APPENDIX 1. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with asymmetric tree topologies and 50 characters in each data set. Each value is the average accuracy from 100 replicated matrices.

   

Branch length

Case

 

0.01

0.15

0.30

0.45

0.60

I

data set 1

0.363

0.849

0.472

0.107

0.021

 

data set 2

0.361

0.832

0.506

0.091

0.012

 

consensus

0.139

0.714

0.261

0.018

0.000

 

combined

0.601

0.955

0.744

0.185

0.021

             

II

data set 1

0.360

0.869

0.455

0.081

0.014

 

data set 2

0.300

0.728

0.398

0.044

0.013

 

consensus

0.106

0.636

0.180

0.008

000

 

combined

0.559

0.915

0.695

0.140

0.025

             

III

data set 1

0.335

0.871

0.473

0.084

0.014

 

data set 2

0.268

0.675

0.320

0.037

0.007

 

consensus

0.089

0.590

0.132

0.003

0.000

 

combined

0.497

0.856

0.641

0.149

0.019

             

IV

data set 1

0.333

0.744

0.402

0.066

0.013

 

data set 2

0.304

0.784

0.412

0.083

0.008

 

consensus

0.097

0.567

0.159

0.003

000

 

combined

0.517

0.858

0.649

0.149

0.014

             

V

data set 1

0.357

0.847

0.426

0.091

0.023

 

data set 2

0.178

0.386

0.223

0.059

0.014

 

consensus

0.060

0.331

0.092

0.008

000

 

combined

0.420

0.613

0.432

0.125

0.022

             

VI

data set 1

0.344

0.846

0.465

0.099

0.027

 

data set 2

0.001

0.005

0.008

0.007

0.003

 

consensus

0.001

0.003

0.008

0.001

0.000

 

combined

0.261

0.370

0.203

0.038

0.012

             

VII

data set 1

0.195

0.364

0.241

0.056

0.009

 

data set 2

0.154

0.293

0.172

0.049

0.019

 

consensus

0.000

0.010

0.004

0.001

000

 

combined

0.264

0.398

0.132

0 044

0.004

 

 

APPENDIX 2. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with symmetric tree topologies and 50 characters in each data set. Each value is the average accuracy from 100 replicated matrices.

   

Branch length

Case

 

0.01

0.15

0.30

0.45

0.60

I

data set 1

0.343

0.807

0.546

0.248

0.047

 

data set 2

0.343

0.829

0.561

0.211

0.037

 

consensus

0.125

0.667

0.315

0.067

0.003

 

combined

0.577

0.956

0.749

0.342

0.052

             

II

data set 1

0.341

0.805

0.551

0.222

0.025

 

data set 2

0.263

0.614

0.399

0.158

0.033

 

consensus

0.093

0.486

0.228

0.048

0.000

 

combined

0.489

0.810

0.624

0.295

0.042

             

III

data set 1

0.353

0.827

0.548

0.183

0.053

 

data set 2

0.208

0.441

0.253

0.098

0.023

 

consensus

0.066

0.350

0.136

0.020

0.000

 

combined

0.423

0.702

0.512

0.241

0.049

             

IV

data set 1

0.267

0.637

0. 394

0.161

0.037

 

data set 2

0.266

0.632

0.395

0.124

0.036

 

consensus

0.069

0.353

0.120

0.015

0.003

 

combined

0.414

0.682

0.523

0.198

0.036

             

V

data set 1

0.343

0.825

0.535

0.207

0.046

 

data set 2

0.190

0.443

0.329

0.153

0.035

 

consensus

0.068

0.375

0.191

0.044

0.001

 

combined

0.420

0.708

0.555

0.267

0.044

             

VI

data set 1

0.363

0.824

0.514

0.219

0.047

 

data set 2

0.087

0.195

0.148

0.057

0.019

 

consensus

0.040

0.163

0.090

0.018

000

 

combined

0.300

0.532

0.386

0.155

0.040

             

VII

data set 1

0.202

0.444

0.312

0.153

0.025

 

data set 2

0.200

0.450

0.348

0.134

0.026

 

consensus

0.031

0.156

0.093

0.029

0.002

 

combined

0.336

0.544

0.383

0.169

0.040

 

 

 

APPENDIX 3. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with asymmetric tree topologies and 250 characters in each data set. Each value is the average accuracy from 100 replicated matrices.

