Table 5. Genes under selection in S morphotype and L morphotype genomes and their q-values (corrected p-values for multiple testing) for the likelihood ratio tests using m12 and m78 nested site models.

				Pfam	AF12/BS01 q-value		AF70/DV901 q-value		AZS/MC04 q-value
	Genes under selection				m12	m78	m12	m78	m12	m78
S	AF12_05817	AF70_02866	AZS_06933	Fungal specific transcription factor domain	0.0056	0.0034	0.0047	0.0048	0.0066	0.0059
morphotype	AF12_08775	AF70_08873	AZS_09471	Fungal specific transcription factor domain	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000
	AF12_10212	AF70_07962	AZS_10444	Polyprenyl synthetase	0.0040	0.0027	0.0049	0.0040	0.0372	0.0299
	AF12_08924	AF70_00133	AZS_07535	Heterokaryon incompatibility protein (HET)	0.0132	0.0130	0.0315	0.0245	0.0161	0.0152
	AF12_04453	AF70_04222	AZS_05654	Eukaryotic cytochrome b561	0.0040	0.0034	0.0047	0.0049	0.0042	0.0035
	AF12_04574	AF70_04341	AZS_05775	No annotation	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000
	AF12_11547	AF70_11889	AZS_12064	Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold	0.0040	0.0034	0.0047	0.0049	0.0042	0.0043
	AF12_12244	AF70_01569	AZS_12604	No annotation	0.0005	0.0005	0.0004	0.0003	0.0003	0.0003
	AF12_12631	AF70_06345	AZS_08864	No annotation	0.0000	0.0000	0.0000	0.0000	0.0000	0.0000
	AF12_11962	AF70_12568	AZS_12704	No annotation	0.0343	0.0252	0.0047	0.0035	0.0039	0.0025
	AF12_02667	AF70_03436	AZS_10736	Protein kinase domain	0.0030	0.0023	0.0039	0.0040	0.0032	0.0027
	AF12_03527	AF70_04870	AZS_05363	No annotation	0.0010	0.0008	0.0011	0.0011	0.0010	0.0003
L	BS01_06841	DV901_08350	MC04_12622	Sugar (and other) transporter	0.0129	0.928	0.0077	0.8656	0.0108	0.0082
morphotype	BS01_09387	DV901_12827	MC04_12342	No annotation	0.0004	0.0003	0.0005	0.0005	0.0006	0.001