Table 4.

GO Analysis of Putative Genes under Positive Selection Detected by Both SM and BSM

Codon substitution Models	Lineage (Branch Number)	Number of Candidates	GO enrichment
			Molecular Function		Biological Process		Interpro Domain
			ID	Fold Enrichment	ID	Fold Enrichment	ID	Fold Enrichment
SM	Drosophila buzzatii versus Drosophila mojavensis	772	Antiporter activity	1.77	Regulation of transcription	4.90	Src homology-3 domain	1.60
			Transcription factor activity	1.56
BSM	D. buzzatii #1	350	DNA binding	1.36	Regulation of transcription DNA dependent	1.36	Immunoglobulin-like	1.33
					Phosphate metabolic process	0.72
	D. mojavensis #2	172	Dopamine beta-monooxigenase activity	2.35	Heterocycle catabolic process	2.35	DOMON (DOpamine beta-MOnooxygenase N-terminal domain)	2.35
					Cation transport	0.98
					Histidine family amino acid catabolic process	2.35
	Cactophilic #3	458	Zinc ion binding	2.01	Cytoeskeleton organization	1.67	Zinc finger, PHD-type	1.93
			Transition metal ion binding	2.01	Regulation of transcription DNA dependent	1.06	Proteinase inhibitor I1 kazal	2.20
			DNA binding	1.66

Note.—Only categories showing an enrichment with a P value less than 1.0e-03 are included.