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Auteur (up) Ben Abdelkrim, A.; Hattab, T.; Fakhfakh, H.; Belkadhi, M.S.; Gorsane, F. url  doi
openurl 
  Titre A landscape genetic analysis of important agricultural pest species in Tunisia: The whitefly Bemisia tabaci Type Article scientifique
  Année 2017 Publication Revue Abrégée Plos One  
  Volume 12 Numéro 10 Pages e0185724  
  Mots-Clés Animal migration; Genetic loci; Melons; Microsatellite loci; Pest control; phylogeography; Population genetics; Tunisia  
  Résumé Combining landscape ecology and genetics provides an excellent framework to appreciate pest population dynamics and dispersal. The genetic architectures of many species are always shaped by environmental constraints. Because little is known about the ecological and genetic traits of Tunisian whitefly populations, the main objective of this work is to highlight patterns of biodiversity, genetic structure and migration routes of this pest. We used nuclear microsatellite loci to analyze B. tabaci populations collected from various agricultural areas across the country and we determine their biotype status. Molecular data were subsequently interpreted in an ecological context supplied from a species distribution model to infer habitat suitability and hereafter the potential connection paths between sampling localities. An analysis of landscape resistance to B. tabaci genetic flow was thus applied to take into account habitat suitability, genetic relatedness and functional connectivity of habitats within a varied landscape matrix. We shed light on the occurrence of three geographically delineated genetic groups with high levels of genetic differentiation within each of them. Potential migration corridors of this pest were then established providing significant advances toward the understanding of genetic features and the dynamic dispersal of this pest. This study supports the hypothesis of a long-distance dispersal of B. tabaci followed by infrequent long-term isolations. The Inference of population sources and colonization routes is critical for the design and implementation of accurate management strategies against this pest.  
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  Langue Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 1932-6203 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2199  
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Auteur (up) Dalongeville, A.; Andrello, M.; Mouillot, D.; Albouy, C.; Manel, S. doi  openurl
  Titre Ecological traits shape genetic diversity patterns across the Mediterranean Sea: a quantitative review on fishes Type Article scientifique
  Année 2016 Publication Revue Abrégée J. Biogeogr.  
  Volume 43 Numéro 4 Pages 845-857  
  Mots-Clés atlantic bluefin tuna; bass dicentrarchus-labrax; climate-change; cod gadus-morhua; ecological traits; effective population-size; genetic diversity; gilthead sea; life-history traits; marine fishes; marine populations; Mediterranean Sea; microsatellite markers; microsatellites; mitochondrial; mitochondrial DNA; molecular markers; population genetics  
  Résumé AimWe set out to identify the determinants of the variation in genetic diversity among fish species and test whether multi-species genetic diversity is randomly distributed in space. LocationMediterranean Sea. MethodsWe collected genetic diversity data from 39 published studies on Mediterranean fishes (31 species) along with the spatial coordinates of the sampling sites. We focused on microsatellite heterozygosity (151 data points) and mitochondrial haplotype diversity (201 data points). We used linear regressions to link genetic diversity and 11 ecological traits. We also tested for spatial autocorrelation and trends in the residuals. ResultsAmong-species variation in microsatellite heterozygosity was explained by three ecological traits: vertical distribution, migration type and body length. Variation in mitochondrial haplotype diversity was also explained by vertical distribution and migration type, and by reproductive strategy (semelparity). However, vertical distribution and migration type showed opposite effects on microsatellites and mitochondrial diversity. After accounting for the effects of ecological traits, no spatial pattern was detected, except for one of the species considered. Main conclusionsEcological factors explain an important proportion of the among-species genetic diversity. These results suggest that life history strategies of the species influence the variation of microsatellite diversity indirectly through their effect on effective population size, while the spatial variations of genetic diversity seem to be too complex to be identified in our analysis. We found very different effects of traits on mitochondrial and nuclear DNA diversity, which can be explained by the specificities of mitochondrial DNA (absence of recombination, maternal inheritance and non-neutrality).  
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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  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ alain.herve @ collection 1627  
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Auteur (up) Dubois, M.; Rossi, V.; Ser-Giacomi, E.; Arnaud-Haond, S.; Lopez, C.; Hernandez-Garcia, E. doi  openurl
  Titre Linking basin-scale connectivity, oceanography and population dynamics for the conservation and management of marine ecosystems Type Article scientifique
  Année 2016 Publication Global Ecology and Biogeography Revue Abrégée Glob. Ecol. Biogeogr.  
