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Table 4 Parameter estimation and likelihood ratio tests for the free-ratio and branch-site models among plant H+-PPase genes

From: The structure, functional evolution, and evolutionary trajectories of the H+-PPase gene family in plants

Cluster

Model

np a

Ln L

Estimates of parameters (ω2)

LRT P-value

Positive selected sites b

Background branch

Foreground branch

Not required

One-ratio

183

− 135,266.4315

–

–

0.000000000*

Not Allowed

Free-ratio

363

−134,256.0879

–

–

Not Allowed

Type I

Model A

186

−132,447.573101

0.03780

999.00000

0.000000002*

1

Model A-null

185

−132,465.522435

1

–

Not Allowed

Type II

Model A

186

−132,461.505672

0.03773

26.50916

0.005794019*

14

Model A-null

185

−132,465.312309

1

–

Not Allowed

Type Ia c

Model A

118

−66,571.582278

0.03457

1.00000

0.000000000*

None

Model A-null

117

−67,324.741260

1

–

 

Not Allowed

  1. Note: *, p < 0.01
  2. aNumber of parameters in the ω distribution
  3. bThe number of positive-selection sites inferred at posterior probabilities > 95%
  4. cPhylogenetic relationships used for the branch-site model analysis (Additional file 10)