Table 2.
Results of multiple analyses of selection in the N gene of the AgV2 recombination-free dataset (220 sequences). (a) Significant positively and negatively selected sites detected by site-based methods FEL, SLAC, FUBAR, and MEME. (b) Analysis of evidence of relaxation (Relax) or Episodic Diversifying Selection (aBSREL, BUSTED).
| (a) Site-Based Methods | |||||
|---|---|---|---|---|---|
| Length (Codons) | Type of Selection | FEL | SLAC | FUBAR | MEME |
| 450 | Positive | 2 | 0 | 0 | 3 |
| Negative | 193 | 162 | 311 | - | |
| Codons | 77,339 | - | - | 158, 419, 443 | |
| (b) Branch-Based Methods | |||||
| Method | Test Group | Reference Group | Result | ||
| aBSREL | All AgV2 | - | No EDS (p ≤ 0.05) | ||
| aBSREL | AM3b MRCA + Brazilian Wild A + B MRCA | - | No EDS (p ≤ 0.05) | ||
| aBSREL | AM3b MRCA + Brazilian Wild A + B | - | No EDS (p = 0.0057 ≤ 0.05) | ||
| Relax | AM3b MRCA + Brazilian Wild A + B | All remaining branches | Selection Relaxation not significant (K = 0.94, p = 0.360, LR = 0.84) | ||
| BUSTED | AM3b MRCA + Brazilian Wild A + B | All remaining branches | Evidence of gene-wide EDS (LRT, p-value = 0.022 ≤ 0.05) | ||