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Table 2 Results of PAML branch-site model analysis

From: Heterogeneous natural selection on oxidative phosphorylation genes among fishes with extreme high and low aerobic performance

Branch

Model A

Null model

LRTs

Site class

0

1

2a

2b

b1

−189631.0183

−189631.0183

0

Proportion

0.94985

0.05015

0.00000

0.00000

Foreground ω

0.02838

1.00000

1.00000

1.00000

b2

−189619.8114

−189623.914

8.2052**

Proportion

0.94260

0.04932

0.00769

0.00040

Foreground ω

0.02825

1.00000

18.30494

18.30494

b3

−189710.2567

−189714.0692

7.6250**

Proportion

0.92062

0.04856

0.02927

0.00154

Foreground ω

0.02811

1.00000

5.60205

5.60205

b4

−189591.2640

−189598.5732

14.6183**

Proportion

0.92700

0.04823

0.02355

0.00123

Foreground ω

0.02799

1.00000

9.01795

9.01795

b5

−189728.0764

−189729.5338

2.9148

Proportion

0.91976

0.04869

0.02997

0.00159

Foreground ω

0.02824

1.00000

292.74200

292.74200

b6

−189719.7435

−189722.2222

4.9573*

Proportion

0.93956

0.04997

0.00994

0.00053

Foreground ω

0.02824

1.00000

5.43888

5.43888

b7

−189738.4458

−189738.4458

0

Proportion

0.94477

0.05030

0.00468

0.00025

Foreground ω

0.02845

1.00000

1.00000

1.00000

b8

−189738.5873

−189738.5873

0

Proportion

0.94946

0.05054

0.00000

0.00000

Foreground ω

0.02848

1.00000

1.00000

1.00000

b9

−189738.5873

−189738.5873

0

Proportion

0.94946

0.05054

0.00000

0.00000

Foreground ω

0.02848

1.00000

1.00000

1.00000

b10

−189738.5873

−189738.5873

0

Proportion

0.94946

0.05054

0.00000

0.00000

Foreground ω

0.02848

1.00000

1.00000

1.00000

b11

−189613.4925

−189622.0967

17.2084**

Proportion

0.94688

0.04932

0.00362

0.00019

Foreground ω

0.02831

1.00000

79.27458

79.27458

b12

−189615.9415

−189619.0732

6.7338**

Proportion

0.92922

0.04889

0.02080

0.00109

Foreground ω

0.02820

1.00000

999.00000

999.00000

b13

−189610.5139

−189616.7321

12.4364**

Proportion

0.94411

0.04933

0.00624

0.00033

Foreground ω

0.02821

1.00000

8.65776

8.65776

b14

−189734.9950

−189736.0673

2.1446

Proportion

0.94724

0.05043

0.00221

0.00012

Foreground ω

0.02842

1.00000

4.83612

4.83612

b16

−189624.9748

−189628.011

6.0725**

Proportion

0.94529

0.04967

0.00479

0.00025

Foreground ω

0.02827

1.00000

7.66238

7.66238

b17

−189621.7633

−189627.8443

12.1622**

Proportion

0.94863

0.04955

0.00173

0.00009

Foreground ω

0.02835

1.00000

336.12589

336.12589

b18

−189738.5873

−189738.5873

0

Proportion

0.94945

0.05055

0.00000

0.00000

Foreground ω

0.02848

1.00000

1.00000

1.00000

b23

−189618.7575

−189625.3146

13.1142*

Proportion

0.93161

0.04861

0.01879

0.00098

Foreground ω

0.02817

1.00000

999.00000

999.00000

b24

−189578.5777

−189597.2838

37.4121**

Proportion

0.90294

0.04769

0.04689

0.00248

Foreground ω

0.02828

1.00000

999.00000

999.00000

b25

−189591.1234

−189603.6533

25.0598**

Proportion

0.93264

0.04910

0.01735

0.00091

Foreground ω

0.02815

1.00000

9.15193

9.15193

  1. Estimated likelihood values under model A (allowing positive selection) and the null model (no positive selection), likelihood ratio tests (LRTs), and estimated parameters of model A. LRT critical values 3.84 at p = 0.05 (*) and 5.99 at p = 0.01 (**). Branches are as identified in Fig. 2