   

Branch length

Case

 

0.01

0.15

0.30

0.45

0.60

I

data set 1

0.905

1.000

0.954

0.391

0.027

 

data set 2

0.915

1.000

0.947

0.368

0.027

 

consensus

0.828

1.000

0.904

0.196

0.004

 

combined

0.990

1.000

0.993

0.597

0.047

             

II

data set 1

0.933

1.000

0.959

0.370

0.110

 

data set 2

0.797

0.888

0.860

0.309

0.082

 

consensus

0.749

0.888

0.823

0.120

0.010

 

combined

0.933

0.949

0.942

0.511

0.131

             

III

data set 1

0.920

1.000

0.939

0.352

0.029

 

data set 2

0.715

0.780

0.749

0.220

0.015

 

consensus

0.656

0.780

0.692

0.072

0.001

 

combined

0.865

0.888

0.881

0.541

0.034

             

IV

data set 1

0.818

0.889

0.867

0.319

0.030

 

data set 2

0.812

0.889

0.853

0.283

0.025

 

consensus

0.654

0.778

0.721

0.077

0.003

 

combined

0.866

0.889

0.882

0.504

0.040

             

V

data set 1

0.910

1.000

0.954

0.354

0.041

 

data set 2

0.405

0.440

0.414

0.179

0.015

 

consensus

0.367

0.440

0.398

0.079

0.002

 

combined

0.733

0.639

0.491

0.308

0.033

             

VI

data set 1

0.894

1.000

0.968

0.382

0.036

 

data set 2

0.000

0.000

0.000

0.001

0.000

 

consensus

0.000

0.000

0.000

0.001

0.000

 

combined

0.537

0.494

0.146

0.035

0.000

             

VII

data set 1

0.398

0.439

0.407

0.195

0.024

 

data set 2

0.309

0.330

0.318

0.165

0.024

 

consensus

0.000

0.000

0.000

0.000

0.000

 

combined

0.565

0.526

0.157

0.025

0.008

 

 

 

APPENDIX 4. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with symmetric tree topologies and 250 characters in each data set. Each value is the average accuracy from 100 replicated matrices.

   

Branch length

Case

 

0.01

0.15

0.30

0.45

0.60

I

data set 1

0.914

1.000

0.923

0.540

0.104

 

data set 2

0.921

0.998

0.920

0.535

0.112

 

consensus

0.843

0.998

0.860

0.334

0.018

 

combined

0.992

1.000

0.974

0.684

0.162

             

II

data set 1

0.892

0.999

0.890

0.572

0.110

 

data set 2

0.696

0.779

0.694

0.394

0.082

 

consensus

0.626

0.778

0.607

0.255

0.010

 

combined

0.862

0.879

0.840

0.601

0.131

             

III

data set 1

0.905

0.996

0.917

0.545

0.090

 

data set 2

0.497

0.559

0.479

0.236

0.063

 

consensus

0.445

0.554

0.424

0.119

0.009

 

combined

0.746

0.769

0.701

0.515

0.112

             

IV

data set 1

0.696

0.778

0.698

0.378

0.066

 

data set 2

0.703

0.777

0.687

0.406

0.067

 

consensus

0.449

0.555

0.412

0.131

0.005

 

combined

0.720

0.772

0.712

0.491

0.097

             

V

data set 1

0.902

0.997

0.905

0.572

0.110

 

data set 2

0.508

0.560

0.516

0.335

0.078

 

consensus

0.458

0.559

0.488

0.217

0.011

 

combined

0.762

0.756

0.668

0.479

0.110

             

VI

data set 1

0.923

0.998

0.911

0.543

0.096

 

data set 2

0.194

0.220

0.203

0.135

0.037

 

consensus

0.179

0.220

0.191

0.083

0.005

 

combined

0.638

0.599

0.438

0.273

0.063

             

VII

data set 1

0.498

0.559

0.511

0.336

0.081

 

data set 2

0.499

0.559

0.511

0.318

0.067

 

consensus

0.180

0.220

0.210

0.095

0.008

 

combined

0.598

0.662

0.465

0.276

0.064

 

 

 

 

APPENDIX 5. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with asymmetric tree topologies and 500 characters in each data set. Each value is the average accuracy from 100 replicated matrices.

