In population genetics, the Watterson estimator is a method for describing the genetic diversity in a population. It is estimated by counting the number of polymorphic sites. It is a measure of the "population mutation rate" (the product of the effective population size and the neutral mutation rate) from the observed nucleotide diversity of a population.
The estimate of
where
is the
This estimate is based on coalescent theory. Watterson's estimator is commonly used for its simplicity. When its assumptions are met, the estimator is unbiased and the variance of the estimator decreases with increasing sample size or recombination rate. However, the estimator can be biased by population structure. For example,
Comparing the value of the Watterson estimator, to nucleotide diversity is the basis of Tajima's D which allows inference of the evolutionary regime of a given locus.