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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