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Table 2 Parameter estimates from tests for selection

From: Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns

Model np Parameters Positively selected sites
M0: One ratio 137 -5654.77 ω= 0.173 None
M1a: Nearly neutral 138 -5539.34 p 0 = 0.885, ω 0 = 0.062; p 1 = 0.114, ω 1 = 1 Not allowed
M2a: Positive selection 140 -5529.73 p 0 = 0.892, ω 0 = 0.07; p 0 = 0.085, ω 1 = 1; p 2 = 0.023, ω 2 = 2.92 K30Q
M3: Discrete 139 -5536.84 p 0 = 0.92, ω 0 = 0.08; p 1 = 0.079, ω 1 = 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 p 0 = 0.96; p= 0.09, q= 0.38; p 1 = 0.039, ω= 2.20 A11V, Q14K, K30Q, S95N, V99A, I133L, L225I
Branch-site models     
Taxaceae-Cephalotaxaceae     
Model A: ω 2 = 1, fixed 139 -5533.19 p 0 =0.857, ω 0 =0.053;p 1 =0.061,ω 1 =1;p 2a +p 2b = 0.082, ω 2 = 1 Not allowed
Model A: ω 2 estimated 140 -5530.95 p 0 =0.891, ω 0 =0.06;p 1 =0.078,ω 1 =1;p 2a +p 2b = 0.03, ω 2 = 2.55 A11V, V99A, I133L
Taxus     
Model A: ω 2 = 1, fixed 139 -5535.98 p 0 =0.852, ω 0 =0.057;p 1 =0.106,ω 1 =1;p 2a +p 2b = 0.042, ω 2 = 1 Not allowed
Model A: ω 2 estimated 140 -5533.12 p 0 =0.86, ω 0 =0.06;p 1 =0.103,ω 1 =1;p 2a +p 2b = 0.027, ω 2 = 5.9 K30Q
Torreya     
Model A: ω 2 = 1, fixed 139 -5538.23 p 0 =0.82, ω 0 =0.059;p 1 =0.106,ω 1 =1;p 2a +p 2b = 0.073, ω 2 = 1 Not allowed
Model A: ω 2 estimated 140 -5538.33 p 0 =0.82, ω 0 =0.059;p 1 =0.106,ω 1 =1;p 2a +p 2b = 0.071, ω 2 = 1.02 None
Podocarpaceae     
Model A: ω 2 = 1, fixed 139 -5527.9 p 0 =0.84, ω 0 =0.049;p 1 =0.057,ω 1 =1;p 2a +p 2b = 0.099, ω 2 = 1 Not allowed
Model A: ω 2 estimated 140 -5523.16 p 0 =0.89, ω 0 =0.065;p 1 =0.063,ω 1 =1;p 2a +p 2b = 0.047, ω 2 = 2.41 A11V, G86D, V99A, I133L
Podocarpus I     
Model A: ω 2 = 1, fixed 139 -5537.56 p 0 =0.786, ω 0 =0.05;p 1 =0.084,ω 1 =1;p 2a +p 2b = 0.129, ω 2 = 1 Not allowed
Model A: ω 2 estimated 140 -5533.91 p 0 =0.727, ω 0 =0.058;p 1 =0.091,ω 1 =1;p 2a +p 2b = 0.181, ω 2 = 1.12 None
Podocarpus II     
Model A: ω 2 = 1, fixed 139 -5530.31 p 0 =0.81, ω 0 =0.054;p 1 =0.093,ω 1 =1;p 2a +p 2b = 0.097, ω 2 = 1 Not allowed
Model A: ω 2 estimated 140 -5526.95 p 0 =0.85, ω 0 =0.056;p 1 =0.096,ω 1 =1;p 2a +p 2b = 0.056, ω 2 = 3.31 S143A, T262V
Model np Parameters Positively selected sites
Cephalotaxaceae     
Model A: ω 2 = 1, fixed 139 -5537.3 p 0 =0.82, ω 0 =0.058;p 1 =0.102,ω 1 =1;p 2a +p 2b = 0.077, ω 2 = 1 Not allowed
Model A: ω 2 estimated 140 -5536.84 p 0 =0.862, ω 0 =0.059;p 1 =0.105,ω 1 =1;p 2a +p 2b = 0.032, ω 2 = 2.68 None
  1. Positive selection sites are identified with posterior probability higher than 95%.