HKA (Hudson, Kreitman, and Agaude) test 

The Hudson, Kreitman, and Agaude (HKA) Test for selection uses data from two different species. The rationale for the HKA test is that under neutral evolution, the diversity within each species depends upon theta, but that the divergence between species depends on theta AND time. The HKA test is based on the neutral theory of molecular evolution (Kimura 1983) which predicts that for a particular region of the genome, its rate of evolution is correlated with the levels of polymorphism within species. The test requires data from at least two regions of the genome both for an interspecific comparison and also data for the intraspecific polymorphism from at least one species. A significant HKA result can be due to a number of causes: Too much polymorphism within species at synonymous sites : This is consistent with purifying selection. Too much polymorphism between species at nonsynonymous sites : This is consistent with positive directional selection. The HKA is also conservative because it assumes complete linkage within each gene and free recombination between genes. (http://www.plantsciences.ucdavis.edu/bit150/2006/DN_Lecture/Lecture_18_2...)