   

Branch length

Case

 

0.01

0.15

0.30

0.45

0.60

I

data set 1

0.996

1.000

0.994

0.579

0.067

 

data set 2

0.989

1.000

0.994

0.625

0.067

 

consensus

0.985

1.000

0.989

0.405

0.008

 

combined

1.000

1.000

1.000

0.861

0.087

             

II

data set 1

0.993

1.000

0.996

0.602

0.047

 

data set 2

0.884

0.890

0.889

0.503

0.042

 

consensus

0.878

0.890

0.884

0.308

0.004

 

combined

0.938

0.939

0.948

0.767

0.076

             

III

data set 1

0.989

1.000

0.993

0.608

0.044

 

data set 2

0.777

0.780

0.776

0.387

0.019

 

consensus

0.767

0.780

0.769

0.202

0.003

 

combined

0.866

0.875

0.888

0.732

0.070

             

IV

data set 1

0.884

0.890

0.888

0.505

0.053

 

data set 2

0.882

0.890

0.887

0466

0.035

 

consensus

0.769

0.780

0.774

0.190

0.000

 

combined

0.869

0.891

0.894

0.713

0.065

             

V

data set 1

0.996

1.000

0.998

0.609

0.059

 

data set 2

0.438

0.440

0.434

0.286

0.026

 

consensus

0.435

0.440

0.433

0.186

0.007

 

combined

0.731

0.655

0.466

0.388

0.040

             

VI

data set 1

0.993

1.000

0.999

0.569

0.045

 

data set 2

0.000

0.000

0.000

0.000

0.000

 

consensus

0.000

0.000

0.000

0.000

0.000

 

combined

0.649

0.500

0.128

0.021

0.000

             

VII

data set 1

0.437

0.440

0.434

0.298

0.027

 

data set 2

0.329

0.330

0.329

0.243

0.041

 

consensus

0.000

0.000

0.000

0.000

0.000

 

combined

0.700

0.516

0.114

0.026

0.003

 

 

 

APPENDIX 6. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with symmetric tree topologies and 500 characters in each data set. Each value is the average accuracy from 100 replicated matrices.

   

Branch length

Case

 

0.01

0.15

0.30

0.45

0.60

I

data set 1

0.989

1.000

0.971

0.695

0.150

 

data set 2

0.997

1.000

0.963

0.674

0.156

 

consensus

0.986

1.000

0.936

0.533

0.033

 

combined

0.999

1.000

0.996

0.790

0.231

             

II

data set 1

0.989

1.000

0.964

0.672

0.147

 

data set 2

0.774

0.780

0.758

0.492

0.092

 

consensus

0.768

0.780

0.724

0.360

0.021

 

combined

0.883

0.886

0.871

0.674

0.174

             

III

data set 1

0.992

1.000

0.976

0.687

0.135

 

data set 2

0.558

0.560

0.518

0.314

0.068

 

consensus

0.554

0.560

0.499

0.219

0.017

 

combined

0.744

0.769

0.722

0.586

0.150

             

IV

data set 1

0.770

0.780

0.750

0.493

0.128

 

data set 2

0.770

0.780

0.759

0.474

0.113

 

consensus

0.547

0.560

0.507

0.198

0.020

 

combined

0.754

0.732

0.723

0.563

0.153

             

V

data set 1

0.996

1.000

0.961

0.708

0.161

 

data set 2

0.220

0.560

0.548

0.395

0.117

 

consensus

0.218

0.560

0.537

0.320

0.025

 

combined

0.637

0.759

0.671

0.532

0.156

             

VI

data set 1

0.996

1.000

0.971

0.699

0.162

 

data set 2

0.220

0.220

0.219

0.187

0.047

 

consensus

0.218

0.220

0.219

0.162

0.005

 

combined

0.637

0.648

0.463

0.290

0.068

             

VII

data set 1

0.555

0.560

0.554

0.410

0.110

 

data set 2

0.553

0.560

0.550

0.410

0.101

 

consensus

0.213

0.220

0.219

0.145

0.012

 

combined

0.713

0.664

0.459

0.294

0.076

 

 

 

APPENDIX 7. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with asymmetric tree topologies and 1000 characters in each data set. Each value is the average accuracy from 100 replicated matrices.

