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Table 1 Substitution frequencies and rate heterogeneity parameters

From: Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics

  

A↔C

A↔G

A↔T

C↔G

C↔Ta

αb

I (ML)c

Id

All sites

Fish

0.778

2.419

1.328

0.984

3.192

1.203

0.262

0.412

 

Reptiles

1.081

4.598

0.907

3.330

2.516

0.392

0.000

0.611

 

Mammals

1.322

4.876

0.838

0.727

4.672

1.473

0.345

0.530

 

Tetrapods

1.091

4.120

0.969

1.431

3.341

1.029

0.244

0.367

 

Vertebrates

0.987

3.326

1.084

1.298

3.115

1.014

0.166

0.263

Codon #1

Fish

2.338

2.645

1.434

0.793

2.877

0.422

0.000

0.334

 

Reptiles

2.383

2.148

0.777

0.579

1.313

0.312

0.000

0.629

 

Mammals

2.504

4.097

0.739

0.828

3.515

1.445

0.447

0.646

 

Tetrapods

2.051

2.781

0.935

0.602

1.891

0.780

0.212

0.457

 

Vertebrates

2.188

2.473

1.008

0.741

2.256

0.837

0.122

0.319

Codon #2

Fish

5.561

9.417

3.878

23.904

10.450

0.411

0.000

0.629

 

Reptiles

0.411

7.219

0.549

5.696

3.547

1.936

0.666

0.806

 

Mammals

1.654

11.198

2.489

6.140

7.073

0.364

0.298

0.747

 

Tetrapods

1.727

8.563

1.226

6.564

4.313

0.403

0.119

0.593

 

Vertebrates

2.435

7.089

1.480

7.343

4.679

0.647

0.108

0.435

Codon #3

Fish

0.454

2.419

1.878

0.286

3.282

3.877

0.013

0.103

 

Reptiles

0.377

4.589

0.000

0.431

4.089

1.002

0.000

0.343

 

Mammals

0.985

5.023

0.810

0.194

4.248

2.907

0.000

0.197

 

Tetrapods

0.623

4.283

0.973

0.679

3.599

3.058

0.028

0.050

 

Vertebrates

0.521

3.386

1.169

0.622

3.027

4.665

0.032

0.036

  1. a Parameters are reversible and measured against the G↔T parameter with a value of 1
  2. b Shape parameter for the gamma distribution.
  3. c Proportion of invariant sites estimated using maximum likelihood methods
  4. d Proportion of invariant sites calculated from raw alignment data using MEGA3 [131].