FN Archimer Export Format
PT J
TI Estimating effective population size using RADseq: Effects of SNP selection and sample size
BT 
AF Marandel, Florianne
   Charrier, Gregory
   Lamy, Jean-Baptiste
   Le Cam, Sabrina
   Lorance, Pascal
   Trenkel, Verena
AS 1:1;2:2;3:3;4:2,3;5:1;6:1;
FF 1:PDG-RBE-EMH;2:;3:PDG-RBE-SGMM-LGPMM;4:PDG-RBE-SG2M-LGPMM;5:PDG-RBE-EMH;6:PDG-RBE-EMH;
C1 Ifremer ,Ecologie et Modèles pour l’Halieutique Nantes ,France
   Laboratoire des Sciences de l’Environnement Marin (LEMAR, UMR 6539 CNRS/IRD/UBO/Ifremer) Université de Bretagne OccidentaleInstitut Universitaire Européen de la Mer Plouzané ,France
   Ifremer, Génétique et Pathologie des Mollusques Marin (SG2M‐LGPMM) La Tremblade, France
   Laboratoire des Sciences de l’Environnement Marin (LEMAR, UMR 6539 CNRS/IRD/UBO/Ifremer) Université de Bretagne OccidentaleInstitut Universitaire Européen de la Mer Plouzané ,France
C2 IFREMER, FRANCE
   IFREMER, FRANCE
   IFREMER, FRANCE
   UBO, FRANCE
SI NANTES
   LA TREMBLADE
SE PDG-RBE-EMH
   PDG-RBE-SGMM-LGPMM
   PDG-RBE-SG2M-LGPMM
UM LEMAR
IN WOS Ifremer UPR
   WOS Cotutelle UMR
   DOAJ
   copubli-france
   copubli-univ-france
IF 2.912
TC 32
UR https://archimer.ifremer.fr/doc/00607/71934/70628.pdf
LA English
DT Article
CR RAIE-JUVES
BO Thalia
DE ;effective population size;linkage disequilibrium;NeEstimator;RADseq;skates and rays
AB Effective population size (Ne) is a key parameter of population genetics. However, Ne remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site‐associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on Ne estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient FIS was positively correlated with the amount of missing data, implying data were missing nonrandomly. The precision of Neestimates decreased with the number of SNPs. Mean Ne estimates (averaged across 50 random data sets with2000 SNPs) ranged between 237 and 1784. Increasing the percentage of missing data from 25% to 50% increased Ne estimates between 82% and 120%, while increasing the minor allele frequency (MAF) threshold from 0.01 to 0.1 decreased estimates between 71% and 75%. Considering these effects is important when interpreting RADseq data‐derived estimates of effective population size in empirical studies. 
PY 2020
PD FEB
SO Ecology And Evolution
SN 2045-7758
PU Wiley
VL 10
IS 4
UT 000512443500001
BP 1929
EP 1937
DI 10.1002/ece3.6016
ID 71934
ER

EF