Table 2. Intraspecific patterns in miRNA and siRNA pathway genes of Ae. aegypti.
Site | N | Ss | Sa | h | p | k | KS | KA | KA/KS | R | PHI | F* |
Dcr1 | ||||||||||||
All Sites | 103 | 158 | 103 | 206 | 0.0068 | 37.94 | 0.0212 | 0.0025 | 0.1163 | 0.0125 | 1.11E-16 | 0.31 |
Poza Rica | 18 | 88 | 44 | 36 | 0.0067 | 40.08 | 0.0210 | 0.0022 | 0.1050 | 0.0087 | 1.31 | |
Chetumal | 18 | 84 | 30 | 36 | 0.0045 | 28.02 | 0.0148 | 0.0013 | 0.0908 | 0.0036 | 0.82 | |
L.d.Tejada | 18 | 59 | 24 | 36 | 0.0041 | 25.46 | 0.0129 | 0.0014 | 0.1053 | 0.0123 | 1.13 | |
Thailand | 20 | 67 | 33 | 40 | 0.0041 | 24.49 | 0.0121 | 0.0016 | 0.1326 | 0.0051 | 0.66 | |
PK10 | 19 | 54 | 21 | 38 | 0.0042 | 23.54 | 0.0126 | 0.0016 | 0.1234 | 0.0062 | 1.42 | |
Mindin | 10 | 82 | 43 | 20 | 0.0065 | 40.41 | 0.0183 | 0.0026 | 0.1424 | 0.0154 | 0.99 | |
Dcr2 | ||||||||||||
All Sites | 104 | 109 | 85 | 190 | 0.0050 | 23.87 | 0.0141 | 0.0023 | 0.1650 | 0.0080 | 1.63E-14 | −0.27 |
Poza Rica | 18 | 32 | 24 | 27 | 0.0023 | 10.92 | 0.0063 | 0.0010 | 0.1651 | 0.0007 | 0.13 | |
Chetumal | 18 | 20 | 12 | 32 | 0.0021 | 9.82 | 0.0060 | 0.0009 | 0.1426 | 0.0072 | 1.25 | |
L.d.Tejada | 18 | 32 | 28 | 33 | 0.0036 | 16.98 | 0.0083 | 0.0021 | 0.2503 | 0.0114 | 0.82 | |
Thailand | 20 | 26 | 14 | 39 | 0.0028 | 13.41 | 0.0088 | 0.0010 | 0.1129 | 0.0090 | 2.06* | |
PK10 | 20 | 47 | 25 | 40 | 0.0047 | 22.19 | 0.0135 | 0.0019 | 0.1421 | 0.0240 | 1.45 | |
Mindin | 10 | 71 | 39 | 20 | 0.0060 | 28.44 | 0.0156 | 0.0028 | 0.1772 | 0.0151 | 0.31 | |
Ago1 | ||||||||||||
All Sites | 104 | 76 | 10 | 136 | 0.0076 | 14.91 | 0.0310 | 0.0002 | 0.0077 | 0.0127 | 6.42E-13 | −0.23 |
Poza Rica | 18 | 37 | 1 | 28 | 0.0057 | 13.52 | 0.0230 | 0.0001 | 0.0026 | 0.0085 | 1.65* | |
Chetumal | 18 | 26 | 0 | 8 | 0.0016 | 3.71 | 0.0063 | 0.0000 | 0.0000 | 0.0000 | 0.17 | |
L.d.Tejada | 18 | 29 | 0 | 22 | 0.0040 | 9.49 | 0.0162 | 0.0000 | 0.0000 | 0.0050 | 1.68* | |
Thailand | 20 | 40 | 2 | 38 | 0.0062 | 14.68 | 0.0244 | 0.0002 | 0.0094 | 0.0118 | 1.87** | |
PK10 | 20 | 37 | 5 | 38 | 0.0074 | 14.41 | 0.0277 | 0.0007 | 0.0268 | 0.0480 | 1.4 | |
Mindin | 10 | 63 | 4 | 20 | 0.0084 | 19.62 | 0.0321 | 0.0002 | 0.0065 | 0.1044 | 0.26 | |
Ago2 | ||||||||||||
All Sites | 104 | 52 | 75 | 165 | 0.0053 | 13.31 | 0.0134 | 0.0029 | 0.2124 | 0.0041 | 2.42E-13 | 0.97 |
Poza Rica | 18 | 15 | 14 | 30 | 0.0032 | 7.86 | 0.0076 | 0.0017 | 0.2224 | 0.0096 | 1.36 | |
