title: cloncase: Estimation of sex frequency and effective population size by clonemate resampling in partially clonal organisms.
abstract: 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.
authors: UMR1290, BIOGER, INRA-AgroParisTech, BP01, 78850, Thiverval-Grignon, France.|Institute of Biotechnology and Genetic Engineering, the University of Agriculture, Peshawar, 25000, Peshawar, Pakistan.
authors: Sajid
authors: S
authors: Ali
authors: UR546 Biostatistics and Spatial Processes, INRA, 84914, Avignon, France.
authors: Samuel
authors: S
authors: Soubeyrand
authors: Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France.|UMR385 Biologie et Génétique des Interactions Plante-Parasite, CIRAD, INRA, F-34398, Montpellier, France.
authors: Pierre
authors: P
authors: Gladieux
authors: Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France.
authors: Tatiana
authors: T
authors: Giraud
authors: UMR1290, BIOGER, INRA-AgroParisTech, BP01, 78850, Thiverval-Grignon, France.
authors: Marc
authors: M
authors: Leconte
authors: UMR1290, BIOGER, INRA-AgroParisTech, BP01, 78850, Thiverval-Grignon, France.
authors: Angélique
authors: A
authors: Gautier
authors: DuPont de Nemours (France) SAS Crop Protection - European Research & Development Center, 24, rue du Moulin, 68740, Nambsheim, France.
authors: Mamadou
authors: M
authors: Mboup
authors: State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
authors: Wanquan
authors: W
authors: Chen
authors: UMR1290, BIOGER, INRA-AgroParisTech, BP01, 78850, Thiverval-Grignon, France.
authors: Claude
authors: C
authors: de Vallavieille-Pope
authors: Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France.|GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91190, Gif-sur-Yvette, France.
authors: Jérôme
authors: J
authors: Enjalbert
mesh_terms: D001487:Basidiomycota / Q000145:classification / Q000235:genetics; D002681:China; D005827:Genetics, Microbial / Q000379:methods*; D005828:Genetics, Population / Q000379:methods*; D005838:Genotype; D011156:Population Density; D011995:Recombination, Genetic; D017678:Sex Distribution; D014908:Triticum / Q000382:microbiology
keywords: Clonality rate; Ne; microorganisms; multilocus genotypes; temporal sampling