A Coalescent Estimator of the Population Recombination Rate (original) (raw)

Population genetic models often use a population recombination parameter 4Nc, where N is the effective population size and c is the recombination rate per generation. In many ways 4_Nc_ is comparable to 4_Nu_, the population mutation rate. Both combine genome level and population level processes, and together they describe the rate of production of genetic variation in a population. However, 4_Nc_ is more difficult to estimate. For a population sample of DNA sequences, historical recombination can only be detected if polymorphisms exist, and even then most recombination events are not detectable. This paper describes an estimator of 4_Nc_, hereafter designated γ (gamma), that was developed using a coalescent model for a sample of four DNA sequences with recombination. The reliability of γ was assessed using multiple coalescent simulations. In general γ has low to moderate bias, and the reliability of γ is comparable, though less, than that for a widely used estimator of 4_Nu_. If there exists an independent estimate of the recombination rate (per generation, per base pair), γ can be used to estimate the effective population size or the neutral mutation rate.

Communicating editor: R. R. Hudson

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