Coalescent Theory for a Partially Selfing Population

A coalescent theory for a sample of DNA sequences from a partially selfing diploid population and an algorithm for simulating such samples are developed in this article. Approximate formulas are given for the expectation and the variance of the number of segregating sites in a sample of k sequences from n individuals. Several new estimators of the important parameters theta = 4N mu and the selfing rate s, where N and mu are, respectively, the effective population size and the mutation rate per sequence per generation, are proposed and their sampling properties are studied.