Table 1.

MK Tests for Positive Selection.

Arp Paralog	Polymorphism		Divergence		No. D. pse Strains	No. D. mir Strains	P-Value	Alpha
	P S	P N	D S	D N
D-ActL1	26	2	8	7	11	8	0.002	0.912
D-ActL2	27	12	4	18	11	8	<0.001	0.901
D-ActL3	17	3	6	22	10	8	<0.001	0.951
Arp2D	9	8	6	23	10	8	0.024	0.768

note.—The MK test compares the ratio of nonsynonymous to synonymous fixed differences between two species (D_N/D_S) with the ratio of nonsynonymous to synonymous polymorphisms within a species (P_N/P_S). Under neutrality, we expect D_N/D_S ∼ P_N/P_S. However, if the ratio of fixed differences is far greater than the polymorphism ratio (D_N/D_S ≫ P_N/P_S), then this excess of fixed nonsynonymous differences (evaluated with a Fisher’s exact test) is inferred to be the result of positive selection. The number of polymorphisms and divergences in the table are the total found for both species (Drosophila pseudoobscura [D. pse] and D. miranda [D. mir]). Alpha, or the neutrality index, represents the proportion of nonsynonymous substitutions likely to have been driven by positive selection (Smith and Eyre-Walker 2002). Alpha is defined as [1 − (D_SP_N/D_NP_S)] and is expected to be zero under neutrality, and approaches 1 if all the nonsynonymous substitutions are likely to be driven by positive selection. Alpha values of 0.8 or higher are considered very strong evidence of positive selection.