Table 3

Inference of balancing selection for 43 black bear DQB variants
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*

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].

Yasukochi et al.

Yasukochi et al. BMC Evolutionary Biology 2012 12:230   doi:10.1186/1471-2148-12-230

Open Data