In population genetics, the Watterson estimator is a method for describing the genetic diversity in a population. It was developed by Margaret Wu and G. A. Watterson in the 1970s., is the effective population size is the per-generation mutation rate of the population of interest ( haploid is used.

, is

is the number of segregating sites (an example of a segregating site would be a single-nucleotide polymorphism) in the sample and

th harmonic number.

This estimate is based on coalescent theory. The Watterson estimator is commonly used for its simplicity. When its assumptions are met, the estimator is unbiased and the variance is downwardly biased in an exponentially growing population. It can also be biased by violation of the infinite-sites mutational model; multiple point mutations at a single site will downwardly bias the estimate.

Comparing the value of the Watterson's estimator to nucleotide diversity) is the basis of Tajima's D, which is used to determine whether a DNA sequence is evolving neutrally or under a non-random process (e.g., selection).

See also

• Coupon collector's problem

• Ewens sampling formula

References

• McVean, Gil; Awadalla, Philip; Fearnhead, Paul (2002) "A Coalescent-Based Method for Detecting and Estimating Recombination From Gene Sequences", Genetics, 160, 12311241.