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Table 1 Nucleotide diversity and divergence in the bindin gene of the sea urchins Strongylocentrotus intermedius, S. pallidus, and S. droebachiensis

From: DNA polymorphism and selection at the bindin locus in three Strongylocentrotus sp. (Echinoidea)

 

Exon I

Exon II

Exon I + Exon II

Intron

Silent

Total

Syn

Nsyn

Total

Syn

Nsyn

Total

Syn

Nsyn

Total

INT (25)

 

 N

57

180

237

78

246

324

135

426

561

871

1009

1435

 S

2

2

4

3

2

5

5

4

9

39

44

48

 π

0.0111

0.0025

0.0046

0.0050

0.0018

0.0026

0.0076

0.0021

0.0034

0.0078

0.0077

0.0060

 θ

0.0092

0.0030

0.0045

0.0136

0.0022

0.0050

0.0117

0.0025

0.0047

0.0119

0.0118

0.0090

  K int-pul

0.1925

0.

0.1165

0.1465

0.

0.0702

0.1654

0.

0.0892

0.0739

0.0851

0.0796

PAL (11)

 

 N

57

180

237

75

234

309

132

414

546

934

1069

1483

 S

4

1

5

1

4

5

5

5

10

53

58

63

 π

0.0271

0.0046

0.0100

0.0022

0.0073

0.0061

0.0131

0.0061

0.0078

0.0205

0.0195

0.0158

 θ

0.0253

n.a.

0.0072

0.0046

0.0058

0.0055

0.0131

n.a.

0.0063

0.0194

n.a.

0.0145

  K pal-pul

0.1408

0.

0.1042

0.1704

0.

0.0755

0.1569

0.

0.0883

0.0736

0.0825

0.0786

DRO (16)

 

 N

56

180

237

75

240

315

131

420

552

919

1054

1474

 S

1

3

4

4

4

8

5

7

11

27

32

38

 π

0.0041

0.0062

0.0057

0.0192

0.0077

0.0105

0.0128

0.0071

0.0084

0.0080

0.0086

0.0081

 θ

0.0053

0.0050

0.0051

0.0160

0.0050

0.0077

0.0114

0.0050

0.0066

0.0089

0.0092

0.0080

  K dro-pul

0.1790

0.

0.1042

0.1630

0.

0.0773

0.1699

0.

0.0890

0.0671

0.0784

0.0748

  1. The region analyzed represents the full mature bindin gene, which includes exon I (excluding the signal peptide), intron, and exon II (excluding the repeat region)
  2. INT = S. intermedius, DRO = S. droebachiensis, PAL = S. pallidus; N, number of sites (indels are excluded); S, number of polymorphic sites; π, average number of nucleotide differences per site among all pairs of sequences ([134], p. 256), obtained for the silent, synonymous, nonsynonymous, and total number of sites; θ, average number of segregating nucleotide sites among all sequences, based on the expected distribution of neutral variants in a panmictic population at equilibrium [135]; K int-pul, K pal-pul, and K dro-pul are the average proportion of nucleotide differences between S. intermedius, S. pallidus, S. droebachiensis and Hemicentrotus pulcherrimus (AF077318 and AF077319), respectively, corrected according to [136]; Syn, synonymous sites; Nsyn, nonsynonymous sites; Silent, silent sites (synonymous and noncoding intronic sites). The segregating sites associated with indels are excluded from the π, θ, and, K calculations