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Auteur Griot, R.; Allal, F.; Brard-Fudulea, S.; Morvezen, R.; Haffray, P.; Phocas, F.; Vandeputte, M.
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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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 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 Lupo, C.; Bougeard, S.; Le Bihan, V.; Blin, J.L.; Allain, G.; Azema, P.; Benoit, F.; Bechemin, C.; Bernard, I.; Blachier, P.; Brieau, L.; Danion, M.; Garcia, A.; Gervasoni, E.; Glize, P.; Laine, A.; Lapegue, S.; Mablouke, C.; Poirier, L.; Raymond, J.C.; Treilles, M.; Chauvin, C.; Le Bouquin, S.
Titre Mortality of marine mussels Mytilus edulis and M. galloprovincialis: systematic literature review of risk factors and recommendations for future research Type Article scientifique
Année 2020 Publication Revue Abrégée Rev. Aquac.
Volume Numéro Pages
Mots-Clés cultured blue mussels; eco-epidemiology; environment; habitat segregation; husbandry practices; indigenous perna-perna; infectious-diseases; mass mortality; mussel health; mussel mytilus-galloprovincialis; natural-populations; northern adriatic sea; pathogens; stress responses; summer mortality
Résumé The aim of this study was to summarise the literature reporting the risk factors for mortality in the mussel speciesMytilus edulisandMytilus galloprovincialisin order to identify potential science-based solutions to prevent or mitigate mussel mortality outbreaks. We followed the PRISMA methodology: Preferred Reporting Items for Systematic Reviews and Meta-Analyses. The studied corpus of 91 publications (114 studies) was highly heterogeneous with respect to the methodological approaches used to define or estimate mussel mortality and the related putative risk factors. Results showed that the mortality risk of both mussel speciesM. edulisandM. galloprovincialisvaried across the seasons, increased with an elevated seawater temperature above a thermal threshold of 20 and 24 degrees C, respectively, decreased by protecting mussels from predation, and was associated with the presence of pathogens inM. edulis. ForM. galloprovincialis, using mussel spat from the same area where the farming is carried out and farming them together with another mussel species appears to reduce the mortality risk. However, forM. edulis, this could be achieved by using pure crosses and in particular mussel spat having a selected genotype. For wild bed conservation, sand accumulation and anthropogenic sedimentation should be minimised. Our analysis showed that current approaches to this research topic are limited and are unlikely to yield actionable evidence to identify mussel mortality prevention or mitigation strategies. Therefore, recommendations are offered to increase the ability of future eco-epidemiological research to identify multiple exposures associated with mussel mortality, underpinned by standardised efforts and cooperative initiatives.
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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 1753-5123 ISBN Médium
Région Expédition Conférence
Notes WOS:000556059500001 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2848
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Auteur Riou, V.; Ndiaye, A.; Budzinski, H.; Dugue, R.; Le Menach, K.; Combes, Y.; Bossus, M.; Durand, J.D.; Charmantier, G.; Lorin-Nebel, C.
Titre Impact of environmental DDT concentrations on gill adaptation to increased salinity in the tilapia Sarotherodon melanotheron Type Article scientifique
Année 2012 Publication Revue Abrégée Comp. Biochem. Physiol. C-Toxicol. Pharmacol.
Volume 156 Numéro 1 Pages 7-16
Mots-Clés DDTs; Na+/K+-ATPase; Osmoregulation; Rainbow trout; Teleost; cell responses; crucian carp; fish; gill; goldfish carassius-auratus; na-k-atpase; natural-populations; polychlorinated-biphenyls; salmo-gairdneri; water
Résumé Estuaries of tropical developing countries suffering from severe droughts induced by climate change are habitats to fish, which face drastic salinity variations and the contact with pollutants. The Western Africa tilapia Sarotherodon melanotheron is highly resistant to hypersalinity, but the effect of human-released xenobiotics on its adaptation is barely known. Controlled experiments were conducted to observe S. melanotheron gill adaptation to abrupt salinity variations in the presence of waterborne DDT, at concentrations detected in their natural habitat. The gills appeared as an important site of DDT conversion to DDD and/or depuration. A 12-days DDT exposure resulted in decreased gill epithelium thickness at all salinities (from fresh- to hypersaline-water), and the structure of gills from freshwater fish was particularly altered, relative to controls. No unbalance in tilapia blood osmolality was observed following DDT exposure, which however caused a decrease in branchial Na+-K+-ATPase (NKA) activity. Gill cellular NKA expression was reduced in salt-water, together with the expression of the CFTR chloride channel in hypersaline water. Although S. melanotheron seems very resistant (especially in seawater) to short-term waterborne DDT contamination, the resulting alterations of the gill tissue, cells and enzymes might affect longer term respiration, toxicant depuration and/or osmoregulation in highly fluctuating salinities. (C) 2012 Elsevier Inc. All rights reserved.
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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 1532-0456 ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 649
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