in the southwest of France where they coexist in sympatryi.e., in the same geographical zonewith little hybridization. In the Mediterranean Sea, two lineages have a mosaic distribution, associated with lagoon-like and marine habitats. A fifth lineage was identified in the Black Sea. Genetic homogeneity over large spatial scales contrasts with isolation maintained in sympatry or close parapatry at a fine scale. A high variation in locus-specific introgression rates provides additional evidence that partial reproductive isolation must be maintaining the divergence. We find that fixed differences between lagoon and marine populations in the Mediterranean Sea belong to the most differentiated SNPs between the two Atlantic lineages, against the genome-wide pattern of structure that mostly follow geography. These parallel outlier SNPs cluster on a single chromosome-wide island of differentiation. Since Atlantic lineages do not map to lagoon-sea habitat variation, genetic parallelism at the genomic island suggests a shared genetic barrier contributes to reproductive isolation in contrasting contexts-i.e., spatial versus ecological. We discuss how a genomic hotspot of parallel differentiation could have evolved and become associated both with space and with a patchy environment in a single study system.  
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  ISSN 0014-3820 ISBN Médium  
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Auteur Mason, N.W.H.; de Bello, F.; Mouillot, D.; Pavoine, S.; Dray, S. url  doi
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  Titre A guide for using functional diversity indices to reveal changes in assembly processes along ecological gradients Type Article scientifique
  Année 2013 Publication Revue Abrégée J Veg Sci  
  Volume 24 Numéro 5 Pages (down) 794-806  
  Mots-Clés Co-existence; Environmental filtering; Functional divergence; Functional evenness; Functional richness; Functional trait; Limiting similarity; Niche complementarity; Null models; species richness  
  Résumé Question Which functional diversity indices have the power to reveal changes in community assembly processes along abiotic stress gradients? Is their power affected by stochastic processes and variations in species richness along stress gradients?

Methods We used a simple community assembly model to explore the power of functional diversity indices across a wide range of ecological contexts. FD) and convex hull volume (FRic) – with a matrix-swap null model (yielding indices SESFD and SESFRic) to remove any trivial effects of species richness. We also compared two indices that measure both functional richness and functional divergence – Rao quadratic entropy (Rao) and functional dispersion (FDis) – with a null model that randomizes abundances across species but within communities. SESRao and SESFDis).

Results When mass effects operated, only SESRao and SESFDis gave reasonable power, irrespective of how species richness varied along the stress gradient. FD, FRic, Rao and FDis had low power when species richness was constant, and variation in species richness greatly influenced their power. SESFRic and SESFD were unaffected by variation in species richness. When priority effects operated, FRic, SESFRic, Rao and FDis had good power and were unaffected by variation in species richness. Variation in species richness greatly affected FD and SESFD. SESRao and SESFDis had low power in the priority effects model but were unaffected by variation in species richness.

Conclusions Our results demonstrate that a reliable test for changes in assembly processes along stress gradients requires functional diversity indices measuring either functional richness or functional divergence. We recommend using SESFRic as a measure of functional richness and either SESRao or SESFDis (which are very closely related mathematically) as a measure of functional divergence. Used together, these indices of functional richness and functional divergence provide good power to test for increasing niche complementarity with declining stress across a broad range of ecological contexts.
 
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  ISSN 1654-1103 ISBN Médium  
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Auteur ARNAUD-HAOND, S.; MOALIC, Y.; HERNANDEZ-GARCIA, E.; EGUILUZ, V.M.; ALBERTO, F.; SERRAO, E.A.; DUARTE, C.M. url  openurl
  Titre Disentangling the Influence of Mutation and Migration in Clonal Seagrasses Using the Genetic Diversity Spectrum for Microsatellites Type Article scientifique
  Année 2014 Publication Revue Abrégée Journal Of Heredity  
  Volume 105 Numéro 4 Pages (down) 532-541  
  Mots-Clés clonality; genetic divergence; Genetic Diversity Spectrum; microsatellites; Seagrass; stepwise mutation  
  Résumé 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 that the lack of isolation by distance, rather than the resulting from rare events of large-scale dispersal, reflects at least for some species a stronger influence of mutation over migration at the scale of the distribution range. The global distribution of genetic polymorphism may, therefore, result predominantly from ancient events of step-by-step (re)colonization followed by local recruitment and clonal growth, rather than contemporary gene flow. The analysis of GDS appears useful to unravel the evolutionary forces influencing the dynamics and evolution at distinct temporal and spatial scales by accounting for phylogenetic information borne by microsatellites, under an appropriate mutation model. This finding adds nuance to the generalization of the influence of large-scale dispersal on the dynamics of seagrasses.  
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  ISSN 0022-1503 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1138  
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