Table 2 Site-specific ExpCM are vastly better than GY94 or ExpCM with preferences averaged or randomized across sites
Gene | Model | ΔAIC | Log likelihood | # free parameters: values of selection parameters |
|---|---|---|---|---|
Gal4 | ExpCM | 0 | –1048 | 6: β=0.82, ω=0.13 |
|  | GY94 M3 | 129 | –1103 | 15: ω 1=0.01, ω 2=0.11, ω 3=0.49, p 1=0.50, p 2=0.29 |
|  | GY94 M0 | 192 | –1139 | 11: ω=0.06 |
|  | averaged ExpCM | 196 | –1146 | 6: β=1.07, ω=0.06 |
|  | randomized ExpCM | 206 | –1151 | 6: β=0.10, ω=0.07 |
β-lactamase | ExpCM | 0 | –3421 | 6: β=1.01, ω=1.02 |
|  | ExpCM (Firnberg data) | 204 | –3523 | 6: β=1.04, ω=0.65 |
|  | GY94 M3 | 564 | –3694 | 15: ω 1=0.07, ω 2=0.55, ω 3=6.24, p 1=0.69, p 2=0.17 |
|  | GY94 M0 | 765 | –3798 | 11: ω=0.34 |
|  | averaged ExpCM | 766 | –3804 | 6: β=0.77, ω=0.35 |
|  | randomized ExpCM | 790 | –3816 | 6: β=0.10, ω=0.34 |
NP | ExpCM | 0 | –8624 | 6: β=2.43, ω=0.61 |
|  | GY94 M3 | 2175 | –9703 | 15: ω 1=0.00, ω 2=0.16, ω 3=1.31, p 1=0.59, p 2=0.24 |
|  | averaged ExpCM | 2584 | –9916 | 6: β=0.43, ω=0.11 |
|  | randomized ExpCM | 2593 | –9921 | 6: β=0.10, ω=0.11 |
|  | GY94 M0 | 2613 | –9926 | 11: ω=0.11 |
HA | ExpCM | 0 | –7461 | 6: β=1.61, ω=0.60 |
|  | GY94 M3 | 1782 | –8343 | 15: ω 1=0.02, ω 2=4.26, ω 3=4.94, p 1=0.59, p 2=0.25 |
|  | averaged ExpCM | 2137 | –8530 | 6: β=0.42, ω=0.23 |
|  | randomized ExpCM | 2157 | –8539 | 6: β=0.10, ω=0.23 |
|  | GY94 M0 | 2176 | –8544 | 11: ω=0.22 |