CLONCASE: Estimation of sex frequency and effective population size by clonemate resampling in partially clonal organisms

文献类型： 外文期刊

第一作者： Leconte, Marc

作者： Leconte, Marc;Gautier, Angelique;De Vallavieille-Pope, Claude;Ali, Sajid;Soubeyrand, Samuel;Gladieux, Pierre;Giraud, Tatiana;Enjalbert, Jerome;Gladieux, Pierre;Mboup, Mamadou;Chen, Wanquan;Enjalbert, Jerome

作者机构：

关键词： Clonality rate;microorganisms;multilocus genotypes;Ne;temporal sampling

期刊名称：MOLECULAR ECOLOGY RESOURCES （ 影响因子：7.09； 五年影响因子：8.745 ）

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收录情况： SCI

摘要： 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 (N-c = 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.

分类号： Q7

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