FN Archimer Export Format
PT J
TI APIS: An Auto‐Adaptive Parentage Inference Software that tolerates missing parents
BT 
AF Griot, Ronan
   Allal, Francois
   Brard‐Fudulea, S
   Morvezen, R
   Haffray, P
   Phocas, F
   Vandeputte, Marc
AS 1:1,2;2:3;3:1;4:1;5:1;6:2;7:2,3;
FF 1:;2:PDG-RBE-MARBEC-LAAAS;3:;4:;5:;6:;7:;
C1 SYSAAF, Station LPGP/INRA Campus de BeaulieuRennes , France
   GABI, INRA, AgroParisTech, Université Paris‐Saclay , France
   MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD Palavas‐les‐Flots , France
C2 SYSAAF, FRANCE
   INRA, FRANCE
   IFREMER, FRANCE
SI PALAVAS
SE PDG-RBE-MARBEC-LAAAS
UM MARBEC
IN WOS Ifremer UMR
   copubli-france
   copubli-p187
IF 1.251
TC 18
UR https://archimer.ifremer.fr/doc/00587/69866/67767.pdf
LA English
DT Article
DE ;microsatellites;missing parents;parentage assignment;pedigree;SNP
AB 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) SNP 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. 
PY 2020
PD MAR
SO Molecular Ecology Resources
SN 1755-098X
PU Wiley
VL 20
IS 2
UT 000496576600001
BP 579
EP 590
DI 10.1111/1755-0998.13103
ID 69866
ER

EF