Table 1.
Polymorphism in Pvs230 and tests for neutrality
Area | Region | No. of polymorphic sites | No. of singletons | No. of haplotypes | Haplotype diversity Hd ± SD | Nucleotide diversity θπ ± SD | dN ± SE | dS ± SE | P value |
---|---|---|---|---|---|---|---|---|---|
Brazil (N=20) | Entire gene | 15 | 4 | 6 | 0.747 ± 0.076 | 0.00060 ± 0.00007 | 0.00059 ± 0.00024 | 0.00065 ± 0.00030 | 0.8752 |
IVP | 1 | 0 | 2 | 0.395 ± 0.101 | 0.00070 ± 0.00018 | 0.00092 ± 0.00092 | 0.00000 ± 0.00000 | 0.3105 | |
ICP | 14 | 4 | 6 | 0.747 ± 0.076 | 0.00059 ± 0.00006 | 0.00056 ± 0.00027 | 0.00070 ± 0.00030 | 0.7405 | |
Turkey (N=20) | Entire gene | 13 | 2 | 6 | 0.763 ± 0.066 | 0.00054 ± 0.00009 | 0.00030 ± 0.00011 | 0.00140 ± 0.00054 | 0.0496 |
IVP | 0 | 0 | 1 | 0.000 ± 0.000 | 0.00000 ± 0.00000 | 0.00000 ± 0.00000 | 0.00000 ± 0.00000 | 1.0000 | |
ICP | 13 | 2 | 6 | 0.763 ± 0.066 | 0.00059 ± 0.00010 | 0.00032 ± 0.00012 | 0.00152 ± 0.00062 | 0.0617 | |
Madagascar (N=7) | Entire gene | 14 | 9 | 7 | 1.000 ± 0.076 | 0.00063 ± 0.00012 | 0.00040 ± 0.00016 | 0.00144 ± 0.00063 | 0.1171 |
IVP | 1 | 0 | 2 | 0.571 ± 0.119 | 0.00101 ± 0.00021 | 0.00133 ± 0.00133 | 0.00000 ± 0.00000 | 0.3105 | |
ICP | 13 | 9 | 7 | 1.000 ± 0.076 | 0.00060 ± 0.00012 | 0.00033 ± 0.00014 | 0.00156 ± 0.00067 | 0.0719 | |
China(N=20) | Entire gene | 13 | 4 | 14 | 0.958 ± 0.028 | 0.00051 ± 0.00005 | 0.00050 ± 0.00018 | 0.00056 ± 0.00035 | 0.8789 |
IVP | 4 | 3 | 4 | 0.574 ± 0.090 | 0.00143 ± 0.00038 | 0.00164 ± 0.00121 | 0.00075 ± 0.00073 | 0.5396 | |
ICP | 9 | 1 | 14 | 0.958 ± 0.028 | 0.00044 ± 0.00003 | 0.00041 ± 0.00018 | 0.00054 ± 0.00037 | 0.7456 | |
Thailand (N=20) | Entire gene | 32 | 14 | 18 | 0.989 ± 0.019 | 0.00084 ± 0.00010 | 0.00065 ± 0.00016 | 0.00153 ± 0.00047 | 0.0723 |
IVP | 5 | 1 | 6 | 0.726 ± 0.090 | 0.00230 ± 0.00045 | 0.00303 ± 0.00172 | 0.00000 ± 0.00000 | 0.0728 | |
ICP | 27 | 13 | 18 | 0.989 ± 0.019 | 0.00073 ± 0.00009 | 0.00047 ± 0.00015 | 0.00165 ± 0.00047 | 0.0241 | |
PNG (N=21) | Entire gene | 28 | 17 | 16 | 0.976 ± 0.020 | 0.00062 ± 0.00010 | 0.00030 ± 0.00011 | 0.00175 ± 0.00056 | 0.0130 |
IVP | 1 | 1 | 2 | 0.095 ± 0.084 | 0.00017 ± 0.00015 | 0.00022 ± 0.00021 | 0.00000 ± 0.00000 | 0.2976 | |
ICP | 27 | 16 | 16 | 0.976 ± 0.020 | 0.00065 ± 0.00011 | 0.00030 ± 0.00012 | 0.00189 ± 0.00060 | 0.0123 | |
Worldwide (N=113) | Entire gene | 77 | 32 | 72 | 0.983 ± 0.005 | 0.00118 ± 0.00003 | 0.00089 ± 0.00022 | 0.00221 ± 0.00064 | 0.0494 |
IVP | 8 | 4 | 9 | 0.731 ± 0.017 | 0.00203 ± 0.00013 | 0.00263 ± 0.00154 | 0.00013 ± 0.00013 | 0.1128 | |
ICP | 69 | 28 | 71 | 0.983 ± 0.005 | 0.00111 ± 0.00003 | 0.00076 ± 0.00020 | 0.00238 ± 0.00067 | 0.0218 |
Sequence lengths are 564 bp and 7437 by for interspecies variable part and interspecies conserved part, respectively. IVP, interspecies variable part; ICP, interspecies conserved part.