Skip to main content

Table 4 Parameter estimates and log-likelihood values under models of variable ω ratios among codons

From: Molecular evolution of psbA gene in ferns: unraveling selective pressure and co-evolutionary pattern

Models

Ts/Tv

np

â„“

Estimated value of parameters

Positively selected codons**

Dataset one*

     

M0: One ratio

4.38

22

-3906.05

ω = 0.0184

None

M1a: Near neutral

4.55

23

-3858.84

p0 = 97.14%, ω0 = 0.00618; p1 = 2.86%, ω1 = 1

Not allowed

M2a: Positive

4.55

25

-3858.83

p0 = 97.14%, ω0 = 0.00618; p1 = 2.86%, ω1 = 1; p2 = 0%, ω2 = 79.26

91 L (97.2%)

M3: Discrete

4.60

26

-3854.64

p0 = 96.31%, ω0 = 0.00488; p1 = 3.39%, ω1 = 0.5646; p2 = 0.3%, ω2 = 3.9847

91 L (99.8%)

M7: β

4.48

23

-3865.36

p = 0.0267, q = 0.614

Not allowed

M8: β &ω > 1

4.53

25

-3857.78

p0 =97.84%, p = 0.01575, q = 0.46508; p1 = 2.15%, ω = 1.08788

91 L (99.7%)

Dataset two*

     

M0: One ratio

5.97

29

-3093.72

ω = 0.02403

None

M1a: Near neutral

6.07

30

-3061.96

p0 = 96.57%, ω0 = 0.00127; p1 = 3.43%, ω1 = 1

Not allowed

M2a: Positive

5.80

32

-3061.96

p0 = 96.57%, ω0 = 0.00127; p1 = 3.43%, ω1 = 1; p2 = 0, ω2 = 34.2681

347E (58.3%)

M3: Discrete

5.71

33

-3060.47

p0 = 46.14%, ω0 = 0; p1 = 49.52%, ω1 = 0; p2 = 4.31%, ω2 = 0.61912

None

M7: β

5.75

30

-3064.99

p = 0.00981, q = 0.19983

Not allowed

M8: β &ω > 1

5.80

32

-3061.93

p0 =96.61%, p = 0.01744, q = 2.58197; p1 = 3.38%, ω = 1

347E (81.6%), 349P (61.5%), 353 G (54.4%)

Dataset three*

     

M0: One ratio

4.66

47

-5742.02

ω = 0.01934

None

M1a: Near neutral

4.87

48

-5654.74

p0 = 96.39%, ω0 = 0.00538; p1 = 3.6%, ω1 = 1

Not allowed

M2a: Positive

4.18

50

-5656.81

p0 = 96.47%, ω0 = 0.0054; p1 = 3.55%, ω1 = 1; p2 = 0, ω2 = 4.46

71 L (72.4%), 91 L (78.0%)

M3: Discrete

4.90

51

-5637.73

p0 = 90.54%, ω0 = 0; p1 = 8.51%, ω1 = 0.5308; p2 = 0.943%, ω2 = 1.71

71 L (96.1%), 91 L (97.1%), 351 V (81.3%)

M7: β

4.78

48

-5648.93

p = 0.03078, q = 0.63009

Not allowed

M8: β &ω > 1

5.09

50

-5641.45

p0 =98.21%, p = 0.01555, q = 0.36594; p1 = 1.78%, ω = 1.19067

71 L (96.4%), 91 L(97.2%), 351 V (84.9%)

  1. *The contexts of the dataset were introduced in Additional file1Table S3. Codons with PP > 95% were in bold. The phylogeny trees applied in the estimation were reconstructed throughout dataset introduced in Additional file1Table S3 accordingly.
  2. **Positions and posterior probability of the positively selected codons were showed in this column. The posterior probabilities were given via Bayes Empirical Bayes (BEB) method.