ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps

Type Article
Date 2017-11
Language English
Author(s) Becheler Ronan1, Masson Jean-Pierre2, Arnaud-Haond SophieORCID3, Halkett Fabien4, Mariette Stephanie5, Guillemin Marie-Laure1, 6, Valero Myriam1, Destombe Christophe1, Stoeckel Solenn2
Affiliation(s) 1 : Univ Paris VI, Sorbonne Univ, Evolutionary Biol & Ecol Algae, CNRS,UPMC,UC,UACH,UMI, F-3614 Roscoff, France.
2 : INRA, Inst Genet Environm & Plant Protect, UMR1349, Le Rheu, France.
3 : IFREMER, MARBEC Marine Biodivers Exploitat & Conservat, Blvd Jean Monet, F-34200 Sete, France.
4 : Univ Lorraine, IAM UMR1136, INRA, Nancy, France.
5 : Univ Bordeaux, BIOGECO UMR1202, INRA, Cestas, France.
6 : Univ Austral Chile, Inst Ciencias Ambientales & Evolut, Fac Ciencias, Valdivia, Chile.
Source Molecular Ecology Resources (1755-098X) (Wiley), 2017-11 , Vol. 17 , N. 6 , P. e251-e267
DOI 10.1111/1755-0998.12698
WOS© Times Cited 1
Keyword(s) inbreeding, instantaneous inference, population genetics model, rate of asexuality, selfing
Abstract

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.

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Becheler Ronan, Masson Jean-Pierre, Arnaud-Haond Sophie, Halkett Fabien, Mariette Stephanie, Guillemin Marie-Laure, Valero Myriam, Destombe Christophe, Stoeckel Solenn (2017). ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps. Molecular Ecology Resources, 17(6), e251-e267. Publisher's official version : https://doi.org/10.1111/1755-0998.12698 , Open Access version : https://archimer.ifremer.fr/doc/00390/50187/