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Auteur Ben Abdelkrim, A.; Hattab, T.; Fakhfakh, H.; Belkadhi, M.S.; Gorsane, F. url  doi
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  Titre (up) 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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  Volume de collection Numéro de collection Edition  
  ISSN 1932-6203 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2199  
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Auteur Griot, R.; Allal, F.; Brard-Fudulea, S.; Morvezen, R.; Haffray, P.; Phocas, F.; Vandeputte, M. doi  openurl
  Titre (up) APIS: An auto-adaptive parentage inference software that tolerates missing parents Type Article scientifique
  Année 2020 Publication Revue Abrégée Mol. Ecol. Resour.  
  Volume 20 Numéro 2 Pages 579-590  
  Mots-Clés errors; fitness; genetic-parameters; guide; identification; impact; markers; microsatellites; missing parents; natural-populations; parentage assignment; pedigree; snp  
  Résumé In the context of parentage assignment using genomic markers, key issues are genotyping errors and an absence of parent genotypes because of sampling, traceability or genotyping problems. Most likelihood-based parentage assignment software programs require a priori estimates of genotyping errors and the proportion of missing parents to set up meaningful assignment decision rules. We present here the R package APIS, which can assign offspring to their parents without any prior information other than the offspring and parental genotypes, and a user-defined, acceptable error rate among assigned offspring. Assignment decision rules use the distributions of average Mendelian transmission probabilities, which enable estimates of the proportion of offspring with missing parental genotypes. APIS has been compared to other software (CERVUS, VITASSIGN), on a real European seabass (Dicentrarchus labrax) single nucleotide polymorphism data set. The type I error rate (false positives) was lower with APIS than with other software, especially when parental genotypes were missing, but the true positive rate was also lower, except when the theoretical exclusion power reached 0.99999. In general, APIS provided assignments that satisfied the user-set acceptable error rate of 1% or 5%, even when tested on simulated data with high genotyping error rates (1% or 3%) and up to 50% missing sires. Because it uses the observed distribution of Mendelian transmission probabilities, APIS is best suited to assigning parentage when numerous offspring (>200) are genotyped. We have demonstrated that APIS is an easy-to-use and reliable software for parentage assignment, even when up to 50% of sires are missing.  
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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 1755-098x ISBN Médium  
  Région Expédition Conférence  
  Notes WOS:000496576600001 Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2760  
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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 (up) 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 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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  Volume de collection Numéro de collection Edition  
  ISSN 0022-1503 ISBN Médium  
  Région Expédition Conférence  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1138  
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Auteur Dalongeville, A.; Andrello, M.; Mouillot, D.; Albouy, C.; Manel, S. doi  openurl
  Titre (up) 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  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 1627  
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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 (up) 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 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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  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 0962-1083 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ alain.herve @ collection 2143  
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