Table 1.
Selection pressures in GALA paralogs
| P-values for LRTs comparing codon modelsa | Proportions of sites in different selection regimesb | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GALA copy | Number of strains | Alignment length (nt) | Population recombination rate, Ner (PLPT)a | Tajima's Da | M0 vs M3 | M1a vs M2a | M7 vs M8 | M8a vs M8 | Strict negative (%) (ω < 0.15) | Relaxed negative (%) (0.15 < ω < 0.9) | Neutral (%) (0.9 < ω < 1) | Positive (%) (ω = 1) |
| GALA1 | 6 | 2046 | 0.00 (1.00) | 2.1 | 0.000 | 1.000 | 0.045 | 0.256 | 42 (ω = 0.08) | 25 (ω = 0.31) | 33 | 0 |
| GALA2 | 7 | 3237 | 0.00 (1.00) | 1.7 | 0.000 | 1.000 | 0.022 | 0.187 | 32 (ω = 0.04) | 4.5 (ω = 0.25) | 63 | 0 |
| GALA3c | 9 | 1971 | 12.25 (0.003) | 4.2 | 0.000 | 0.023 | 0.001 | 0.000 | 28 (ω = 0.05) | 57 (ω = 0.53) | 10 | 5 (ω = 3.28) |
| GALA4c | 8 | 1677 | 14.29 (0.001) | 3.5 | 0.000 | 0.040 | 0.002 | 0.002 | 39 (ω = 0.06) | 58 (ω = 0.49) | 0 | 3 (ω = 5.90) |
| GALA5 | 8 | 1683 | 0.00 (0.000) | 2.1 | 0.000 | 1.000 | 0.170 | 0.457 | 57 (ω = 0.06) | 19 (ω = 0.24) | 24 | 0 |
| GALA6c | 9 | 1866 | 6.12 (0.000) | 4.2 | 0.000 | 0.653 | 0.035 | 0.048 | 48 (ω = 0.06) | 48 (ω = 0.54) | 0 | 4 (ω = 2.58) |
| GALA7c | 9 | 2052 | 16.33 (0.000) | 4.3 | 0.000 | 0.000 | 0.000 | 0.000 | 46 (ω = 0.05) | 28 (ω = 0.51) | 18 | 8 (ω = 3.7) |
Significant values for selection, recombination and neutrality tests are shown in bold.
Estimates of selection regimes are reported according to the model M8 if the likelihood ratio test (LRT) comparing M8a and M8 was significant. Otherwise, selection regimes are reported according to model M8a. For strict and relaxed negative selection, the average ω -value over respective selection classes (with either ω < 0.15 or 0.15 < ω < 0.9) is shown. In each of four selection categories shown, the highest frequency value of sites is underlined.
GALAs where positive selection was detected using at least two LRTs for positive selection. Note that the LRT comparing M0 and M3 is not a test for positive selection but for variability of selection pressure among sites.