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Table 4 Genetic variability determinants and neutrality tests on Tomato leaf curl virus Arusha virus-like populations from Kenya with other worldwide tomato begomoviruses

From: Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya

Population Genea Nb hc Sd Hde Etaf πg kh θ-Wi θ-Etaj Tajima's D Fu and Li's D Fu and Li's F
Tomato begomoviruses Genome 2920 46 1666 1.000 2985 0.22424 569.5749 0.14924 0.2674  − 0.5971  − 0.2912  − 0.4859
(n = 46) V1 372 43 241 0.996 419 0.22538 76.1768 0.16224 0.28206  − 0.7389  − 0.8229  − 0.9463
  V2 1261 46 752 1.000 1334 0.22421 271.971 0.14106 0.25023  − 0.3842  − 0.0052  − 0.1764
  C1 1179 46 692 1.000 1213 0.21165 225.4106 0.14784 0.25915  − 0.6771  − 0.3609  − 0.5737
  C2 431 45 264 0.999 458 0.23777 97.486 0.14651 0.25417  − 0.2374  − 0.0923  − 0.1752
  C3 469 45 303 0.999 550 0.24589 108.1903 0.15669 0.28442  − 0.4989  − 0.3631  − 0.4949
  C4 316 44 210 0.997 360 0.21015 65.1459 0.15414 0.26423  − 0.7516  − 0.4512  − 0.6736
Kenyan ToLCArV-like Genome 2766 12 211 1.000 224 0.0264 72.955 0.0253 0.0268  − 0.0774  − 0.4189  − 0.3751
isolates (n = 12) V1 360 9 22 0.939 24 0.02298 8.2727 0.02024 0.02208 0.1819 0.1216 0.1564
  V2 1239 12 71 1.000 72 0.0209 25.8788 0.01899 0.01926 0.3958  − 0.0631 0.0659
  C1 1116 12 94 1.000 102 0.02744 30.6212 0.02789 0.03027  − 0.4355  − 0.7775  − 0.7841
  C2 422 11 39 0.985 40 0.02761 11.6515 0.0306 0.03139  − 0.5481  − 1.072  − 1.065
  C3 450 11 23 0.985 23 0.01872 8.4242 0.01692 0.01692 0.4703  − 0.3193  − 0.1286
  C4 312 10 11 0.955 11 0.00869 2.7121 0.01167 0.01167  − 1.0628  − 1.4718  − 1.552
  1. aV1: Movement protein gene, V2: Coat protein gene, C1: Replication-associated protein gene, C2: Transcriptional activator protein gene, C3: Replication enhancer protein gene, C4: C4 protein gene
  2. bN: Number of nucleotide sites
  3. ch: Haplotype number
  4. dS: Total number of variable or segregation sites
  5. eHd: Haplotype diversity
  6. fEta: Total number of mutations
  7. gπ: Nucleotide diversity
  8. hk: Average number of nucleotide differences between sequences
  9. iθ-W: Waterson’s estimate of population mutation rate based on the total number of segregating sites
  10. jθ-Eta: Waterson’s estimate of population mutation rate based on the total number of mutations
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