454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher

Table 1 Evaluation of the goodness of fit for different models of codon evolution and estimated parameter values

Model	lnL	ΔAIC	Parameters
	Cluster I putative pseudogenes
M0 - one ω	-525.2	7.0	ω = 0.568
M7 - nearly neutral with beta	-520.7	best
M8 - positive selection with beta (ω₀ ≤ 1, ω₁ > 1)	-520.3	3.2	p₀ = 0.925, p₁ = 0.075, ω₁ = 3.133
	Cluster II putative expressed alleles
M0 - one ω	-4108.8	931.4	ω = 0.687
M7 - nearly neutral with beta	-3744.3	118.2
M8 - positive selection with beta (ω₀ ≤ 1, ω₁ > 1)	-3685.6	best	p₀ = 0.748, p₁ = 0.252, ω₁ = 3.238
	Group II.A (putative pseudogenes)
M0 - one ω	-353.5	48.0	ω = 2.332
M7 - nearly neutral with beta	-343.1	29.2
M8 - positive selection with beta (ω₀ ≤ 1, ω₁ > 1)	-326.5	best	p₀ = 0.962, p₁ = 0.038, ω₁ = 50.098

ω - dN/dS; nearly neutral with beta - for all sites ω ≤ 1 and the beta distribution approximates ω variation; positive selection - a proportion of sites evolves with ω > 1; p₀ - proportion of sites with ω ≤ 1, p₁ - proportion of positively selected sites (ω > 1), ω₁ - estimated value of ω for sites under positive selection; ΔAIC - the difference between the value of the Akaike Information Criterion (AIC) of a given model and the best model.

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