Table 3.

Site models and tests of selection

Model	Parameter estimates	ĸ	lnL	p
M0	ω = 0.070	1.01	−1961.39	<<0.001
M3	p0 = 0.585 p1 = 0.383, p2 = 0.032	0.98	−1922.15
	ω0 = 0.001, ω1 = 0.151, ω2 = 0.615
M1	p0 = 0.952, p1 = 0.048,	1.13	−1946.80	--
	ω0 = 0.057 ω1 = 1.000
M2	p0 = 0.952, p1 = 0.048, p2 = 0.000,	1.13	−1946.80
	ω0 = 0.057, ω1 = 1.000, ω2 = 42.1
M7	p = 0.260, q = 2.948	0.94	−1924.53	--
M8	p0 = 1.000, p = 0.260	0.94	−1924.53
	q = 2.95, (p1 = 0.000), ω = 2.51

Model refers to the Nsites value in codeml (e.g. M0 is nSites = 0); other parameter values for all tests were: codon frequency =3, model =0, omega = 0; ω is dN/dS and p_n is the proportion of codons with ration ω_n; κ is the transition:transversion ratio; LnL is the log likelihood, p is the result of χ² test, which was not performed when the likelihoods were identical.