Estimating the recombination parameter of a finite population model without selection

Abstract

An estimator is proposed for the parameter C = 4Nc. where N is the population size and c is the recombination rate. The estimator is appropriate for use with sequence or restriction site data from random samples from within populations. Properties of the estimator are investigated for an infinite-sites neutral model using Monte Caro simulations. The median and mode of the distribution of the estimator are close to the true value for all parameter values examined, but large data sets are required to obtain reliable estimates. © 2008 Cambridge University Press.