TABLE 1

MLEs of parameters and sites inferred to be under positive selection for the HLA data set

ModelpκEstimates of parametersPositively selected sites
M0: one-ratio1−9114.232.0ω̂ = 0.557None
M1: neutral1−8497.191.80 = 0.661 (1 = 0.339)Not allowed
M2: selection3−8045.421.90 = 0.620, 1 = 0.316
 (2 = 0.064), ω̂2 = 7.6879F 24A 45M 63E 67M 70H 71S 73T
   77N 80T 81L 82R 83G 94T 95I
   97I 99Y 113Y 114R 116D 151H
   152A 156R 163R 167G
M1a: nearly neutral2−8260.211.70 = 0.878 (1 = 0.122)Not allowed
ω̂0 = 0.038
M2a: positive selection4−7983.711.90 = 0.795, 1 = 0.148
   (2 = 0.057),
 ω̂0 = 0.049, ω̂2 = 5.3799F 24A 63E 67M 70H 71S 73T 77N
   80T 81L 82R 83G 95I 97I 99Y
   114R 116D 152A 156R 163R
M3: discrete5−7983.701.90 = 0.794, 1 = 0.149,
   (2 = 0.057)
 ω̂0 = 0.048, ω̂1 = 0.982,
   ω̂2 = 5.3449F 24A 45M 63E 67M 70H 71S 73T
   77N 80T 81L 82R 83G 95I 97I
   99Y 114R 116D 152A 156R 163R
M7: beta2−8258.281.7 = 0.064, = 0.333Not allowed
M8: beta&ω4−7981.311.90 = 0.943, = 0.132,
    = 0.611
 (1 = 0.057), ω̂ = 4.9059F 24A 45M 63E 67M 70H 71S 73T
   77N 80T 81L 82R 83G 94T 95I
   97I 99Y 113Y 114R 116D 151H
   152A 156R 163R
  • 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.