TABLE 2.

Codon model parameter estimates for AP1/FUL paralogs

Model	p	ℓ	Estimates of parameters	Positively selected sites
M0: one ratio	1	−3714.44	= 0.1181	None
Branch-specific models
Two ratios	2	−3714.27	0 = 0.1167, 1 = 0.1525	None
Three ratios	3	−3714.22	0 = 0.1223, 1 = 0.1527 2 = 0.1147	None
Site-specific models
M1a: near neutral	2	−3635.68	p0 = 0.87366, (p1 = 0.12634)	Not allowed
M2a: selection	4	−3635.68	p0 = 0.87368, p1 = 0.12632 (p2 = 0.00000), 2 = ∞	None
M3: discrete (K = 3)	3	−3614.81	p0 = 0.52591, (p1 = 0.39457), p2 = 0.07953, 0 = 0.01531 1 = 0.18259, 2 = 0.89122	None
M7: β	2	−3618.86	p = 0.32839, q = 1.74796	Not allowed
M8: β and ω	4	−3619.31	p0 = 0.99707, p = 0.32866 q = 1.75003, (p1 = 0.00293) = 118.19	167V (P = 0.86) 207T (P = 0.60) 208T (P = 0.73) 215L (P = 0.68)
Branch-site models
Model A: FUL1 (= null Model A)	4	−3635.68	p0 = 0.87366, p1 = 0.12634, (p2a + p2b = 0.000) 0 = 0.0729 2a = 1.00000, 2b = 1.00000	None
Model B: FUL1 (= null Model B)	5	−3626.84	p0 = 0.80202, p1 = 0.19798, (p2 + p3 = 0.00), 0 = 0.05027 1 = 0.52984, 2 = ∞	None
Model A: FUL2 (= null Model A)	4	−3635.19	p0 = 0.77157, p1 = 0.11071 (p2a + p2b = 0.11773) 0 = 0.0714, 2a = 1.00000 2b = 1.00000	45L (P = 0.69) 50T (P = 0.62) 145Q (P = 0.61) 206D (P = 0.51)
Model B: FUL2 (= null Model B)	5	−3626.84	p0 = 0.80202, p1 = 0.19798, (p2 + p3 = 0.00), 0 = 0.05027 1 = 0.52984, 2 = ∞

Parameter estimates that are underlined indicate positive selection; those in parentheses are not free parameters (p). Putative sites under positive selection are based on the coding region of rice OsMADS14. Estimates of κ ranged between 1.74 and 1.9. ℓ, log likelihood; p, number of parameters; q, free parameter.