Chetumal | 18 | 13 | 18 | 32 | 0.0030 | 7.37 | 0.0068 | 0.0017 | 0.2442 | 0.0063 | 0.47 | |
L.d.Tejada | 18 | 12 | 18 | 34 | 0.0034 | 8.48 | 0.0071 | 0.0019 | 0.2630 | 0.0164 | 1.07 | |
Thailand | 20 | 8 | 11 | 19 | 0.0020 | 4.90 | 0.0041 | 0.0012 | 0.2995 | 0.0039 | 0.57 | |
PK10 | 20 | 7 | 9 | 34 | 0.0020 | 5.05 | 0.0046 | 0.0012 | 0.2604 | 0.0464 | 1.68* | |
Mindin | 10 | 33 | 23 | 19 | 0.0076 | 21.91 | 0.0186 | 0.0039 | 0.2086 | 0.0063 | 1.71* | |
R3D1 | ||||||||||||
All Sites | 104 | 21 | 9 | 87 | 0.0046 | 4.47 | 0.0163 | 0.0009 | 0.0572 | 0.0131 | 2.64E-03 | 0.69 |
Poza Rica | 18 | 14 | 2 | 17 | 0.0041 | 3.98 | 0.0131 | 0.0011 | 0.0861 | 0.0091 | 1.23 | |
Chetumal | 18 | 9 | 2 | 9 | 0.0023 | 2.20 | 0.0064 | 0.0009 | 0.1415 | 0.0009 | 0.96 | |
L.d.Tejada | 18 | 13 | 3 | 16 | 0.0040 | 3.92 | 0.0152 | 0.0004 | 0.0270 | 0.0075 | 0.64 | |
Thailand | 20 | 4 | 0 | 4 | 0.0012 | 1.14 | 0.0048 | 0.0000 | 0.0000 | 0.0000 | 1.02 | |
PK10 | 20 | 12 | 4 | 37 | 0.0048 | 4.67 | 0.0159 | 0.0012 | 0.0763 | 0.1607 | 1.56 | |
Mindin | 10 | 12 | 2 | 16 | 0.0053 | 5.20 | 0.0194 | 0.0006 | 0.0325 | 0.0675 | 1.33 | |
R2D2 | ||||||||||||
All Sites | 104 | 6 | 5 | 19 | 0.0064 | 2.81 | 0.0243 | 0.0014 | 0.0557 | 0.0162 | 6.65E-01 | 0.46 |
Poza Rica | 18 | 3 | 2 | 6 | 0.0012 | 1.04 | 0.0037 | 0.0004 | 0.1005 | 0.0000 | 0.79 | |
Chetumal | 18 | 7 | 1 | 16 | 0.0026 | 2.32 | 0.0089 | 0.0006 | 0.0683 | 0.0263 | 0.21 | |
L.d.Tejada | 18 | 4 | 1 | 14 | 0.0022 | 2.00 | 0.0074 | 0.0006 | 0.0823 | 0.0436 | 1.52 | |
Thailand | 20 | 6 | 2 | 8 | 0.0019 | 1.73 | 0.0056 | 0.0008 | 0.1441 | 0.0006 | 0.97 | |
PK10 | 20 | 0 | 2 | 3 | 0.0012 | 0.51 | 0.0000 | 0.0015 | 0.0000 | 0.0000 | 0.69 | |
Mindin | 10 | 10 | 5 | 15 | 0.0066 | 5.90 | 0.0198 | 0.0022 | 0.1122 | 0.0290 | 1.18 |
Sample size (N), numbers of segregating sites that were synonymous (Ss) or led to amino acid replacements (Sa), the number of haplotypes (h), the overall pi(the average number of nucleotide differences per site between two sequences) are listed for each gene and collection. Also listed are the average number of nucleotide differences, k and K among synonymous sites (Ks) and among replacement sites (Ka) and their ratio (Ka/Ks). The effective recombination rate between adjacent sites (R) and the PHI test for recombination are listed alongside Fu and Li's F* test and associated significance tests (*P<0.05, **P<0.01).