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.