Probability of a segregating pattern in a sample of DNA sequences.
Mutations that result in segregating sites (polymorphic sites) in a sample of DNA sequences can be classified into different types. A pattern of segregating sites is an array of the numbers of various types of mutations. Using an urn model, the probability of a pattern of segregating sites can be expressed as a recurrence equation and its value can be computed sequentially. Among those that can be computed by this method are the probability of obtaining k external mutations (mutations that occur in external branches of the genealogy of a sample), the probability of obtaining k internal mutations (mutations that occur in internal branches), the probability of obtaining k singletons (segregating sites at which one of the two segregating nucleotides is present in only one sequence), and the probability of obtaining k non-singletons. Two applications of the method are discussed. One is a maximum likelihood estimation of straight theta and another is a Bayesian statistical test of the hypothesis of neutral mutations.
Human Genetics Center, University of Texas, Houston, Texas 77225, USA.
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D001499:Bayes Theorem; D004252:DNA Mutational Analysis / Q000706:statistics & numerical data*; D006801:Humans; D016013:Likelihood Functions; D008957:Models, Genetic; D018807:Polymorphism, Single-Stranded Conformational