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

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 = 1.80^a	ω: 0.30 - 12.49^a (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 = d_N / d_S. 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].

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