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Table 2 Comparative rate distribution tests of non-synonymous and synonymous substitutions across datasets

From: Differential strengths of selection on S-RNases from Physalis and Solanum(Solanaceae)

HA: Rates free to vary

Log likelihood: -16749.63

Parameters: 229

Inferred rates for Physalis:

Inferred rates for Solanum:

dN/dS

dS

dN

Prob

dN/dS

dS

dN

Prob

2.663

1.047

2.788

0.463

1.139

0.942

1.073

0.353

1.000

0.814

0.814

0.311

1.000

2.000

2.000

0.094

0.000

0.580

0.000

0.081

0.496

0.800

0.397

0.274

0.177

1.487

0.262

0.144

0.083

0.933

0.077

0.279

a) H 0 : Same strength of selection

 

Log likelihood: -16765.49

Parameters: 228

Inferred rates for Physalis:

Inferred rates for Solanum:

dN/dS

dS

dN

Prob

dN/dS

dS

dN

Prob

1.664

1.261

2.099

0.466

1.664

0.781

1.300

0.337

1.000

0.647

0.647

0.312

1.000

2.241

2.241

0.086

0.000

0.470

0.000

0.081

0.527

0.884

0.466

0.290

0.171

1.222

0.209

0.141

0.087

1.001

0.087

0.286

Are selection strengths (dN/dS) different?

LRT = 31.722 p < 0.0001; DF = 1

b) H 0 : Same proportion of selected sites

Log likelihood: -16750.60

Parameters: 228

Inferred rates for Physalis:

Inferred rates for Solanum:

dN/dS

dS

dN

Prob

dN/dS

dS

dN

Prob

2.737

1.042

2.851

0.397

1.143

0.949

1.085

0.397

1.000

0.900

0.900

0.339

1.000

2.065

2.065

0.081

0.000

0.573

0.000

0.084

0.491

0.804

0.395

0.258

0.216

1.297

0.280

0.180

0.082

0.939

0.077

0.264

Are the proportions of codons under selection different?

LRT = 1.929 p < 0.165; DF = 1

c) H 0 : Same dN/dS and proportions

Log likelihood: -16766.96

Parameters: 228

Inferred rates for Physalis:

Inferred rates for Solanum:

dN/dS

dS

dN

Prob

dN/dS

dS

dN

Prob

1.636

1.318

2.157

0.397

1.636

0.805

1.318

0.397

1.000

0.703

0.703

0.348

1.000

2.341

2.341

0.074

0.000

0.472

0.000

0.087

0.517

0.894

0.463

0.265

0.193

1.136

0.219

0.169

0.086

1.022

0.088

0.264

Are selective regimes (dN/dS and proportions) different?

LRT = 34.647 p < 0.0001; DF = 2

d) H 0 : Shared distributions of rates

Log likelihood: -16764.30

Parameters: 219

Inferred joint rates:

    

dN/dS

dS

dN

Prob

    

2.507

1.034

2.593

0.189

    

1.000

1.139

1.139

0.338

    

0.543

0.797

0.433

0.251

    

0.086

0.988

0.085

0.222

    

Are the distributions different?

LRT = 29.350 p < 0.001; DF = 10

  1. NOTE: Null models (a-d) were tested using likelihood ratio tests (LRTs) against the alternative model HA where dN and dS rates are free to vary in each dataset. Significance of p ≤ 0.05 was determined using χ2 with degrees of freedom (DF) equal to the number different parameters between models