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. 2012 Sep 21;7(9):e44198. doi: 10.1371/journal.pone.0044198

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).