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Table 1 Genetic diversity and Tajima's D in 54 loci in Daphnia pulex and an outgroup species

From: Immune genes undergo more adaptive evolution than non-immune system genes in Daphnia pulex

Gene

Classa

No. individuals(D. pulex,outgroup)

Outgroup

Basepairs sequenced

No. of alleles found

Ï€sb

Ï€ac

Ksd

Kae

Ka/Ks

Tajima's D

     

D. pulex

D. parvula

     

D. pulex

p

D. parvula

p

Actin

NI

11, 2

D. parvula

421

4

1

0.0082

0.0000

0.0882

0.0000

0.0000

-0.265

0.54

-

-

Caspase 1

NI

11, 4

D. parvula

707

9

1

0.0213

0.0000

0.0806

0.0009

0.0114

0.003

0.48

-

-

Caspase 2

NI

7, 1

D. parvula

655

13

2

0.0375

0.0202

0.0533

0.0236

0.4438

0.564

0.25

-

-

Caspase 3

NI

5, 1

D. parvula

529

8

2

0.0456

0.0109

0.1375

0.0693

0.5041

1.0170

0.14

-

-

Caspase 4

NI

11, 3

D. parvula

513

17

6

0.0342

0.0227

0.0923

0.0470

0.5096

0.857

0.16

1.267

0.06

Caspase 5

NI

9, 2

D. parvula

587

13

2

0.0354

0.0112

0.1882

0.0249

0.1323

0.201

0.36

-

-

Caspase 6

NI

8, 3

D. parvula

547

13

2

0.0259

0.0161

0.0804

0.0475

0.5904

0.889

0.17

0.851

0.11

Chitinase 15

NI

11, 3

D. parvula

877

19

5

0.0338

0.0049

0.1050

0.0215

0.2049

0.563

0.24

-0.826

0.67

Chitinase 16

NI

11, 4

D. parvula

931

14

6

0.0190

0.0013

0.1164

0.0174

0.1490

0.814

0.18

0.585

0.24

Chitinase 17

NI

10, 3

D. parvula

909

16

2

0.1514

0.0291

0.2285

0.0516

0.2260

1.808

0.02

-0.933

0.46

Eukaryotic translation initiation factor 2γ

NI

10, 3

D. parvula

1237

9

3

0.0102

0.0000

0.0350

0.0000

0.0000

0.592

0.26

-1.132

0.65

Enolase

NI

10, 4

D. parvula

336

3

1

0.0079

0.0000

0.1845

0.0000

0.0000

0.282

0.32

-

-

Fumerate

NI

10, 1

D. parvula

1103

10

2

0.0149

0.0006

0.1459

0.0039

0.0266

0.270

0.33

-

-

Glutamine-oxaloacetic transaminase

NI

10, 4

D. parvula

777

9

2

0.0321

0.0000

0.1368

0.0057

0.0414

1.211

0.09

1.167

0.09

Glyceraldehyde 3-phosphate dehydrogenase

NI

11, 4

D. parvula

701

8

1

0.0104

0.0000

0.0656

0.0038

0.0579

-0.125

0.49

-

-

Lactose dehydrogenase

NI

11, 2

D. parvula

840

10

1

0.0263

0.0016

0.1092

0.0024

0.0223

0.201

0.37

-

-

Mannose phosphase isomerase

NI

9, 3

D. parvula

751

8

2

0.0058

0.0010

0.0870

0.0010

0.0120

-0.437

0.63

-

-

Phosphoglucose isomerase

NI

11, 2

D. parvula

1387

17

3

0.0552

0.0025

0.1105

0.0052

0.0471

1.065

0.11

-0.780

0.53

Phosphoglycerate mutase

NI

8, 1

D. parvula

1184

15

2

0.0883

0.0011

0.1492

0.0056

0.0377

1.148

0.08

-

-

Scavenger 5

NI

9, 3

D. parvula

1440

16

5

0.0325

0.0001

0.1319

0.0069

0.0519

1.091

0.10

1.150

0.09

Scavenger 6

NI

7, 3

D. parvula

1119

6

5

0.0300

0.0026

0.1027

0.0113

0.1095

0.816

0.18

-0.496

0.58

Ultraspiracle

NI

10, 4

D. parvula

336

3

1

0.0079

0.0000

0.1845

0.0000

0.0000

0.282

0.31

-

-

Average

   

813.0

11

3

0.0331

0.0057

0.1188

0.0159

0.1443

    

