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Auteur Dalongeville, A.; Benestan, L.; Mouillot, D.; Lobreaux, S.; Manel, S. doi  openurl
  Titre Combining six genome scan methods to detect candidate genes to salinity in the Mediterranean striped red mullet (Mullus surmuletus) Type Article scientifique
  Année 2018 Publication Revue Abrégée BMC Genomics  
  Volume 19 Numéro Pages 217  
  Mots-Clés Adaptive genomics; Candidate genes; climate; genetics; Genome scan; landscape genomics; local adaptation; Mediterranean Sea; methionine sulfoxide reductase; Mullus surmuletus; population genomics; principal component analysis; r package; Salinity; selection; threespine sticklebacks  
  Résumé Background: Adaptive genomics may help predicting how a species will respond to future environmental changes. Genomic signatures of local adaptation in marine organisms are often driven by environmental selective agents impacting the physiology of organisms. With one of the highest salinity level, the Mediterranean Sea provides an excellent model to investigate adaptive genomic divergence underlying salinity adaptation. In the present study, we combined six genome scan methods to detect potential genomic signal of selection in the striped red mullet (Mullus surmuletus) populations distributed across a wide salinity gradient. We then blasted these outlier sequences on published fish genomic resources in order to identify relevant potential candidate genes for salinity adaptation in this species. Results: Altogether, the six genome scan methods found 173 outliers out of 1153 SNPs. Using a blast approach, we discovered four candidate SNPs belonging to three genes potentially implicated in adaptation of M. surmuletus to salinity. The allele frequency at one of these SNPs significantly increases with salinity independently from the effect of longitude. The gene associated to this SNP, SOCS2, encodes for an inhibitor of cytokine and has previously been shown to be expressed under osmotic pressure in other marine organisms. Additionally, our results showed that genome scan methods not correcting for spatial structure can still be an efficient strategy to detect potential footprints of selection, when the spatial and environmental variation are confounded, and then, correcting for spatial structure in a second step represents a conservative method. Conclusion: The present outcomes bring evidences of potential genomic footprint of selection, which suggest an adaptive response of M. surmuletus to salinity conditions in the Mediterranean Sea. Additional genomic data such as sequencing of a full-genome and transcriptome analyses of gene expression would provide new insights regarding the possibility that some striped red mullet populations are locally adapted to their saline environment.  
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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 1471-2164 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2324  
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Auteur Dalongeville, A.; Andrello, M.; Mouillot, D.; Lobreaux, S.; Fortin, M.-J.; Lasram, F.; Belmaker, J.; Rocklin, D.; Manel, S. doi  openurl
  Titre Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale Type Article scientifique
  Année 2018 Publication Revue Abrégée Evol. Appl.  
  Volume 11 Numéro 8 Pages 1437-1447  
  Mots-Clés caribbean reef fish; connectivity; divergent selection; ecological data; ecological genetics; landscape genetics; marine connectivity; marine fish; Mediterranean Sea; Mullus surmuletus; neighbor matrices; oceanography; population-structure; sea; seascape genetics; single nucleotide polymorphism; surmuletus  
  Résumé Genetic variation, as a basis of evolutionary change, allows species to adapt and persist in different climates and environments. Yet, a comprehensive assessment of the drivers of genetic variation at different spatial scales is still missing in marine ecosystems. Here, we investigated the influence of environment, geographic isolation, and larval dispersal on the variation in allele frequencies, using an extensive spatial sampling (47 locations) of the striped red mullet (Mullus surmuletus) in the Mediterranean Sea. Univariate multiple regressions were used to test the influence of environment (salinity and temperature), geographic isolation, and larval dispersal on single nucleotide polymorphism (SNP) allele frequencies. We used Moran's eigenvector maps (db-MEMs) and asymmetric eigenvector maps (AEMs) to decompose geographic and dispersal distances in predictors representing different spatial scales. We found that salinity and temperature had only a weak effect on the variation in allele frequencies. Our results revealed the predominance of geographic isolation to explain variation in allele frequencies at large spatial scale (>1,000km), while larval dispersal was the major predictor at smaller spatial scale (<1,000km). Our findings stress the importance of including spatial scales to understand the drivers of spatial genetic variation. We suggest that larval dispersal allows to maintain gene flows at small to intermediate scale, while at broad scale, genetic variation may be mostly shaped by adult mobility, demographic history, or multigenerational stepping-stone dispersal. These findings bring out important spatial scale considerations to account for in the design of a protected area network that would efficiently enhance protection and persistence capacity of marine species.  
