HKA test

[2] Neutral Evolution Theory, first proposed by Kimura in a 1968 paper, and later fully defined and published in 1983, is the basis for many statistical tests that detect selection at the molecular level.

[4] Hudson et al. proposed applying these variables to a chi-squared, goodness-of-fit test.

The test statistic proposed by Hudson et al., Χ2, is: This states that, for each locus (L) (for which there must be at least two) the sum of the difference in number of observed polymorphic sites in sample A minus the estimate of expected polymorphism squared, all of which is divided by the variance.

If the polymorphism within species A, and B, and the divergence between them are all independent, then the test statistic should fall approximately onto a chi-squared distribution.

In this case the rate of mutation in each locus is equal, so this can only be explained by a reduction in the effective population size Ne of species B, which is inferred as an act of selection.