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

Table 4 Results of maximum-likelihood models for exon 2 of the DQA1 gene

Model code	P	Log-likelihood	Parameter estimates	Positively selected sites
M0(one ratio)	1	−774.550	ω=0.643	None
M1a(nearly neutral)	1	−760.293	p₀= 0.723 (p₁= 0.277)	Not allowed
M2a(positive selection)	3	−752.443	p₀= 0.911, p₁= 0.033(p₂= 0.056) ω₂= 5.148	13T,16F,35G,42R,45E,46L,48K,50G,54P,56G,59R,61L,63T,64S,70I,71M,74R
M3(discrete)	4	−752.206	p₀= 0.736, p1= 0.244 (p₂= 0.018) ω₁= 1.298, ω₂= 8.174	Not allowed
M7(beta)	2	−761.268	p= 0.008, q= 0.028	Not allowed
M8(beta and omega)	4	−752.248	p₀= 0.974 (p₁= 0.025) p= 0.008, q= 0.023, ω= 7.292	10L,13T,16F,29Q,35G,42R,43W,45E,46L,48K,50G,51G,54P,56G,59R,61L, 63T,64S,70I,71M,74R,79A

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.

ISSN: 2730-7182