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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 1752-4571 ISBN Médium  
  Région Expédition Conférence  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2422  
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Auteur Tserpes, G.; Massuti, E.; Fiorentino, F.; Facchini, M.T.; Viva, C.; Jadaud, A.; Joksimovic, A.; Pesci, P.; Piccinetti, C.; Sion, L.; Thasitis, I.; Vrgoc, N. doi  openurl
  Titre Distribution and spatio-temporal biomass trends of red mullets across the Mediterranean Type Article scientifique
  Année 2019 Publication Revue Abrégée Sci. Mar.  
  Volume 83 Numéro Pages 43-55  
  Mots-Clés distribution; egg size; fishery; gamma; history; management; Mediterranean; mullus-barbatus l.; perciformes; red mullet; sea; stock structure; striped red mullet; surmuletus; trends  
  Résumé The present work examines the spatio-temporal biomass trends of Mullus barbatus and Mullus sunnuletus in the Mediterranean Sea through the analysis of a time series of data coming from the Mediterranean International Trawl Surveys (MEDITS), accomplished annually from 1994 to 2015. The biomass of both species showed clear declining trends below 150 to 200 m depth, which were steeper in the case of M. barbatus. Increases in temporal biomass trends were observed for M. barbatus from 2008 onward in most geographic sub-areas (GSAs), while stability was mostly observed for M. stumuletus. For both species, dynamic factor analysis revealed similarities among neighbouring GSAs and the subsequent cluster analysis identified two major GSA groups corresponding to the eastern and western basins of the Mediterranean. Overall, the results suggested that the combined effects of fishing and environmental conditions determine species abundance variations, but the relative importance of each component may vary among areas.  
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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 0214-8358 ISBN Médium  
  Région Expédition Conférence  
  Notes WOS:000504829900004 Approuvé (up) pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2714  
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Auteur Boulanger, E.; Dalongeville, A.; Andrello, M.; Mouillot, D.; Manel, S. doi  openurl
  Titre Spatial graphs highlight how multi-generational dispersal shapes landscape genetic patterns Type Article scientifique
  Année 2020 Publication Revue Abrégée Ecography  
  Volume Numéro Pages  
  Mots-Clés connectivity; fish populations; flow; genetic connectivity; habitat; Mediterranean Sea; migration rates; models; Mullus surmuletus; mullus-surmuletus; ocean currents; r-package; seascape genetics; spatial graphs; stepping-stone dispersal; unsampled populations  
  Résumé Current approaches that compare spatial genetic structure of a given species and the dispersal of its mobile phase can detect a mismatch between both patterns mainly due to processes acting at different temporal scales. Genetic structure result from gene flow and other evolutionary and demographic processes over many generations, while dispersal predicted from the mobile phase often represents solely one generation on a single time-step. In this study, we present a spatial graph approach to landscape genetics that extends connectivity networks with a stepping-stone model to represent dispersal between suitable habitat patches over multiple generations. We illustrate the approach with the case of the striped red mullet Mullus surmuletus in the Mediterranean Sea. The genetic connectivity of M. surmuletus was not correlate with the estimated dispersal probability over one generation, but with the stepping-stone estimate of larval dispersal, revealing the temporal scale of connectivity across the Mediterranean Sea. Our results highlight the importance of considering multiple generations and different time scales when relating demographic and genetic connectivity. The spatial graph of genetic distances further untangles intra-population genetic structure revealing the Siculo-Tunisian Strait as an important corridor rather than a barrier for gene flow between the Western- and Eastern Mediterranean basins, and identifying Mediterranean islands as important stepping-stones for gene flow between continental populations. Our approach can be easily extended to other systems and environments.  
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  Auteur institutionnel Thèse  
  Editeur Lieu de Publication Éditeur  
  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 0906-7590 ISBN Médium  
  Région Expédition Conférence  
  Notes WOS:000533549700001 Approuvé (up) pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2789  
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