Table 5.

Codon-based tests for positive selection for exon 2 and 3 of the major histocompatibility complex (MHC) class I based on the different models of evolution available in PAML

	Likelihood model	Par	Log-likelihood	Parameter estimate	Positively selected sites
CODEML	M1a (exon 2)	2	−10753.43	p0 = 0.963 (p1 = 0.036)	Not allowed
	M2a (exon 2)	4	−10499.79	p0 = 0.862, p1 = 0.116 (p2 = 0.022), ω2 = 3.430	1, 16, 35, 38, 56, 59, 60, 63, 66, 70, 73
	M7 (exon 2)	2	−10721.29	p0 = 0.045, q = 0.294	Not allowed
	M8 (exon 2)	4	−10464.3	p0 = 0.984 (p1 = 0.016), p = 0.173, q = 0.936, ω = 2.829	1, 16, 35, 38, 55, 56, 59, 60, 63, 66, 67, 70, 73
	M1a (exon 3)	2	−8181.64	p0 = 0.976 (p1 = 0.024)	Not allowed
	M2a (exon 3)	4	−7950.48	p0 = 0.945, p1 = 0.051 (p2 = 0.004), ω2 = 4.665	11, 46, 50, 54, 61
	M7 (exon 3)	2	−8191.56	p0 = 0.054, q = 0.347	Not allowed
	M8 (exon 3)	4	−7926.8	p0 = 0.997 (p1 = 0.003), p = 0.090, q = 0.543, ω = 4.463	11, 46, 50, 54, 61
MEME	Exon 2				1, 4, 16, 26, 35, 54, 55, 56, 60, 63, 66, 70, 73, 75
	Exon 3				2, 6, 8, 11, 22, 26, 34, 42, 47, 50, 53, 54, 56, 61

The table summarizes the results for M1a (nearly neutral gene evolution), M2a (a model allowing positive selection with ω ≥ 1 [d_N/d_S ratio]), M7 (beta distributed variable selective pressure), and M8 (beta plus positive selection [ω]) models of evolution. Par is the number of parameters in the ω distribution, ω is the selection parameter, and p_i is the proportion of sites falling into the ω_i site class. p_i refers to p₀, p₁ and p₂, while ω_i to ω₂. p₀ proportion of sites with ω = < 1. p₁ and p₂ refer to the proportion of positively selected sites (ω > 1). ω₂ is the estimated value of ω for sites under positive selection for the M2a model. For models M7 and M8, p and q refer to the shape parameters of the β function. Positively selected sites were identified in models M2a and M8 by the Bayes empirical Bayes procedure. The output from MEME is also given. With bold are the sites that belong at the antigen-binding region