New paradigms in genetics have increased the chance of finding genes that appear redundant but in fact may have been preserved due to a small level of positive selection potential acting during each generation. Monitoring changes in genotypic frequencies within and between generations allows the dissection of the fertility, viability and meiotic drive selection components acting on such genes in natural and experimental populations. Here, a formal maximum likelihood procedure is developed to identify and estimate these selection components in highly selfing populations by fitting the time-dependent solutions for genotypic frequencies to observed multigenerational counts. With adult census alone, we can not simultaneously estimate all three selection components considered. In such cases, we instead consider a hierarchy of 11 models with either fewer selection components, complete dominance, or multiplicative meiotic drive with a single parameter. We identify the best-fitting of these models by applying likelihood ratio tests to nested models and Akaike's Information Criterion (AIC) and the Bayesian Information Criterion (BIC) to non-nested models. With seed census, fertility and viability selection are not distinguishable and thus can only be estimated jointly. A combination of joint seed and adult census data allows us to estimate all three selection components simultaneously. Simulated data validate the estimation procedure and provide some practical guidelines for experimental design. An application to Arabidopsis data establishes that viability selection is the major selective force acting on the ACT2 actin gene in laboratory-grown Arabidopsis populations.
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