High polymorphism in MHC-DRB genes in golden snub-nosed monkeys reveals balancing selection in small, isolated populations

Table 7 Results of maximum likelihood models of the Rhro-DRB sequences

Model	k	l	Parameters estimates	Positively selected sites
M0 (one ratio)	1	− 1830.09	ω = 0.559	None
M1a (nearly neutral)	1	− 1690.63	p₀ = 0.603 (p₁ = 0.397)	Not allowed
M2a (positive selection)	3	− 1653.33	p₀ = 0.576, p₁ = 0.400 (p₂ = 0.025), ω₂ = 12.820	11F, 13S
M3 (discrete)	5	− 1651.07	p₀ = 0.602, p₁ = 0.374 (p₂ = 0.025), ω₀ = 0.035, ω₁ = 1.496, ω₂ = 16.973	6R, 9E, 10Q, 11F, 13S, 15C, 25R, 26Y, 28Q, 30Y, 31F, 32Y, 37Y, 38 V, 47F, 49A, 56P, 57 V, 60 N, 61F, 63S, 64Q, 67F, 70Q, 71R, 72R, 74Q, 77 N, 78Y, 84G, 85 V, 86 V
M7 (beta)	2	− 1686.84	p = 0.079, q = 0.125	Not allowed
M8 (beta and omega)	4	−1651.44	p₀ = 0.975 (p₁ = 0.025), p = 0.019, q = 0.035, ω = 11.880	11F, 13S

K represents the number of parameters in the ω distribution, ω is the parameter of selection, p_n is the proportion of sites falling into the ω_n sites class. For models M7 and M8, p and q are the shape parameters of the β function. 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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