FN Archimer Export Format
PT J
TI ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps
BT 
AF BECHELER, Ronan
   MASSON, Jean-Pierre
   ARNAUD-HAOND, Sophie
   HALKETT, Fabien
   MARIETTE, Stephanie
   GUILLEMIN, Marie-Laure
   VALERO, Myriam
   DESTOMBE, Christophe
   STOECKEL, Solenn
AS 1:1;2:2;3:3;4:4;5:5;6:1,6;7:1;8:1;9:2;
FF 1:;2:;3:PDG-RBE-MARBEC-LHM;4:;5:;6:;7:;8:;9:;
C1 Univ Paris VI, Sorbonne Univ, Evolutionary Biol & Ecol Algae, CNRS,UPMC,UC,UACH,UMI, F-3614 Roscoff, France.
   INRA, Inst Genet Environm & Plant Protect, UMR1349, Le Rheu, France.
   IFREMER, MARBEC Marine Biodivers Exploitat & Conservat, Blvd Jean Monet, F-34200 Sete, France.
   Univ Lorraine, IAM UMR1136, INRA, Nancy, France.
   Univ Bordeaux, BIOGECO UMR1202, INRA, Cestas, France.
   Univ Austral Chile, Inst Ciencias Ambientales & Evolut, Fac Ciencias, Valdivia, Chile.
C2 UNIV PARIS 06, FRANCE
   INRA, FRANCE
   IFREMER, FRANCE
   UNIV LORRAINE, FRANCE
   UNIV BORDEAUX, FRANCE
   UNIV AUSTRAL CHILE, CHILE
SI SETE
SE PDG-RBE-MARBEC-LHM
UM MARBEC
IN WOS Ifremer jusqu'en 2018
   copubli-france
   copubli-p187
   copubli-univ-france
   copubli-int-hors-europe
   copubli-sud
IF 7.059
TC 15
UR https://archimer.ifremer.fr/doc/00390/50187/50810.pdf
LA English
DT Article
DE ;inbreeding;instantaneous inference;population genetics model;rate of asexuality;selfing
AB Partial clonality is commonly used in Eukaryotes and has large consequences for their evolution and ecology. Assessing accurately the relative importance of clonal versus sexual reproduction matters for studying and managing such species. Here, we proposed a Bayesian approach, ClonEstiMate, to infer rates of clonality c from populations sampled twice over a short time interval, ideally one generation time. The method relies on the likelihood of the transitions between genotype frequencies of ancestral and descendent populations, using an extended Wright-Fisher model explicitly integrating reproductive modes. Our model provides posterior probability distribution of inferred c, given the assumed rates of mutation, as well as inbreeding and selfing when occurring. Tested under various conditions, this model provided accurate inferences of c, especially when the amount of information was modest, i.e. low sample sizes, few loci, low polymorphism and strong linkage disequilibrium. Inferences remained robust when mutation models and rates were misinformed. However, the method was sensitive to moderate frequencies of null alleles and when the time interval between required samplings exceeding two generations. Misinformed rates on mating modes (inbreeding and selfing) also resulted in biased inferences. Our method was tested on eleven datasets covering five partially clonal species, for which the extent of clonality was formerly deciphered. It delivered highly consistent results with previous information on the biology of those species. ClonEstiMate represents a powerful tool for detecting and inferring clonality in finite populations, genotyped with SNPs or microsatellites. It is freely available at "h t tp://https://w">https://w w w 6.rennes.inra.fr / igepp_eng/ Productions/ Software. 
PY 2017
PD NOV
SO Molecular Ecology Resources
SN 1755-098X
PU Wiley
VL 17
IS 6
UT 000415921900022
DI 10.1111/1755-0998.12698
ID 50187
ER

EF