Table 4

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

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.

Sepil et al.

Sepil et al. BMC Evolutionary Biology 2012 12:68   doi:10.1186/1471-2148-12-68

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