Table 4. PAML codeml module likelihood scores and parameter estimates for MAFFT nucleotide alignments of the plant SK, SKL1 and SKL2 families.

Gene Family	Model	likelihood	ts/tv	Average dN/dS	Parameter Estimates
					Frequency	dN/dS
SK	M0, one-ratio	−9019.68	1.98	0.157	p = 1.000	ω = 0.157
	M3, discrete	−8809.15	2.13	0.184	p0 = 0.344	ω0 = 0.025
					p1 = 0.398	ω1 = 0.145
					p2 = 0.258	ω2 = 0.457
	M1a, neutral	−8909.16	2.30	0.311	p0 = 0.78848	ω0 = 0.12549
					p1 = 0.21152	ω1 = 1.00000
	M2a, selection	−8909.16	2.30	0.311	p0 = 0.78847	ω0 = 0.12548
					p1 = 0.21153	ω1 = 1.0000
					p2 = 0.00000	ω2 = 6.99385
SKL1	M0, one-ratio	−6310.96	1.89	0.189	p = 1.000	ω = 0.189
	M3, discrete	−6187.15	1.95	0.231	p0 = 0.252	ω0 = 0.022
					p1 = 0.591	ω1 = 0.178
					p2 = 0.157	ω2 = 0.761
	M1a, neutral	−6216.0363	2.02	0.281	p0 = 0.82812	ω0 = 0.13190
					p1 = 0.17188	ω1 = 1.00000
	M2a, selection	−6216.0363	2.02	0.281	p0 = 0.82812	ω0 = 0.13190
					p1 = 0.17181	ω1 = 1.00000
					p2 = 0.00006	ω2 = 1.00000
SKL2	M0, one-ratio	−8244.72	1.46	0.272	p = 1.000	ω = 0.272
	M3, discrete	−8087.24	1.46	0.123	p0 = 0.899	ω0 = 0.020
					p1 = 0.081	ω1 = 0.695
					p2 = 0.020	ω2 = 2.498
	M1a, neutral	−8623.98	1.31	0.087	p0 = 0.91628	ω0 = 0.00346
					p1 = 0.08372	ω1 = 1.00000
	M2a, selection	−8165.8	1.46	0.122	p0 = 0.92524	ω0 = 0.02280
					p1 = 0.06438	ω1 = 1.00000
					p2 = 0.01038	ω2 = 3.49887

Ts = transition, tv = transversion, Df = degrees of freedom, P = probability, 2ΔL = twice the difference of log likelihood values.