Table 1

Characterization of Nuclear introns and mt genes examined in the present study

Sequence type

Fragments name

TEs

Aligneda

Final datab

Parsimony-informative sites

Nucleotide Composition

Ti/Tv

Best fit model

Among-site Rate Variation

Pairwise Distance (%)



A

T

G

C

I

α


Nucear introns

Cidea-1

YES

1590

1134

343

0.308

0.240

0.230

0.222

1.5

TrN+G

0

0.9770

7.5

Coro1c-4

YES

1435

1332

339

0.242

0.280

0.234

0.243

2.4

K81uf+G

0

0.9379

6.3

Coro1c-5

YES

1380

1099

140

0.309

0.321

0.210

0.160

2.2

TVM+G

0

0.9084

4.7

Guca1b-3

YES

711

711

149

0.230

0.186

0.289

0.295

1.6

HKY+G

0

0.7174

6.1

Ociad1-4

YES

1576

1014

200

0.328

0.393

0.145

0.134

1.9

TVM+G

0

1.3754

4.1

Plod2-13

NO

1317

1230

236

0.293

0.325

0.229

0.153

2.0

GTR+G

0

1.555

3.3

Plod2-14

YES

1685

1068

263

0.342

0.327

0.180

0.151

1.4

TVM+G

0

1.4866

3.7

Ssr1-5

YES

1180

783

131

0.324

0.382

0.160

0.134

2.2

GTR+G

0

1.4043

3.6

Tbc1d7-6

YES

1153

1095

326

0.247

0.293

0.261

0.199

1.5

TIM+G

0

0.7365

8.2

Tinagl1-1

YES

1263

1260

250

0.208

0.208

0.295

0.290

2.4

HKY+G

0

0.7637

3.2

Tinagl1-3

YES

1115

1014

193

0.179

0.238

0.281

0.301

1.9

K81uf+G

0

0.7201

3.7

Wasf1-3

YES

1195

1021

161

0.314

0.345

0.170

0.171

1.8

GTR+G

0

1.6253

3.9

Wasf1-6

YES

1276

1077

207

0.308

0.354

0.191

0.147

2.2

TVM+G

0

1.7531

4.1

Wasf1-7

NO

1380

1147

223

0.314

0.355

0.165

0.166

2.0

GTR+G

0

0.6571

3

Ttr-1

YES

1130

895

159

0.263

0.279

0.227

0.231

2.4

TVM+G

0

1.3403

4.6

Fgb-4

YES

847

523

71

0.307

0.307

0.215

0.171

2.0

HKY

0

equal

4.5

Fgb-7

YES

642

611

102

0.292

0.327

0.186

0.195

1.4

GTR

0

equal

5.1


Com1c

15893

12570

1735

0.279

0.301

0.219

0.201

2.0

TVM+I+G

0.17

0.9090

4.4

Com2c

15893

15038

2137

0.279

0.302

0.218

0.201

1.9

GTR+I+G

0.18

0.9078

4.6

Com3c

15893

15688

2170

0.279

0.303

0.218

0.200

1.8

GTR+I+G

0.18

0.9052

4.6


Mt genes

ND1

957

357

0.309

0.274

0.122

0.295

2.6

GTR+I+G

0.53

0.7988

17.3

ND2

1044

483

0.363

0.263

0.098

0.275

2.1

GTR+I+G

0.35

0.859

23

COX1

1545

556

0.282

0.302

0.175

0.241

3.1

GTR+I+G

0.58

1.1772

19.1

COX2

684

252

0.323

0.276

0.142

0.260

3.3

K81uf+I+G

0.56

1.0711

19.6

ATP8

204

92

0.388

0.291

0.077

0.243

2.2

GTR+I+G

0.42

1.3437

22.8

ATP6

681

290

0.306

0.291

0.116

0.287

3.3

GTR+I+G

0.46

0.7582

21.6

COX3

784

303

0.273

0.286

0.154

0.286

2.6

TrN+I+G

0.53

0.8079

20.2

ND3

348

160

0.320

0.279

0.130

0.272

2.5

TrN+I+G

0.38

0.956

22.3

ND4L

297

127

0.287

0.324

0.124

0.265

2.9

TVM+I+G

0.43

0.7530

22.5

ND4

1378

609

0.323

0.278

0.115

0.284

2.8

GTR+I+G

0.42

0.835

22.1

ND5

1830

739

0.331

0.274

0.115

0.280

2.6

TIM+I+G

0.42

0.8367

19.6

ND6

534

192

0.417

0.203

0.101

0.278

2.7

K81uf+I+G

0.46

0.656

16.3

CYTB

1140

446

0.295

0.278

0.134

0.293

2.8

TVM+I+G

0.5

1.1027

18.7

12SrRNA

988

236

0.371

0.229

0.178

0.223

2.8

GTR+I+G

0.37

0.3532

9.2

16SrRNA

1626

403

0.369

0.243

0.174

0.213

2.1

GTR+I+G

0.47

0.5765

10.5

tRNA

1558

301

0.353

0.281

0.157

0.209

4.0

GTR+I+G

0.48

0.4371

7.3

D-loop

941

315

0.308

0.277

0.166

0.249

1.9

HKY+I+G

0.3

0.4867

11.4


Combined

16537

5855

0.329

0.272

0.140

0.259

2.7

GTR+I+G

0.5

0.9372

16.9


Note: Ti = Transition; Tv = Transversion; I = Proportion of invariable sites; α = Gamma distribution shape parameter; TEs = Transposible Elements. If TEs were detected in introns, it indicated YES, otherwise it indicated NO.

a The length of sequences which were aligned using the CLUSTAL software with default settings.

b The length of analyzed data, after the ambiguous areas of the alignment were removed by Gblocks 0.91b.

c The length of all introns concatenated, after the ambiguous areas of the alignment were removed by Gblocks 0.91b with no gap (Com1), half gap (Com2), and all gap (Com3) parameters.

Yu et al. BMC Evolutionary Biology 2011 11:92   doi:10.1186/1471-2148-11-92

Open Data