TABLE 3.
HMM PBP codons sites evolving under nonneutral selection
| PBP allele seta | Selectionb | No. (%) of sites | Significant sites |
Combined |
||||
|---|---|---|---|---|---|---|---|---|
| FUBAR | MEME | SLAC | Gene-wide | TG/DM | TP | |||
| pbp1a-389 | Neg | 671 (91.4) | 42 | – | 23 | 42 | 9 | 17 |
| Pos | 63 (8.6) | 4 | 3 | 0 | 4 | 1 | 2 | |
| pbp1b-426 | Neg | 682 (88.8) | 66 | – | 49 | 67 | 20 | 14 |
| Pos | 86 (11.2) | 3 | 3 | 2 | 4 | 1 | 0 | |
| pbp1b-427* | Neg | 714 (93.0) | 75 | – | 55 | 76 | 22 | 17 |
| Pos | 54 (7.0) | 2 | 5 | 2 | 5 | 1 | 1 | |
| pbp2a-564 | Neg | 663 (85.1) | 70 | – | 60 | 78 | 24 | 24 |
| Pos | 116 (14.9) | 12 | 9 | 5 | 14 | 2 | 3 | |
| pbp2x-462 | Neg | 700 (93.1) | 53 | – | 36 | 53 | 17 | 24 |
| Pos | 52 (6.9) | 3 | 1 | 2 | 3 | 0 | 1 | |
| pbp2x-463* | Neg | 733 (97.6) | 299 | – | 53 | 299 | 75 | 132 |
| Pos | 18 (2.4) | 4 | 16 | 1 | 18 | 3 | 6 | |
a
*, allele sets include recombinant outliers (pbp1b-143 and pbp2x-286) with exogenous SDSE-like sequences.
b
Selection as determined with FUBAR: negative = dN/dS < 1, positive = dN/dS > 1. Neg, negative; Pos, positive.