Caspase 8

I

2, 2

D. parvula

672

4

2

0.1456

0.0906

0.1994

0.1465

0.7347

2.291

0.01

-

-

Dicer2

I

3, 1

D. parvula

265

6

1

0.0731

0.0098

0.1889

0.0597

0.3162

0.029

0.37

-

-

Dorsal

I

11, 4

D. parvula

624

8

1

0.0242

0.0000

0.1105

0.0000

0.0000

0.003

0.43

-

-

Galectin 1

I

11, 2

D. parvula

715

14

4

0.0235

0.0014

0.1004

0.0142

0.1419

0.604

0.23

-0.065

0.29

Galectin 2

I

10, 4

D. parvula

864

8

1

0.0162

0.0005

0.2106

0.0118

0.0559

1.065

0.12

-

-

Gemini

I

11, 2

D. parvula

1083

15

2

0.0342

0.0002

0.0962

0.0028

0.0295

0.774

0.17

-0.755

0.45

Gram-negative binding protein 1

I

11, 3

D. parvula

825

13

2

0.0182

0.0027

0.1266

0.0314

0.2478

1.203

0.11

0.851

0.14

Gram-negative binding protein 10

I

11, 4

D. parvula

638

7

5

0.0119

0.0000

0.1150

0.0043

0.0375

0.649

0.25

-0.163

0.55

Gram-negative binding protein 11

I

11, 3

D. parvula

787

14

5

0.0241

0.0037

0.1419

0.0232

0.1633

0.167

0.36

0.338

0.30

Gram-negative binding protein 2

I

10, 2

D. parvula

748

10

3

0.0398

0.0044

0.0420

0.0099

0.2351

1.483

0.04

0.168

0.23

Gram-negative binding protein 6

I

10, 2

D. parvula

836

10

2

0.0229

0.0019

0.0775

0.0116

0.1495

1.366

0.07

1.633

0.27

IMD

I

10, 3

D. parvula

489

12

4

0.0333

0.0056

0.1504

0.0200

0.1326

-0.007

0.43

-0.933

0.43

MyD88

I

11, 3

D. parvula

834

8

3

0.0139

0.0016

0.1498

0.0229

0.1527

-0.243

0.52

-0.826

0.68

Nitric oxide synthase 1

I

11, 3

D. parvula

662

14

2

0.0229

0.0011

0.0665

0.0062

0.0926

0.056

0.44

0.851

0.14

Nitric oxide synthase 2

I

9, 2

D. parvula

549

13

3

0.0203

0.0047

0.1689

0.0212

0.1253

0.333

0.33

-0.612

0.26

Pelle

I

12, 2

D. parvula

797

7

4

0.0087

0.0000

0.0636

0.0054

0.0846

-0.523

0.66

0.592

0.38

Prophenol Oxidase

I

5, 2

D. parvula

1224

8

4

0.0224

0.0040

0.0235

0.0029

0.1222

-0.284

0.57

1.198

0.11

Scavenger 2

I

10, 2

D. parvula

1463

15

4

0.0218

0.0087

0.1355

0.0410

0.3027

-0.537

0.68

0.592

0.39

Scavenger 4

I

6, 3

D. parvula

841

11

2

0.0840

0.0036

0.1327

0.0108

0.0816

0.842

0.15

-

-

Stat

I

11, 3

D. parvula

844

8

3

0.0174

0.0000

0.5590

0.0000

0.0000

1.197

0.10

-0.144

0.54

TEP 1

I

6, 2

D. parvula

1067

7

3

0.0098

0.0004

0.0565

0.0102

0.1798

0.307

0.36

-0.710

0.39

TEP 2

I

4, 2

D. parvula

865

8

3

0.0369

0.0018

0.1556

0.0078

0.0504

0.389

0.29

-

-

TEP 3

I

9, 3

D. parvula

1013

14

6

0.0319

0.0009

0.1398

0.0056

0.0399

0.314

0.31

0.878

0.15

Tequila

I

3, 1

D. parvula

834

6

2

0.0591

0.0011

0.0581

0.0005

0.0091

0.670

0.22

-

-

Toll 1

I

9, 4

D. parvula

468

10

2

0.0214

0.0006

0.0938

0.0541

0.5768

1.025

0.13

-

-

Toll 2

I

10, 4

D. parvula

836

10

1

0.0169

0.0026

0.1106

0.0161

0.1456

0.512

0.25

-

-

Toll 3

I

9, 4

D. parvula

523

12

5

0.0282

0.0004

0.0887

0.0031

0.0354

-0.015

0.45

-0.431

1.39

Average

   

791.3

11

3

0.0335

0.0056

0.1292

0.0188

0.1512

    

Average over NI and I classes

   

801.1

10

3

0.0329

0.0057

0.1260

0.0182

0.1514

    

Scavenger 3

I

5, 1

D. arenata

552

8

1

0.0715

0.0057

0.0741

0.0163

0.2192

0.065

0.47

-

-

Gram-negative binding protein 7

I

9, 1

D. arenata

788

12

1

0.0474

0.0016

0.1150

0.0117

0.1014

-0.160

0.51

-

-

Galectin 3

I

8, 1

D. arenata

974

10

1

0.0232

0.0026

0.0518

0.0035

0.0678

0.326

0.31

-

-

Chitinase 1

NI

8, 1

D. arenata

885

13

1

0.0364

0.0072

0.0721

0.0153

0.2127

0.718

0.18

-

-

Chitinase 9

NI

6, 1

D. arenata

908

10

2

0.0793

0.0089

0.0748

0.0101

0.1350

0.484

1.00

-

-

Average

   

821.4

10.6

1.2

0.0516

0.0052

0.0775

0.0114

0.1472

    
  1. Table Legend: Significant P-values are indicated in bold text, (a) NI= non-immune, I: immune, (b) πs: average pairwise synonymous nucleotide diversity, (c) πa: average pairwise non-synonymous nucleotide diversity, (d) Ks: average pairwise synonymous nucleotide divergence, (e) Ka: average pairwise non-synonymous nucleotide divergence.
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BMC Ecology and Evolution

ISSN: 2730-7182

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