Table 2.

Parameter estimates from tests for selection

Model	np	ℓ	Parameters	Positively selected sites
M0: One ratio	137	-5654.77	ω = 0.173	None
M1a: Nearly neutral	138	-5539.34	p0 = 0.885, ω0 = 0.062; p1 = 0.114, ω1 = 1	Not allowed
M2a: Positive selection	140	-5529.73	p0 = 0.892, ω0 = 0.07; p0 = 0.085, ω1 = 1; p2 = 0.023, ω2 = 2.92	K30Q
M3: Discrete	139	-5536.84	p0 = 0.92, ω0 = 0.08; p1 = 0.079, ω1 = 1.46	A11V, Q14K, E28Q, K30Q, G86D, S95N, V99A, I133L, L225I, I251M, K305R
M7: β	138	-5547.37	p = 0.015, q = 0.074	Not allowed
M8: β &ω	140	-5527.82	p0 = 0.96; p = 0.09, q = 0.38; p1 = 0.039, ω = 2.20	A11V, Q14K, K30Q, S95N, V99A, I133L, L225I
Branch-site models
Taxaceae-Cephalotaxaceae
Model A: ω2 = 1, fixed	139	-5533.19	p0=0.857, ω0=0.053;p1=0.061,ω1=1;p2a+p2b = 0.082, ω2 = 1	Not allowed
Model A: ω2 estimated	140	-5530.95	p0=0.891, ω0=0.06;p1=0.078,ω1=1;p2a+p2b = 0.03, ω2 = 2.55	A11V, V99A, I133L
Taxus
Model A: ω2 = 1, fixed	139	-5535.98	p0=0.852, ω0=0.057;p1=0.106,ω1=1;p2a+p2b = 0.042, ω2 = 1	Not allowed
Model A: ω2 estimated	140	-5533.12	p0=0.86, ω0=0.06;p1=0.103,ω1=1;p2a+p2b = 0.027, ω2 = 5.9	K30Q
Torreya
Model A: ω2 = 1, fixed	139	-5538.23	p0=0.82, ω0=0.059;p1=0.106,ω1=1;p2a+p2b = 0.073, ω2 = 1	Not allowed
Model A: ω2 estimated	140	-5538.33	p0=0.82, ω0= 0.059;p1=0.106,ω1=1;p2a+p2b = 0.071, ω2 = 1.02	None
Podocarpaceae
Model A: ω2 = 1, fixed	139	-5527.9	p0=0.84, ω0=0.049;p1=0.057,ω1=1;p2a+p2b = 0.099, ω2 = 1	Not allowed
Model A: ω2 estimated	140	-5523.16	p0=0.89, ω0=0.065;p1=0.063,ω1=1;p2a+p2b = 0.047, ω2 = 2.41	A11V, G86D, V99A, I133L
Podocarpus I
Model A: ω2 = 1, fixed	139	-5537.56	p0=0.786, ω0=0.05;p1=0.084,ω1=1;p2a+p2b = 0.129, ω2 = 1	Not allowed
Model A: ω2 estimated	140	-5533.91	p0=0.727, ω0=0.058;p1=0.091,ω1=1;p2a+p2b = 0.181, ω2 = 1.12	None
Podocarpus II
Model A: ω2 = 1, fixed	139	-5530.31	p0=0.81, ω0=0.054;p1=0.093,ω1=1;p2a+p2b = 0.097, ω2 = 1	Not allowed
Model A: ω2 estimated	140	-5526.95	p0=0.85, ω0=0.056;p1=0.096,ω1=1;p2a+p2b = 0.056, ω2 = 3.31	S143A, T262V
Model	np	ℓ	Parameters	Positively selected sites
Cephalotaxaceae
Model A: ω2 = 1, fixed	139	-5537.3	p0=0.82, ω0=0.058;p1=0.102,ω1=1;p2a+p2b = 0.077, ω2 = 1	Not allowed
Model A: ω2 estimated	140	-5536.84	p0=0.862, ω0=0.059;p1=0.105,ω1=1;p2a+p2b = 0.032, ω2 = 2.68	None

Positive selection sites are identified with posterior probability higher than 95%.