Table 3. Parameter estimates and likelihood values of the various models of codon evolution using CODEML in PAML.
| Model | Model Parameters | -lnL | Models Comparison | 2ΔL | Pr. | Sites Under Positive Selection (Bayes Empirical Bayes, Pr. ω>1) | |
|---|---|---|---|---|---|---|---|
| A. Test on the truncated and full-length MAT1-1-1 genes within a species (datasets with positive selection detected) | |||||||
| G. clavigera (9 isolates) | M1a (neutral) | P0 = 0.26, P1 = 0,74 | 2172.75 | M1a vs. M2a | 17.70 | <0.001 | 2 G (0.99**), 3 I (0.99**), 8 N (0.99**) |
| M2a (selection) | P0 = 0.99, P1 = 0.00, P2 = 0.004, ω2 = 227.05 | 2163.90 | |||||
| M7 (beta) | P = 2.30, q = 0.005 | 2172.75 | M7 vs. M8 | 17.41 | <0.001 | 2 G (0.99**), 3 I (0.99**), 8 N (0.99**) | |
| M8 (beta + ω) | P0 = 0.98, P = 0.005, q = 3.27, P1 = 0.02, ω = 81.42 | 2164.05 | |||||
| G. aurea (four isolates) | M1a (neutral) | P0 = 0.77, P1 = 0.23 | 2102.86 | M1a vs. M2a | 21.18 | <0.001 | 3 A (0.94), 8 A (0.94) |
| M2a (selection) | P0 = 0.99, P1 = 0.00, P2 = 0.003, ω2 = 282.78 | 2092.27 | |||||
| M7 (beta) | P = 0.005, q = 0,012 | 2102.96 | M7 vs. M8 | 21.37 | <0.001 | 3 A (0.97*), 8 A (0.97*) | |
| M8 (beta + ω) | P0 = 0.99, P = 0.005, q = 15.47, P1 = 0.003, ω = 282.82 | 2092.27 | |||||
| L. longiclavatum (five isolates) | M1a (neutral) | P0 = 0.72, P1 = 0.28 | 2183.24 | M1a vs. M2a | 18.88 | <0.001 | 3 A (0.93), 8 A (0,93) |
| M2a (selection) | P0 = 0.99, P1 = 0.00, P2 = 0.002, ω2= 209.51 | 2173.80 | |||||
| M7 (beta) | P = 0.005, q= 0.011 | 2183.25 | M7 vs. M8 | 18.90 | <0.001 | 3 A (0.97*), 8 A (0.97*) | |
| M8 (beta + ω) | P0 = 0.99, P = 0.51, q = 1.49, P1 = 0.001, ω = 209.58 | 2173.80 | |||||
| B. Test on the truncated and full-length MAT1-1-1 genes within a species (dataset without positive selection detected) | |||||||
| L. terebrantis (4 isolates) | M1a (neutral) | 2462.37 | M1a vs. M2a | 1.30 | ns | ||
| M2a (selection) | 2461.72 | ||||||
| M7 (beta) | 2462.54 | M7 vs. M8 | 1.65 | ns | |||
| M8 (beta + ω) | 2461.72 | ||||||
Parameter estimates and likelihood values of the various models of codon evolution using CODEML in PAML. Notes for G. clavigera: Models assuming positive selection (M2a and M8) fit better the data than neutral models (M1a and M7) according to likelihood ratio tests. Model M2 assumes that 0.4% of the sites have dN/dS value = 227.05. Three sites under strong positive selection (P > 0.99) are identified by this model with Bayes empirical Bayes methods. Model M8 showed that approximately 98% of sites have dN/dS from a U-shaped beta distribution (hence, data fit strongly this model) and approximately 2% of site are under strong positive selection with dN/dS = 81.4. Both models M2 and M8 identified the same positive selection sites with Bayes empirical Bayes methods (even if model M8 would assume more sites under positive selection).