Table 1.

Comparison of modelled amino acid model change in the Suaedoideae ppc-1 gene, to identify sites under positive selection

Model with positive selectiona				Null modela			LRTb	P-value
Model	Log-likelihood	Parametersc	Positively selected sitesd	Model	Log-likelihood	Parametersc	2L
Analysis for positively selected sites common for C3 and C4 clades
M2a	–6741.7	κ=2.94, p0=0.82, ω0=0.07, ps=0.003, ωS=3.24	None	M1a	–6742.34	κ=2.92, p0=0.82, ω0=0.07	1.28	0.5273
M8	–6740.28	κ=2.89, p0=0.98, p=0.24, q=1.0, ωS=1.93	None	M8a	–6743.02	κ=2.86, p0=0.96, p=0.19, q=0.7	5.48	0.0192
Analysis for positive selection along branches leading to C4 clades
A	–6729.78	κ=2.95, p0=0.81, ω0=0.08, ps=0.04, ωS=4.2	733, 868	A1	–6737.24	κ=2.89, p0=0.77, ω0=0.06	14.9	0.0001
Analysis for positive selection along branches leading to Kranz C4 clades
A	–6732.25	κ=2.94, p0=0.77,ω0=0.06, ps=0.06, ωS=3.64	485, 519, 735	A1	–6735.67	κ=2.91, p0=0.71, ω0=0.06	6.8	0.0091
Analysis for positive selection along branches leading to single-cell C4 clades
A	–6742.34	κ=2.92, p0=0.82, ω0=0.07, ps=0.00, ωS=NA	None	A1	–6742.34	κ=2.92, p0=0.82, ω0=0.07	0	1
Analysis for positive selection along all C4 branches
A	–6702.46	κ=2.91, p0=0.74, ω0=0.05, ps=0.18, ωS=1.5	480, 513, 627, 662, 695, 707, 733, 744, 794, 863, 868, 880, 931	A1	–6705.34	κ=2.86, p0=0.69, ω0=0.04	5.08	0.0242

^a M1a (nearly neutral), M2a (positive selection), M8a (beta and ω=1), and M8 (beta and ω) are PAML site models; A1 and A are PAML branch-site models.

^b LRT is the likelihood ratio test; 2L is twice the difference of model log-likelihoods.

^c κ is the transition/transversion rate ratio; ω is the dN/dS ratio; ω_s is the dN/dS ratio in a class under putative positive selection; p₀ and p_s are the proportion of codons with ω<1 and ω>1, respectively; p and q are parameters of beta distribution in the range (0, 1).

^d Sites listed are those at which positive selection is detected at the significance level of >95%, or >99% in bold italics.