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Table 3 Analysis of potential natural selection analysis among Amy1 genes

From: Structural organization and functional divergence of high isoelectric point α-amylase genes in bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.)

Model

p a

b

Estimates of Parameters

Positive Selected Sites

M0: one-ratio

1

− 7710.25

ω0 = 0.0519

NAc

Branch model

    

Two-ratios

2

− 7708.92

ω0 = 0.0513, ω1 = 0.182

None

Site-specific model

    

M1a: neutral

2

− 7606.65

p0 = 0.938 (p1 = 0.0620)

NAc

   

ω0 = 0.0409 (ω1 = 1.000)

 

M2a:selection

4

−7606.65

p0 = 0.938, p1 = 0.0620 (p2 = 0.000)

397S (P = 0.57)

   

ω0 = 0.0409 (ω1 = 1.000),

ω2 = 1.000

 

M3: discrete (K = 2)

3

− 7500.24

p0 = 0.776 (p1 = 0.224)

None

   

ω0 = 0.0131, ω1 = 0.219

 

M3: discrete (K = 3)

5

− 7487.11

p0 = 0.705, p1 = 0.240 (p2 = 0.0549)

None

   

ω0 = 0.009, ω1 = 0.131, ω2 = 0.446

 

M7: beta

2

− 7490.53

p = 0.254 q = 3.432

NAc

M8: beta&ω > 1

4

− 7488.21

p0 = 0.989 (p1 = 0.0108)

None

   

p = 0.281, q = 4.425, ωs = 1.000

 

Branch-site model

    

Model A

3

− 7604.85

p0 = 0.878, p1 = 0.0484,

Foreground lineage ω2 (BEBd):

   

(p2a + p2b = 0.0736)

56 V 119H 189 K 254D

   

ω2 = 1.000

(0.70 < P < 0.95)

Model B

5

− 7498.40

p0 = 0.620,

Foreground lineage ω2 (NEBd):

   

p1 = 0.183 (p2a + p2b = 0.197)

119H 254D (P > 0.95*)

   

ω0 = 0.0125, ω1 = 0.216,

Foreground lineage ω2 (BEBd):

   

ω2 = 1.197

56 V 119H 189 K 254D

    

(0.50 < P < 0.85)

  1. aThe number of free parameters for ω distribution. bValue of log likelihoods. cNot allowed. dNEB Naive Empirical Bayes, BEB Bayes Empirical Bayes. Amino acids refer to the first sequence: BdAmy1