Skip to main content

Table 2 Parameter estimates from tests for selection

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

Model

np

â„“

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

â„“

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%.