Table 4.

Likelihood ratio test analyses to compare different models of codon evolution implemented in CODEML for the exon 2 sequences at the DQB and DRB loci in S. chinensis

Models compared	df	DQB		DRB
		2Δl	P value	2Δl	P value
M3 versus M0	4	348.6	<0.0001	888.4	<0.0001
M2a versus M1a	2	91.4	<0.0001	268.2	<0.0001
M8 versus M7	2	91.6	<0.0001	258.2	<0.0001

Differences in log-likelihood values (2(lb – la)) were compared with degrees of freedom using the χ² distribution. df indicates the number of free parameters in the ω distribution, ω the selection parameter, and 2Δl the likelihood ratio statistic computed as 2(lb – la), where la and lb are the log-likelihood values for each of the models being compared.