Table 6.
Neutrality tests, haplotype and nucleotide diversity of each Turnip mosaic virus population in China and Japan
| Geographical group | Genetic group | Tajima's D | Fu & Li's D | Fu & Li's F | Haplotype diversity | Nucleotide diversity |
|---|---|---|---|---|---|---|
| China | ||||||
| Mainland | World‐B | −0.918 | −0.535 | −0.761 | 1.000 (0.016) | 0.036 (0.008) |
| Asian‐BR | −0.999 | −0.708 | −0.896 | 1.000 (0.034) | 0.024 (0.007) | |
| Taiwan | World‐B | −1.062 | −1.020 | −1.132 | 1.000 (0.096) | 0.035 (0.024) |
| Japan | ||||||
| Kyushu | World‐B | −1.059 | −1.062 | −1.167 | 1.000 (0.096) | 0.024 (0.008) |
| Asian‐BR | −1.700* | −2.165* | −2.374* | 1.000 (0.011) | 0.018 (0.006) | |
| Basal‐BR II | −0.861 | −0.861 | −0.903 | 1.000 (0.177) | 0.005 (0.002) | |
| Basal‐BR III | −2.179‡ | −2.869† | −3.102† | 1.000 (0.017) | 0.005 (0.002) | |
| Honshu & Hokkaido | World‐B | −0.574 | −0.546 | −0.601 | 1.000 (0.126) | 0.029 (0.012) |
| Basal‐BR I | — | — | — | 1.000 (0.500) | 0.005 (0.000) | |
0.05 < P < 0.1,
P < 0.02,
P < 0.01; Tajima's D test compares the nucleotide diversity with the proportion of polymorphic sites, which are expected to be equal under selective neutrality. Fu & Li's D test is based on the differences between the number of singletons (mutations appearing only once among the sequences) and the total number of mutations. Fu & Li's F test is based on the differences between the number of singletons and the average number of nucleotide differences between pairs of sequences. Nucleotide diversity was estimated by the average pairwise difference among sequence in a sample, based on all sites. Numbers in parentheses indicate standard deviations. An isolate from Hokkaido is not included in the analysis because it had interlineage recombination site in the genome (interlineage recombinant). Tajima's D, Fu & Li's D and F statistical tests are not performed because basal‐BR I group in Honshu and Hokkaido only has two isolates. For details of the genogroups, basal‐BR, Asian‐BR and world‐B, see Ohshima et al. (2002). Basal‐BR I, basal‐BR II and basal‐BR III are subgroups of basal‐BR.