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Auteur (up) 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  
  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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