   

Branch length

Case

 

0.01

0.15

0.30

0.45

0.60

I

data set 1

1.000

1.000

1.000

0.839

0.101

 

data set 2

1.000

1.000

1.000

0.862

0.091

 

consensus

1.000

1.000

1.000

0.726

0.021

 

combined

1.000

1.000

1.000

0.965

0.159

             

II

data set 1

1.000

1.000

1.000

0.823

0.090

 

data set 2

0.890

0.890

0.890

0.719

0.070

 

consensus

0.890

0.890

0.890

0.585

0.014

 

combined

0.939

0.946

0.934

0.913

0.115

             

III

data set 1

1.000

1.000

1.000

0.802

0.091

 

data set 2

0.780

0.780

0.780

0.623

0.034

 

consensus

0.780

0.780

0.780

0.466

0.004

 

combined

0.891

0.883

0.873

0.873

0.088

             

IV

data set 1

0.890

0.890

0.890

0.748

0.080

 

data set 2

0.890

0.890

0.890

0.705

0.081

 

consensus

0.780

0.780

0.780

0.486

0.008

 

combined

0.884

0.883

0.882

0.851

0.130

             

V

data set 1

1.000

1.000

1.000

0.818

0.087

 

data set 2

0.440

0.440

0.439

0.364

0.052

 

consensus

0.440

0.440

0.439

0.301

0.009

 

combined

0.768

0.602

0.480

0.417

0.070

             

VI

data set 1

1.000

1.000

1.000

0.836

0.103

 

data set 2

0.000

0.000

0.000

0.000

0.000

 

consensus

0.000

0.000

0.000

0.000

0.000

 

combined

0.715

0.479

0.080

0.008

0.001

             

VII

data set 1

0.440

0.440

0.440

0.363

0.044

 

data set 2

0.330

0.330

0.330

0.295

0.037

 

consensus

0.000

0.000

0.000

0.000

0.000

 

combined

0.733

0.551

0.093

0.003

0.000

 

 

 

 

APPENDIX 8. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, with symmetric tree topologies and 1000 characters in each data set. Each value is the average accuracy from 100 replicated matrices.

   

Branch length

Case

 

0.01

0.15

0.30

0.45

0.60

I

data set 1

1.000

1.000

0.996

0.792

0.230

 

data set 2

1.000

1.000

0.993

0.782

0.210

 

consensus

1.000

1.000

0.989

0.681

0.055

 

combined

1.000

1.000

0.999

0.868

0.293

             

II

data set 1

1.000

1.000

0.994

0.790

0.219

 

data set 2

0.780

0.780

0.776

0.567

0.141

 

consensus

0.780

0.780

0.770

0.475

0.037

 

combined

0.875

0.892

0.880

0.750

0.252

             

III

data set 1

1.000

1.000

0.996

0.785

0.221

 

data set 2

0.560

0.560

0.555

0.362

0.087

 

consensus

0.560

0.560

0.551

0.278

0.025

 

combined

0.716

0.771

0.765

0.603

0.212

             

IV

data set 1

0.780

0.780

0.774

0.578

0.172

 

data set 2

0.780

0.780

0.774

0.563

0.161

 

consensus

0.560

0.560

0.548

0.273

0.023

 

combined

0.701

0.760

0.746

0.604

0.204

             

V

data set 1

1.000

1.000

0.994

0.789

0.214

 

data set 2

0.560

0.560

0.558

0.474

0.148

 

consensus

0.560

0.560

0.558

0.426

0.046

 

combined

0.837

0.735

0.674

0.565

0.195

             

VI

data set 1

1.000

1.000

0.993

0.781

0.247

 

data set 2

0.220

0.220

0.220

0.201

0.053

 

consensus

0.220

0.220

0.220

0.189

0.018

 

combined

0.670

0.651

0.463

0.286

0.088

             

VII

data set 1

0.560

0.560

0.556

0.489

0.146

 

data set 2

0.560

0.560

0.556

0.475

0.153

 

consensus

0.220

0.220

0.220

0.200

0.025

 

combined

0.746

0.701

0.469

0.278

0.095

 

 

 

 

APPENDIX 9. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, asymmetric tree topologies, slightly unequal branch lengths (range 0.00--0.15) and different numbers of characters. Each value is the average accuracy from 100 replicated matrices.

