The extent to which we can make evolutionary inferences from current
sequence data depends on our ability to estimate the recombination rate.
Simulations for statistical 'tests of neutrality' and neutral null models
require a recombination rate; assuming that there is no recombination is
not always appropriate, and can hinder our ability to distinguish between
alternative hypotheses. Three new estimators of the population
recombination rate C = 4Nr are introduced. These estimators summarize the
data using the number of distinct haplotypes and the estimated minimum
number of recombination events, then calculate the value of C that
maximizes the likelihood of obtaining the summarized data. They are
compared with all previously proposed estimators of the recombination rate.
One of the newly proposed estimators is generally better than the others
for the parameter values considered here, while the three programs that
calculate maximum likelihood estimates give conflicting results.
 

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