Table 6.
Selection pressures acting on codons of PCV2 cap gene nucleotide sequences. Proportion of codons under statistically significant positive and negative selective pressure were identified. Selection pressure inferring methods applied were FUBAR, FEL and SLAC for both positive and negative selection; with an additional method MEME for positive pressure. Statistical significance was set at pp > 0.9 for FUBAR and p < 0.05 for FEL, SLAC and MEME.
| PCV2 Genotype | Positive Selection | Negative Selection | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total Positively Selected Codon | Selection Pressure Inference Methods | Statistical Consensus across Methods | Total Negatively Selected Codons |
Selection Pressure Inference Methods | Statistical Consensus across Methods | |||||||||||
| FUBAR | FEL | SLAC | MEME | n = 1 | n = 2 | n = 3 | n = 4 | FUBAR | FEL | SLAC | n = 1 | n = 2 | n = 3 | |||
| PCV2a | 3.86% (9/233) |
3 | 1 | 0 | 7 | 8 | 0 | 1 | 0 | 13.73% (32/233) | 29 | 31 | 14 | 4 | 14 | 14 |
| PCV2b | 1.72% (4/233) | 3 | 0 | 0 | 1 | 4 | 0 | 0 | 0 | 13.73% (32/233) | 30 | 22 | 9 | 12 | 11 | 9 |
| PCV2d | 3.00% (7/233) | 3 | 1 | 1 | 6 | 5 | 1 | 0 | 1 | 13.30% (31/233) | 27 | 26 | 9 | 9 | 13 | 9 |