Balancing selection and genetic drift at major histocompatibility complex class II genes in isolated populations of golden snub-nosed monkey (Rhinopithecus roxellana)

Table 5 Results of maximum-likelihood models for exon 2 of the DQB1 gene

Model code	P	Log-likelihood	Parameter estimates	Positively selected sites
M0(one ratio)	1	−1067.274	ω=0.496	None
M1a(nearly neutral)	1	−1007.026	p₀= 0.869 (p₁= 0.131)	Not allowed
M2a(positive selection)	3	−989.138	p₀=0.818, p₁=0.176(p₂= 0.006) ω₂= 8.276	1V,6M,18L,20T,48S,49S,67L,72R,77L,79L,81T
M3(discrete)	4	−994.628	p₁= 0.059 (p₂= 0.018) ω₁= 0.076, ω₂= 3.390	Not allowed
M7(beta)	2	−1007.600	p= 0.006, q= 0.036	Not allowed
M8(beta and omega)	4	−989.309	p₀= 0.994 (p₁= 0.006) p= 0.005, q= 0.020, ω= 8.643	1V,6M,18L,20T,22Y,29Y,30A,38E,48S,49S,62G,63T,67L,72R,77L,79L, 81T

P is the number of parameters in the ω distribution, ω is the selection parameter, and p_n is the proportion of sites falling into the ω_n site class. For models M7 and M8, p and q are the shape parameters of the β function. Positively selected sites were identified in models M2a and M8 by the Bayes empirical Bayes procedure (Yang et al. 2005). Sites inferred under selection at the 99% level are listed in bold, and those inferred at the 95% level are shown in italics.

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