TABLE 1.
MLEs of parameters and sites inferred to be under positive selection for the HLA data set
| Model | p | ℓ | κ | Estimates of parameters | Positively selected sites |
|---|---|---|---|---|---|
| M0: one-ratio | 1 | −9114.23 | 2.0 | ω̂ = 0.557 | None |
| M1: neutral | 1 | −8497.19 | 1.8 | p̂0 = 0.661 (p̂1 = 0.339) | Not allowed |
| M2: selection | 3 | −8045.42 | 1.9 |
p̂0 = 0.620, p̂1 = 0.316 (p̂2 = 0.064), ω̂2 = 7.687 |
9F24A45M63E67M70H71S73T 77N80T81L82R83G94T95I 97I99Y113Y114R116D151H 152A156R163R167G |
| M1a: nearly neutral | 2 | −8260.21 | 1.7 | p̂0 = 0.878 (p̂1 = 0.122) | Not allowed |
| ω̂0 = 0.038 | |||||
| M2a: positive selection | 4 | −7983.71 | 1.9 |
p̂0 = 0.795, p̂1 = 0.148 (p̂2 = 0.057), ω̂0 = 0.049, ω̂2 = 5.379 |
9F24A63E67M70H71S73T77N 80T81L82R83G95I97I99Y 114R116D152A156R163R |
| M3: discrete | 5 | −7983.70 | 1.9 |
p̂0 = 0.794, p̂1 = 0.149, (p̂2 = 0.057) ω̂0 = 0.048, ω̂1 = 0.982, ω̂2 = 5.344 |
9F24A45M63E67M70H71S73T 77N80T81L82R83G95I97I 99Y114R116D152A156R163R |
| M7: beta | 2 | −8258.28 | 1.7 | p̂ = 0.064, q̂ = 0.333 | Not allowed |
| M8: beta&ω | 4 | −7981.31 | 1.9 |
p̂0 = 0.943, p̂ = 0.132, q̂ = 0.611 (p̂1 = 0.057), ω̂ = 4.905 |
9F24A45M63E67M70H71S73T 77N80T81L82R83G 94T95I 97I99Y113Y114R116D151H 152A156R163R |
p, the number of free parameters in the ω-distribution. Sites inferred to be under positive selection at the 99% level are underlined and those at the 95% level are in italic. The reference sequence is A-0101 in Suzuki and Nei (2001), and the site numbering is the same as in the structural file 1AKJ, used by Yang and Swanson (2002). The F61 model is used, with branch lengths fixed at three times the estimates from the Kimura (1980) substitution model.