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Auteur Griot, R.; Allal, F.; Brard-Fudulea, S.; Morvezen, R.; Haffray, P.; Phocas, F.; Vandeputte, M. doi  openurl
  Titre 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  
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  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 (down) 2760  
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Auteur Ben Abdelkrim, A.; Hattab, T.; Fakhfakh, H.; Belkadhi, M.S.; Gorsane, F. url  doi
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  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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  Volume de collection Numéro de collection Edition  
  ISSN 1932-6203 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection (down) 2199  
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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 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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  Volume de collection Numéro de collection Edition  
  ISSN 0962-1083 ISBN Médium  
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Auteur Pirog, A.; Jaquemet, S.; Soria, M.; Magalon, H. doi  openurl
  Titre First evidence of multiple paternity in the bull shark (Carcharhinus leucas) Type Article scientifique
  Année 2017 Publication Revue Abrégée Mar. Freshw. Res.  
  Volume 68 Numéro 1 Pages 195-201  
  Mots-Clés brown smoothhound shark; convenience polyandry; genetic benefits; hammerhead shark; mating-behavior; microsatellite; microsatellite null alleles; mustelus-henlei; paternity test; polyandry; population sizes; triaenodon-obesus; whitetip reef shark  
  Résumé The present study assessed the occurrence of multiple paternity in four litters of bull shark Carcharhinus leucas (n = 5, 8, 9 and 11 embryos) sampled at Reunion Island in the Western Indian Ocean. Using 21 microsatellite loci, we revealed that two litters were generated from two sires each, demonstrating for the first time multiple paternity for this species. We also reported a high paternal skew (10 : 1 in Litter 1 and 7 : 1 in Litter 3), which may be because of post-copulatory or post-zygotic selection processes. These results contribute to a better understanding of the reproductive behaviour of the bull shark, which remains poorly documented. The present study must be expanded to assess the frequency of multiple paternity in this species, and to test for genetic or cryptic benefits (convenience polyandry), which is important for long-term conservation and management plans.  
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  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 1323-1650 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection (down) 2073  
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Auteur Viricel, A.; Simon-Bouhet, B.; Ceyrac, L.; Dulau-Drouot, V.; Berggren, P.; Amir, O.A.; Jiddawi, N.S.; Mongin, P.; Kiszka, J.J. doi  openurl
  Titre Habitat availability and geographic isolation as potential drivers of population structure in an oceanic dolphin in the Southwest Indian Ocean Type Article scientifique
  Année 2016 Publication Revue Abrégée Mar. Biol.  
  Volume 163 Numéro 10 Pages 219  
  Mots-Clés biologically meaningful; bottle-nosed dolphins; genetic differentiation; marine populations; megaptera-novaeangliae; microsatellite loci; mozambique channel; spinner dolphins; stenella-longirostris; tursiops-truncatus  
  Résumé Delphinid populations show highly variable patterns of genetic diversity and population structure. Previous studies indicate that habitat discontinuities and geographic isolation are major drivers of population division in cetaceans. Spinner dolphins (Stenella longirostris) are distributed in all tropical oceans, but they are particularly common around islands and atolls. This species occurs in shallow waters at daytime to rest and socialise, and feeds on offshore mesopelagic prey overnight. Here, we investigated the genetic population structure of spinner dolphins in the Southwest Indian Ocean along a west-east geographic gradient, from eastern Africa to the Mascarene archipelago. We combined analyses of 12 microsatellite loci, mtDNA control region sequences, and sighting data to assess genetic differentiation and characterise habitat preferences of these populations. Significant genetic structure among the three sampled sites (Zanzibar, Mayotte and La Reunion) was observed using both types of molecular markers. Overall, our results indicate that geographic isolation and potentially other factors, such as shallow-water habitats to rest and socialise, may be important drivers of the genetic population structure of insular spinner dolphins in this region.  
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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 0025-3162 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection (down) 1700  
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