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Table 3 Inference of balancing selection for 43 black bear DQB variants

From: MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus

Method Model code Parameter estimates Likelihood or confidential interval Positively selected sites
Maximum likelihood (PAML) M0 (one ratio) ω = 0.41 −1570  
M1a (nearly neutral) p0 = 0.85, p1 = 0.15 −1386  
M2a (balancing selection) ω2 = 7.00 −1326 β9**, β26**, β28**, β30**, β37**
M3 (discrete) ω2 = 7.98 −1325  
M7 (beta) p = 0.05, q = 0.07 −1394  
M8 (beta and ω) ω = 5.71 −1337 β9**, β26**, β28**, β30**, β37**
Bayesian inference (OmegaMap) ω = 1.80a ω: 0.30 - 12.49a
(95% HPD)
β9**, β22**, β26**, β28*, β29**, β30**, β37*, β50*, β57*, β68*, β84*
  1. The putative pseudogene (Urth-DQB*3201) is excluded from this analysis. ω = dN / dS. p0: the proportion of conserved sites with 0 < ω < 1. p1 (=1 - p0): the proportion of neutral sites. Values of p and q are parameters of the beta distribution. *: posterior probability, P < 0.95; **: posterior probability, P < 0.99. a: a mean value. Bold characters indicate positions of the putative peptide binding residues (PBRs) deduced from the amino acid position in the human DR molecule [40].