   

Number of characters

Case

 

50

250

500

1000

I

data set 1

0.747

0.926

0.957

0.978

 

data set 2

0.753

0.919

0.959

0.975

 

consensus

0.606

0.880

0.931

0.965

 

combined

0.878

0.955

0.965

0.985

           

II

data set 1

0.734

0.949

0.959

0.970

 

data set 2

0.646

0.850

0.847

0.865

 

consensus

0.523

0.822

0.829

0.849

 

combined

0.790

0.913

0.915

0.928

           

III

data set 1

0.727

0.938

0.959

0.979

 

data set 2

0.582

0.728

0.752

0.761

 

consensus

0.463

0.694

0.737

0.754

 

combined

0.742

0.850

0.866

0.879

           

IV

data set 1

0.670

0.832

0.847

0.867

 

data set 2

0.673

0.818

0.864

0.871

 

consensus

0.470

0.694

0.728

0.751

 

combined

0.772

0.849

0.869

0.867

           

V

data set 1

0.760

0.935

0.961

0.977

 

data set 2

0.348

0.420

0.429

0.431

 

consensus

0.295

0.401

0.418

0.423

 

combined

0.639

0.708

0.747

0.705

           

VI

data set 1

0.741

0.944

0.966

0.969

 

data set 2

0.004

0.001

0.001

0.001

 

consensus

0.003

0.001

0.001

0.001

 

combined

0.431

0.514

0.547

0.538

           

VII

data set 1

0.346

0.424

0.429

0.433

 

data set 2

0.263

0.316

0.321

0.321

 

consensus

0.007

0.005

0.000

0.001

 

combined

0.465

0.540

0.575

0.646

 

 

 

 

APPENDIX 10. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, symmetric tree topologies, slightly unequal branch lengths (range 0.00--0.15) and different numbers of characters. Each value is the average accuracy from 100 replicated matrices.

   

Number of characters

Case

 

50

250

500

1000

I

data set 1

0.732

0.923

0.957

0.980

 

data set 2

0.740

0.922

0.957

0.987

 

consensus

0.601

0.888

0.936

0.974

 

combined

0.843

0.949

0.977

0.988

           

II

data set 1

0.757

0.941

0.967

0.976

 

data set 2

0.575

0.720

0.754

0.752

 

consensus

0.482

0.696

0.741

0.743

 

combined

0.748

0.848

0.858

0.838

           

III

data set 1

0.702

0.931

0.963

0.975

 

data set 2

0.408

0.519

0.541

0.548

 

consensus

0.314

0.506

0.530

0.539

 

combined

0.632

0.684

0.757

0.708

           

IV

data set 1

0.554

0.722

0.732

0.758

 

data set 2

0.544

0.718

0.747

0.758

 

consensus

0.289

0.488

0.503

0.535

 

combined

0.642

0.724

0.720

0.739

           

V

data set 1

0.727

0.912

0.954

0.974

 

data set 2

0.413

0.522

0.523

0.547

 

consensus

0.332

0.487

0.510

0.537

 

combined

0.643

0.753

0.798

0.800

           

VI

data set 1

0.715

0.939

0.959

0.969

 

data set 2

0.169

0.207

0.212

0.217

 

consensus

0.134

0.197

0.205

0.212

 

combined

0.504

0.607

0.608

0.632

           

VII

data set 1

0.398

0.507

0.541

0.546

 

data set 2

0.408

0.509

0.526

0.549

 

consensus

0.145

0.194

0.211

0.213

 

combined

0.496

0.623

0.661

0684

 

 

 

APPENDIX 11. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, asymmetric tree topologies, highly unequal branch lengths (range 0.00-0.75) and different numbers of characters. Each value is the average accuracy from 100 replicated matrices.

   

Number of characters

Case

 

50

250

500

1000

I

data set 1

0.132

0.307

0.327

0.423

 

data set 2

0.159

0.298

0.323

0.416

 

consensus

0.072

0.192

0.224

0.314

 

combined

0.215

0.373

0.370

0.445

           

II

data set 1

0.142

0.278

0.357

0.401

 

data set 2

0.114

0.249

0.316

0.340

 

consensus

0.049

0.143

0.214

0.252

 

combined

0.200

0.319

0.412

0.419

           

III

data set 1

0.154

0.296

0.348

0.417

 

data set 2

0.107

0.215

0.250

0.271

 

consensus

0.048

0.118

0.150

0.202

 

combined

0.152

0.340

0.350

0.403

           

IV

data set 1

0.128

0.233

0.318

0.287

 

data set 2

0.126

0.247

0.328

0.329

 

consensus

0.033

0.112

0.173

0.168

 

combined

0.175

0.294

0.412

0.373

           

