Table 3. Genes that show significant and nominal evidence of amino acid divergence on the D. melanogaster lineage and on the D. simulans lineage.

D. melanogaster
Gene ID	Gene Name	Pn	Dn	Ps	Ds	MKcodons	Function	FETpval	FET corrected	DoS	DoS rank	DoS rank against null rank
FBgn0260935	Ird1	30	1	47	59	1119	Autophagy/Phagocytosis: Phagosome maturation; autophagosome nucleation	<0.001	<0.001	-0.372943723	17 (26.15%)	39 (16.46%)
D. simulans
Gene ID	Gene Name	Pn	Dn	Ps	Ds	MKcodons	Function	FETpval	FET corrected	DoS	DoS rank	DoS rank against null rank
FBgn0189637	gb	4	7	53	8	447	Phagocytosis: Phagosome maturation	0.001	0.047	0.396	51 (100%)	179 (95.21%)
FBgn0187055	polyph	3	4	47	5	320	Phagocytosis: Phagosome maturation	0.008	0.138	0.384	47 (92.16%)	173 (92.02%)
FBgn0182861	scb	11	12	75	21	814	Phagocytosis: Recognition—receptor	0.008	0.138	0.236	49 (96.08%)	174 (92.55%)
FBgn0045586	Rbsn-5	4	4	45	4	397	Phagocytosis: Phagosome maturation	0.010	0.142	0.418	50 (98.04%)	178 (94.68%)

Pn, the number of non-synonymous polymorphisms; Dn, the number of non-synonymous substitutions; Ps, the number of synonymous polymorphisms; Ds, the number of synonymous substitutions; MKcodons, the total number of codons subjected to the MK test; FETpval, P-value from Fisher’s exact test; FET corrected, P-value from Fisher’s exact test with multiple testing correction; DoS, direction of selection; For each focal-control pair, comparison score was calculated for DoS and the scores were ranked from largest to smallest in the ‘rank’ column. Random assignment of a control gene to be “focal” and re-calculating the ranks of comparison scores created a distribution of ranks. The ranks of comparison scores from true coupling of focal and control genes compared to this distribution are listed in the ‘rank against null’ column.