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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