CloNcaSe


CloNcaSe (Nc and s estimator) is an R-package for estimating effective size (Nc) and sex rate (s) of a partially clonal population sampled at two different times.

Inferring reproductive and demographic parameters of populations is crucial to our understanding of species ecology and evolutionary potential but can be challenging, especially in partially clonal organisms. Here, we describe a new and accurate method, cloncase, for estimating both the rate of sexual vs. asexual reproduction and the effective population size, based on the frequency of clonemate resampling across generations. Simulations showed that our method provides reliable estimates of sex frequency and effective population size for a wide range of parameters. The cloncase method was applied to Puccinia striiformis f.sp. tritici, a fungal pathogen causing stripe/yellow rust, an important wheat disease. This fungus is highly clonal in Europe but has been suggested to recombine in Asia. Using two temporally spaced samples of P. striiformis f.sp. tritici in China, the estimated sex frequency was 75% (i.e. three-quarter of individuals being sexually derived during the yearly sexual cycle), indicating strong contribution of sexual reproduction to the life cycle of the pathogen in this area. The inferred effective population size of this partially clonal organism (Nc = 998) was in good agreement with estimates obtained using methods based on temporal variations in allelic frequencies. The cloncase estimator presented herein is the first method allowing accurate inference of both sex frequency and effective population size from population data without knowledge of recombination or mutation rates. cloncase can be applied to population genetic data from any organism with cyclical parthenogenesis and should in particular be very useful for improving our understanding of pest and microbial population biology.


Informations générales
Partenaire externe
aucun
Suivi
Maintenu
Informations spécifiques
Langage(s) de développement
R
N° de version courante
V2.0
Date de la version courante
OS supporté
Type de licence


Porteur(s)
Unité
BioSP
Département co-porteur
SPE
Auteur(s)
Samuel Soubeyran
Contact
samuel.soubeyrand@inra.fr


 

 

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