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Table 4 Genetic sequences used in this study with their inferred models of evolution.

From: Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset

 

Phylogeny estimation

Fitting to supertree topology

 

Gene

Number of taxa

Number of bps

Model selected

Nonclock ln L

Model selected

Nonclock ln L

Clock ln L

Chi-squared

df

LRT P-value

Clock?

ALDOA

7

120

K80 *

228.5901

K80

228.5901

228.98093

0.78166

5

0.9782

yes

ALDOC

7

129

K3P *

213.1006

K81+I

216.4168

218.7521

4.6706

5

0.4574

yes

APOB (editing region)

5

175

TVM *

317.7049

TVM+G

317.3427

319.90041

5.1154

3

0.1635

yes

APOB (exon 26)

6

963

HKY

1701.6729

HKY

1701.673

1705.76283

8.1797

4

0.08521

yes

APOB (exon 29)

3

621

n/a

n/a

TVM+G

1380.1937

1381.96031

3.5332

1

0.06015

yes

CYP1A1

5

1560

HKY

2641.2015

HKY+I

2913.9797

3546.2776

1264.6

3

0

 

CYP1A2

5

1539

TVM+G

2859.5616

TVM+I

2861.4082

2863.05456

3.2927

3

0.3487

yes

H2AFZ

7

52

TrNef *

95.5468

TrNef

97.6302

99.00264

2.7449

5

0.7392

yes

HLA-DOA

5

399

HKY *

598.9182

HKY

598.9182

599.15301

0.46962

3

0.9255

yes

LEP

5

504

GTR *

1110.6539

GTR

1110.6539

1126.3367

31.366

3

7.12E-07

 

LYZ

3

447

n/a

n/a

K80

677.5543

677.71442

0.32024

1

0.5715

yes

MHC-DQA1

7

162

TVMef *

393.3731

TVMef

393.7065

395.79033

4.1677

5

0.5255

yes

MHC-DQA2

7

230

HKY+G *

455.7005

HKY+I

458.4345

460.01745

3.1659

5

0.6744

yes

MHC-DQB1

5

141

K3Puf+G *

307.2022

TVM+I

306.0257

306.25311

0.45482

3

0.9287

yes

MT-ATP6

22

681

GTR+I+G *

4821.8578

TVM+I+G

4823.9243

4837.61057

27.373

20

0.1251

yes

MT-ATP8

22

204

HKY+I+G *

1598.4148

TVM+I+G

1597.1221

1609.01567

23.787

20

0.2518

yes

MT-CO1

25

1545

GTR+I+G *

10168.6228

TVM+I+G

10171.9424

10194.06882

44.253

23

0.004901

yes

MT-CO2

25

687

HKY+I+G *

4427.0054

HKY+I+G

4428.0015

4446.36885

36.735

23

0.03465

yes

MT-CO3

22

784

HKY+I+G *

4896.904

TVM+I+G

4893.5391

4909.02367

30.969

20

0.0556

yes

MT-CYB

35

1140

TrN+I+G *

8835.9098

GTR+I+G

8836.9434

8872.23839

70.59

33

0.0001522

 

MT-ND1

22

957

HKY+I+G *

5866.8206

TVM+I+G

5863.5283

5882.62305

38.19

20

0.008394

yes

MT-ND2

24

1044

TrN+I+G *

7689.7091

TIM+I+G

7698.3613

7720.88041

45.038

22

0.002625

yes

MT-ND3

22

350

HKY+G *

2365.8095

TVM+I+G

2363.5559

2374.43717

21.763

20

0.3535

yes

MT-ND4

21

1378

GTR+I+G *

9587.3198

TVM+I+G

9586.7549

9609.42621

45.343

19

0.0006135

 

MT-ND4L

22

300

HKY+I+G *

1900.4839

HKY+I+G

1897.8574

1909.16103

22.607

20

0.3085

yes

MT-ND5

22

1836

GTR+I+G *

13444.3742

TVM+I+G

13450.124

13482.66844

65.089

20

1.13E-06

 

MT-ND6

13

528

HKY+I+G *

2457.8525

HKY+I+G

2457.8848

2466.38674

17.004

11

0.1078

yes

MT-RNR1

18

984

GTR+G *

4033.2182

GTR+I+G

4033.6277

4047.13902

27.023

16

0.04123

yes

MT-RNR2

14

1608

GTR+I+G

5722.1966

GTR+I+G

5710.8447

5730.04437

38.399

12

0.0001321

 

MT-TA

7

69

HKY+G *

193.586

HKY+G

192.1818

197.11463

9.8657

5

0.07913

yes

MT-TC

7

69

K80+G *

190.9928

K80+G

190.9817

192.76403

3.5647

5

0.6136

yes

MT-TD

7

68

HKY+G *

177.8663

HKY+G

177.7805

178.50213

1.4433

5

0.9195

yes

MT-TE

9

72

HKY+G *

205.1879

HKY+I

204.3486

208.84935

9.0015

7

0.2525

yes

MT-TF

7

72

TrNef *

201.267

TrN+G

197.1401

202.84986

11.42

5

0.04366

yes

MT-TG

7

72

TrNef+G *

269.0899

HKY+G

267.3327

271.41557

8.1657

5

0.1473

yes

MT-TH

7

69

HKY+G *

201.8982

HKY+G

203.5126

205.11176

3.1983

5

0.6694

yes

MT-TI

7

71

HKY+G *

141.7316

HKY+I

142.4105

145.12331

5.4256

5

0.3662

yes

MT-TK

7

70

HKY+G *

219.0096

HKY+G

221.4528

228.78366

14.662

5

0.01191

yes

MT-TM

7

71

K80+G *

140.5878

TrNef+I+G

135.8801

145.67015

19.58

5

0.001498

yes

MT-TN

7

73

K80+G *

204.0605

HKY+I

201.8885

205.49416

7.2113

5

0.2054

yes

MT-TP

8

68

HKY+G *

200.9591

HKY+G

202.8423

204.98693

4.2893

6

0.6376

yes

MT-TQ

7

76

HKY+G *

202.9076

TrN+G

203.4861

222.92371

38.875

5

2.52E-07

 

MT-TR

8

71

HKY+G *

197.8915

K81uf+G

196.7379

201.8366

10.197

6

0.1166

yes

MT-TT

9

74

K80+G *

226.9842

HKY+I

224.7003

230.34978

11.299

7

0.1261

yes

MT-TV

8

76

K80+G *

231.1146

HKY+G

230.1562

233.04494

5.7775

6

0.4486

yes

MT-TW

7

68

K80+I+G *

215.6285

HKY+I+G

211.9622

218.25694

12.589

5

0.02755

yes

MT-TY

7

70

K80+G *

225.9578

HKY+I

222.7287

230.7563

16.055

5

0.006689

yes

MX1

4

1980

TrN+G

3887.1331

TrN+G

3887.1331

3892.79094

11.316

2

0.003489

yes

RAG1

5

741

HKY+G

1713.0793

TVM+I

1709.8627

1712.53176

5.3381

3

0.1486

yes

RHO

5

1077

HKY+I+G

2055.8504

HKY+I

2056.0244

2056.56021

1.0716

3

0.7839

yes

SERPINA7

7

442

TrNef *

869.6311

TrNef

869.631

870.82096

2.3799

5

0.7945

yes

SRY

21

231

HKY *

488.8158

HKY

488.3143

494.82962

13.031

19

0.837

yes

TOTAL

 

26818

         
  1. Models followed by an asterisk were determined using AICc; all others were determined using AIC. LYZ and APOB (exon 29) were not used to construct the supertree. Gene symbols follow Wain et al. [126].