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Table 1 Parameters reflecting changes in selection pressure predicted by models

From: Genome-wide analysis of purple acid phosphatase structure and expression in ten vegetable species

Lineage-based tests for selection

model

clade No.

np

lnL

2|ΔlnL|

Significant (p < 0.05)

ω

ω (background)

ω (foreground)

one-ratio model

 

537

−37,685.482872

  

0.08013

  

two-ratio model

A

538

−37,681.586780

7.792184

yes

 

0.08013

0.00200

B

538

−37,678.998415

12.968914

yes

 

0.08020

0.00049

C

538

−37,683.604012

3.757720

no

 

0.08030

0.00916

D

538

−37,685.271690

0.422364

no

 

0.08011

0.01379

E

538

−37,684.446480

2.072784

no

 

0.08031

0.00402

F

538

−37,684.155074

2.655596

no

 

0.08034

0.00301

G

538

−37,685.056969

0.851806

no

 

0.08018

0.00755

H

538

−37,682.302812

6.360120

yes

 

0.08020

inf.

I

538

−37,683.897444

3.170856

no

 

0.08019

inf.

Branch-sites test for positive selection of clade H

model

np

lnL

2|ΔlnL|

Significant

Class 0

Class 1

Class 2a

Class 2b

Null (neutral)

539

−37,663.562931

  

p = 0.56355

ω (background) = 0.08032

ω (foreground) = 0.08032

p = 0.00407

ω (background) = 1

ω (foreground) = 1

p = 0.42929

ω (background) = 0.08032

ω (foreground) = 1

p = 0.00310

ω (background) = 1

ω (foreground) = 1

Positive Selection

540

−37,661.849118

3.427626

no (vs Null)

p = 0.52279

ω (background) = 0.08042

ω (foreground) = 0.08042

p = 0.00377

ω (background) = 1

ω (foreground) = 1

p = 0.47005

ω (background) = 0.08042

ω (foreground) = inf.

p = 0.00339

ω (background) = 1

ω (foreground) = inf.