Table 2. Evidence of positive Darwinian selection from site-specific model analyses for the HAMP gene of mammalians.

	1	−989.958		K = 2.090,ω = 0.357	None
M3 (discrete)	5	−962.409	M3 vs M0, 2ΔLnL = 55.10, df = 4, p = 0.00	K = 2.375, p 0 = 0.467, p 1 = 0.185, p 2 = 0.348,ω 0 = 0.043ω 1 = 0.459,ω 2 = 1.303	Not analyzed
M1a (Nearly Neutral)	1	−962.584		K = 2.317, p 0 = 0.526, p 1 = 0.474,ω 0 = 0.056,ω 1 = 1.0	Not allowed
M2a (Positive Selection)	3	−962.462	M2 vs M1, 2ΔLnL = 0.24, df = 2, p = 0.88	K = 2.374, p 0 = 0.531, p 1 = 0.381, p 2 = 0.087,ω 0 = 0.061,ω 1 = 1,ω 2 = 1.664	M0 (One ration)
M7 (beta)	2	−963.172		K = 2.284, P = 0.180, q = 0.206	Not allowed
M8 (beta and omega)	4	−962.411	M8 vs M7, 2ΔLnL = 1.52, df = 2, p = 0.47	K = 2.369, P 0 = 0.623, p 1 = 0.377, p = 0.469, q = 2.968,ω = 1.258

Note: P number of parameters in the ω distribution, K estimated transition/transversion rate ration, ω selection parameter, and p _n proportion of sites that fall into the ω_n site class. p, q shape parameters of the β function (for models M7 and M8).