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Table 4 Results of the likelihood ratio tests for different models of codon evolution and estimated parameter values

From: Characterization and 454 pyrosequencing of Major Histocompatibility Complex class I genes in the great tit reveal complexity in a passerine system

Model

lnL

ΔAIC

Parameters

 

Group 1

 

M0 – one ω

−2975.2

454.8

ω = 0.53

M7 – nearly neutral with β

−2788.9

100.2

 

M8 – positive selection with β (ω0 ≤ 1, ω1 >1)

−2737.8

Best

p0 = 0.83, p1 = 0.17, ω1 = 2.92

 

Group 2

 

M0 – one ω

−1154.5

68.5

ω = 0.74

M7 – nearly neutral with β

−1124

25.5

 

M8 – positive selection with β (ω0 ≤ 1, ω1 >1)

−1110.2

Best

p0 = 0.93, p1 = 0.07, ω1 = 5.26

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