  Volume 25 Numéro 5 Pages 503-515  
  Mots-Clés coral-reef fish; dispersal; genetic-structure; Larval dispersal; local retention; local retention; marine connectivity; marine ecosystems; marine protected areas; mediterranean littoral fishes; Mediterranean Sea; metapopulation; pelagic larval duration; population dynamics; Population Genetics; protected-area design; sea; self-recruitment; sink dynamics; source  
  Résumé AimAssessing the spatial structure and dynamics of marine populations is still a major challenge in ecology. The need to manage marine resources from ecosystem and large-scale perspectives is recognized, but our partial understanding of oceanic connectivity limits the implementation of globally pertinent conservation planning. Based on a biophysical model for the entire Mediterranean Sea, this study takes an ecosystem approach to connectivity and provides a systematic characterization of broad-scale larval dispersal patterns. It builds on our knowledge of population dynamics and discusses the ecological and management implications. LocationThe semi-enclosed Mediterranean Sea and its marine ecosystems are used as a case study to investigate broad-scale connectivity patterns and to relate them to oceanography and population dynamics. MethodsA flow network is constructed by evenly subdividing the basin into sub-regions which are interconnected through the transport of larvae by ocean currents. It allows for the computation of various connectivity metrics required to evaluate larval retention and exchange. ResultsOur basin-scale model predicts that retention processes are weak in the open ocean while they are significant in the coastal ocean and are favoured along certain coastlines due to specific oceanographic features. Moreover, we show that wind-driven divergent (convergent, respectively) oceanic regions are systematically characterized by larval sources (sinks, respectively). Finally, although these connectivity metrics have often been studied separately in the literature, we demonstrate they are interrelated under particular conditions. Their integrated analysis facilitates the appraisal of population dynamics, informing both genetic and demographic connectivities. Main conclusionsThis modelling framework helps ecologists and geneticists to formulate improved hypotheses of population structures and gene flow patterns and to design their sampling strategy accordingly. It is also useful in the implementation and assessment of future protection strategies, such as coastal and offshore marine reserves, by accounting for large-scale dispersal patterns, a missing component of current ecosystem management.  
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  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 1466-822x ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ alain.herve @ collection 1655  
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Auteur (up) KIVELA, M.; ARNAUD-HAOND, S.; SARAMAKI, J. url  doi
openurl 
  Titre EDENetworks: A user-friendly software to build and analyse networks in biogeography, ecology and population genetics Type Article scientifique
  Année 2015 Publication Revue Abrégée Molecular Ecology Resources  
  Volume 15 Numéro 1 Pages 117-122  
  Mots-Clés Biogeography; biological communities; graph theory; microbial ecology; network analysis; population genetics  
  Résumé 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 then transformed into a network by manual or automatic thresholding based on percolation theory or by building the minimum spanning tree. The networks can be visualized along with auxiliary data and analysed with various metrics such as degree, clustering coefficient, assortativity and betweenness centrality. The statistical significance of the results can be estimated either by resampling the original biological data or by null models based on permutations of the data.  
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  Langue Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 1755-098x ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1119  
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Auteur (up) Lapegue, S.; Heurtebise, S.; Cornette, F.; Guichoux, E.; Gagnaire, P.-A. doi  openurl
  Titre Genetic Characterization of Cupped Oyster Resources in Europe Using Informative Single Nucleotide Polymorphism (SNP) Panels Type Article scientifique
  Année 2020 Publication Revue Abrégée Genes  
  Volume 11 Numéro 4 Pages 451  
  Mots-Clés population genetics; conservation; population-structure; r-package; ostreid herpesvirus; introgression; pacific oyster; angulata; crab carcinus-maenas; crassostrea-gigas thunberg; cupped oysters; differential introgression; invasion genetics; portuguese oyster; shellfisheries  
  Résumé The Pacific oyster, Crassostrea gigas, was voluntarily introduced from Japan and British Columbia into Europe in the early 1970s, mainly to replace the Portuguese oyster, Crassostrea angulata, in the French shellfish industry, following a severe disease outbreak. Since then, the two species have been in contact in southern Europe and, therefore, have the potential to exchange genes. Recent evolutionary genomic works have provided empirical evidence that C. gigas and C. angulata exhibit partial reproductive isolation. Although hybridization occurs in nature, the rate of interspecific gene flow varies across the genome, resulting in highly heterogeneous genome divergence. Taking this biological property into account is important to characterize genetic ancestry and population structure in oysters. Here, we identified a subset of ancestry-informative makers from the most differentiated regions of the genome using existing genomic resources. We developed two different panels in order to (i) easily differentiate C. gigas and C. angulata, and (ii) describe the genetic diversity and structure of the cupped oyster with a particular focus on French Atlantic populations. Our results confirm high genetic homogeneity among Pacific cupped oyster populations in France and reveal several cases of introgressions between Portuguese and Japanese oysters in France and Portugal.  
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  ISSN ISBN Médium  
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  Notes WOS:000537224600052 Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2910  
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