Table 1.

Substitution frequencies and rate heterogeneity parameters

		A↔C	A↔G	A↔T	C↔G	C↔Ta	αb	I (ML)c	Id
All sites	Fish	0.778	2.419	1.328	0.984	3.192	1.203	0.262	0.412
	Reptiles	1.081	4.598	0.907	3.330	2.516	0.392	0.000	0.611
	Mammals	1.322	4.876	0.838	0.727	4.672	1.473	0.345	0.530
	Tetrapods	1.091	4.120	0.969	1.431	3.341	1.029	0.244	0.367
	Vertebrates	0.987	3.326	1.084	1.298	3.115	1.014	0.166	0.263
Codon #1	Fish	2.338	2.645	1.434	0.793	2.877	0.422	0.000	0.334
	Reptiles	2.383	2.148	0.777	0.579	1.313	0.312	0.000	0.629
	Mammals	2.504	4.097	0.739	0.828	3.515	1.445	0.447	0.646
	Tetrapods	2.051	2.781	0.935	0.602	1.891	0.780	0.212	0.457
	Vertebrates	2.188	2.473	1.008	0.741	2.256	0.837	0.122	0.319
Codon #2	Fish	5.561	9.417	3.878	23.904	10.450	0.411	0.000	0.629
	Reptiles	0.411	7.219	0.549	5.696	3.547	1.936	0.666	0.806
	Mammals	1.654	11.198	2.489	6.140	7.073	0.364	0.298	0.747
	Tetrapods	1.727	8.563	1.226	6.564	4.313	0.403	0.119	0.593
	Vertebrates	2.435	7.089	1.480	7.343	4.679	0.647	0.108	0.435
Codon #3	Fish	0.454	2.419	1.878	0.286	3.282	3.877	0.013	0.103
	Reptiles	0.377	4.589	0.000	0.431	4.089	1.002	0.000	0.343
	Mammals	0.985	5.023	0.810	0.194	4.248	2.907	0.000	0.197
	Tetrapods	0.623	4.283	0.973	0.679	3.599	3.058	0.028	0.050
	Vertebrates	0.521	3.386	1.169	0.622	3.027	4.665	0.032	0.036

^a Parameters are reversible and measured against the G↔T parameter with a value of 1

^b Shape parameter for the gamma distribution.

^c Proportion of invariant sites estimated using maximum likelihood methods

^d Proportion of invariant sites calculated from raw alignment data using MEGA3 [131].