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Table 5 Nucleotide diversity, selection pressure, and neutrality tests of the LT-Ag genes and two domains of the PyV groups

From: Codon usage patterns of LT-Ag genes in polyomaviruses from different host species

  Genetic variability Neutrality tests Selection pressure
Region Group m n S η k π Tajima’s D Fu and Li’s D Fu and Li’s F dN/dS
LT-Ag All 86 944 837 2129 418.245 0.44306 −0.04390ns 1.45113ns 0.96702ns 2.163
Group A 9 1725 1283 2383 737.889 0.42776 −0.82814ns 0.0858ns −0.15345ns 0.282
Group F 3 1657 1209 1522 910.333 0.54939 NA NA NA 0.684
Group H 13 1648 1336 2725 725.192 0.44004 −0.80590ns 0.16114ns −0.11521ns 1.673
Group M 36 1404 1205 2813 615.989 0.43874 −0.35097ns 0.89680ns 0.54139ns 0.523
Group P 25 1602 1268 2653 666.147 0.41582 − 0.20916ns 0.88010ns 0.62234ns 0.318
DnaJ domain All 54 160 144 352 71.204 0.44503 −0.28170ns 1.14715ns 0.71186ns 0.261
Group A 9 162 119 214 68.083 0.42027 −0.70347ns 0.14282ns −0.07065ns 0.298
Group H 7 192 146 237 82.143 0.42783 −0.88626ns −0.18339ns − 0.37879ns 0.417
Group M 19 162 136 277 63.474 0.39181 −0.83778ns 0.31536ns −0.03513ns 0.289
Group P 19 192 153 291 78.585 0.4093 −0.23632ns 0.71490ns 0.50101ns 0.262
Helicase domain All 86 424 348 827 165.867 0.3912 0.02756ns 1.22733ns 0.85387ns 0.316
Group A 9 471 288 499 159.361 0.33835 −0.68870ns 0.11803ns −0.08782ns 0.150
Group F 3 453 285 345 210 0.46358 NA NA NA 0.379
Group H 13 477 326 632 174.667 0.36618 −0.65740ns 0.21440ns −0.02451ns 0.260
Group M 36 447 346 738 170.876 0.38227 −0.15171ns 0.86494ns 0.60171ns 0.503
Group P 25 471 317 619 161.56 0.34301 −0.05815ns 0.97206ns 0.75361ns 0.142
  1. m, number of sequences used; n, total number of sites (excluding sites with gaps/missing data); S, number of segregating sites; η, total number of mutations; k, average number of pairwise nucleotide differences; π, nucleotide diversity; dS, average number of synonymous substitutions per site; dN, average number of non-synonymous substitutions per site; NA, not available due to limited sequences for analysis of the gene-specific sequence dataset; ns, not significant