Table 1

Genetic diversity and Tajima's D in 54 loci in Daphnia pulex and an outgroup species
Gene Classa No. individuals(D. pulex,outgroup) Outgroup Basepairs sequenced No. of alleles found πsb πac 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

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.

McTaggart et al.

McTaggart et al. BMC Evolutionary Biology 2012 12:63   doi:10.1186/1471-2148-12-63

Open Data