V

data set 1

0.122

0.294

0.351

0.408

 

data set 2

0.089

0.153

0.186

0.216

 

consensus

0.042

0.000

0.112

0.138

 

combined

0.154

0.241

0.277

0.305

           

VI

data set 1

0.159

0.337

0.335

0.397

 

data set 2

0.024

0.020

0.009

0.018

 

consensus

0.012

0.018

0.009

0.018

 

combined

0.102

0.120

0.107

0.145

           

VII

data set 1

0.108

0.169

0.186

0.197

 

data set 2

0.102

0.134

0.156

0.191

 

consensus

0.013

0.018

0.014

0.017

 

combined

0.104

0.117

0.111

0.120

 

 

 

 

APPENDIX 12. Accuracy of separate, combined, and consensus analysis for two genes (data sets) with different phylogenetic histories, symmetric tree topologies, highly unequal branch lengths (range 0.00--0.75) and different numbers of characters. Each value is the average accuracy from 100 replicated matrices.

   

Number of characters

Case

 

50

250

500

1000

I

data set 1

0.311

0.445

0.537

0.576

 

data set 2

0.293

0.442

0.522

0.558

 

consensus

0.180

0.341

0.416

0.489

 

combined

0.393

0.503

0.582

0.598

           

II

data set 1

0.253

0.454

0.525

0.517

 

data set 2

0.191

0.349

0.372

0.378

 

consensus

0.108

0.258

0.289

0.301

 

combined

0.283

0.440

0.493

0.485

           

III

data set 1

0.292

0.464

0.492

0.553

 

data set 2

0.123

0.213

0.237

0.250

 

consensus

0.073

0.148

0.173

0.203

 

combined

0.261

0.373

0.422

0.427

           

IV

data set 1

0.196

0.318

0.355

0.415

 

data set 2

0.182

0.322

0.368

0.411

 

consensus

0.065

0.136

0.162

0.221

 

combined

0.234

0.379

0.391

0.444

           

V

data set 1

0.303

0.413

0.486

0.567

 

data set 2

0.199

0.270

0.316

0.347

 

consensus

0.126

0.211

0.262

0.302

 

combined

0.309

0.373

0.406

0.449

           

VI

data set 1

0.300

0.452

0.492

0.539

 

data set 2

0.092

0.123

0.142

0.151

 

consensus

0.065

0.107

0.122

0.138

 

combined

0.245

0.270

0.272

0.301

           

VII

data set 1

0.189

0.306

0.311

0.367

 

data set 2

0.194

0.310

0.320

0.345

 

consensus

0.072

0.121

0.122

0.152

 

combined

0.231

0.296

0.273

0.320

 

APPENDIX 13. Accuracy of separate, consensus, and combined analysis in different parts of a phylogeny where there is a localized mismatch between gene and species trees in one of two data sets (data set 2). For each tree shape, one column represents the part of the phylogeny directly affected by the mismatch, the other represents those parts that share the same phylogenetic history. There are 250 characters in each data set. Each value is the average accuracy from 100 replicated matrices.

 

   

Tree shape

   

Asymmetric

Symmetric

Branch length

Method

Area of mismatch

Rest of tree

Area of mismatch

Rest of tree

0.01

data set 1

0.890

0.933

0.885

0.910

 

data set 2

0.000

0.896

0.000

0.904

 

consensus

0.000

0.836

0.000

0.828

 

combined

0.460

0.992

0.435

0.984

           

0.15

data set 1

1.000

1.000

1.000

1.000

 

data set 2

0.000

1.000

0.000

0.998

 

consensus

0.000

1.000

0.000

0.998

 

combined

0.460

1.000

0.450

1.000

           

0.30

data set 1

0.990

0.960

0.970

0.942

 

data set 2

0.000

0.963

0.000

0.956

 

consensus

0.000

0.924

0.000

0.904

 

combined

0.500

0.998

0.360

0.990

           

0.45

data set 1

0.790

0.347

0.830

0.700

 

data set 2

0.080

0.388

0.010

0.684

 

consensus

0.060

0.169

0.010

0.502

 

combined

0.450

0.600

0.345

0.832

           

0.60

data set 1

0.380

0.052

0.305

0.222

 

data set 2

0.250

0.049

0.105

0.174

 

consensus

0.080

0.002

0.020

0.050

 

combined

0.300

0.091

0.180

0.264