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Table 5 Parameter estimates, log-likelihood values and predicted sites under selection for codon evolution models

From: Adaptive molecular evolution of the Major Histocompatibility Complex genes, DRA and DQA, in the genus Equus

Locus Model code P Parameter estimates Sites under positive selection 2Δℓ ( p -value)
  M0 (one ratio) 1 -481.93 ω = 0.353 None  
       14.34 (p = 0.006)
  M3 (discrete) 5 -474.76 ω0 = 0.044, p0 = 0.589,
ω1 = 0.044, p1 = 0.315,
ω 2 = 3.40 p2 = 0.096
Not analysed  
DRA M1a (nearly neutral) 1 -476.43 ω0 = 0, p0 = 0.787,
ω1 = 1, p1 = 0.213
Not allowed  
       3.34 (p = 0.188)
  M2a (positive selection) 3 -474.76 ω0 = 0.044, p0 = 0.904,
ω1 = 1, p1 = 0
ω 2 = 3.40 p2 = 0.096
14,19, 47, 49  
  M7 (beta) 2 -476.35 p = 0.005, q = 0.020 Not allowed  
       3.18 (p = 0.204)
  M8 (beta and omega) 4 -474.76 p0 = 0.904, p1 = 0.096,
p = 4.61, q = 99.0, ω = 3.40
14,19, 47, 49  
  M0 (one ratio) 1 -1612.03 ω = 0.984 None  
       197.68 (p < 0.001)
  M3 (discrete) 5 -1513.2 ω0 = 0.078, p0 = 0.556,
ω 1 = 1.68, p1 = 0.364,
ω 2 = 6.80, p2 = 0.080
Not analysed  
DQA M1a (nearly neutral) 1 -1545.23 ω0 = 0.043, p0 = 0.556,
ω1 = 1, p1 = 0.444
Not allowed  
       66.8 (p < 0.001)
  M2a (positive selection) 3 -1516.86 ω0 = 0.047, p0 = 0.521,
ω1 = 1, p1 = 0.389,
ω 2 = 4.91, p2 = 0.090
2*, 43*, 53*, 57*, 67*  
  M7 (beta) 2 -1548.22 p = 0.104, q = 0.119 Not allowed  
       29.65 (p < 0.001)
  M8 (beta and omega) 4 -1518.57 p0 = 0.909, p1 = 0.091,
p = 0.02, q = 0.02, ω = 5.15
2*, 43*, 52, 53*, 57*, 64, 67*  
  1. P = number of free parameters in the ω distribution; ℓ = log-likelihood; Model parameter estimates include the nonsynonymous to synonymous rate ratio (ω) and proportion of sites (p) under each ω site class. Estimates for ω that are evidence for positive selection are bolded. Sites under selection were predicted using the Bayes Empirical Bayes (BEB) approach: sites inferred to be under positive selection with posterior probabilities >95% are in bold and sites with posterior probabilities of > 99% are indicated by an asterisk (*).