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Table 1 Site-models, log-likelihood values, transition: transversion ratio (κ) and parameter estimates for Phrynocephalus mitochondrial gene sequences. ω and ωi are nonsynonymous: synonymous ratios, pi refers to the proportion of sites in class i (see PAML manual for more details on these site models)

From: Evolutionary analysis of mitochondrially encoded proteins of toad-headed lizards, Phrynocephalus, along an altitudinal gradient

Model Number Log Likelihood κ Parameter Estimates
M0 (one ratio) −53,947.45 8.02 ω = 0.0755
M1A (nearly neutral) −53,215.56 8.69 p0 = 0.9173, p1 = 0.0827
ω0 = 0.0410, ω1 = 1.0000
M2A (positive selection) −53,215.56 8.69 p0 = 0.9173, p1 = 0.0827, p2 = 0.0000
ω0 = 0.0410, ω1 = 1.0000, ω2 = 30.1188
M3 (discrete) −52,976.30 8.20 p0 = 0.7920, p1 = 0.0003, p2 = 0.2077
ω0 = 0.0149, ω1 = 0.0533, ω2 = 0.3429
M7 (beta) −52,936.28 8.27 p = 0.1797, q = 1.7626
M8 (beta & ω) −52,926.55 8.29 p0 = 0.9981, p1 = 0.0020, ωs = 2.2162,
p = 0.1863, q = 1.9069