Table 2.

Maximum likelihood estimates of parameters from PAML analyses of cadherins.

(Abbreviations are as follows: Data=dataset. M=ML model; np=number of parameters in model; ω₀, ω₁, ω₂=dN/dS category for sites under negative, neutral and positive selection, respectively; p₀, p₁, p₂=proportion of sites in first category, etc.; pand q=parameters of the beta distribution (continuous distribution approximation); logL=log likelihood of the estimated distribution under a particular model; 2dL=two times the difference in log likelihoods between specific models; P=Pvalue for the specific comparisons (e.g. M0 versus M3), assuming a chi-square distribution.)

data	M	np	ω0	p0	ω1	p1	ω2	p2	p	q	logL	2dL	P
Ecad	M0	7	0.187	1							−7421.03
Ecad	M1	7	0	0.672	1	0.328					−7341.76
Ecad	M2	9	0	0	1	0.193	0.057	0.807			−7320.62
Ecad	M3	11	0.065	0.828	1.151	0.172	1.222	0			−7320.27	201.52	p<0.01
Ecad	M7	8							0.144	0.484	−7323.33
Ecad	M8	10		0.992			89.35	0.008	0.163	0.578	−7314.9	16.86	p<0.01
Pcad	M0	9	0.134	1							−5220.66
Pcad	M1	9	0	0.731	1	0.269					−5218.62
Pcad	M2	11	0	0	1	0.089	0.077	0.911			−5197.62
Pcad	M3	13	0	0.031	0.102	0.931	2.629	0.037			−5194.99	51.34	p<0.01
Pcad	M7	10							0.24	1.223	−5201.19
Pcad	M8	12		0.964			2.661	0.036	10.998	98.994	−5194.99	12.4	p<0.01
VEcad	M0	9	0.174	1							−6932.12
VEcad	M1	9	0	0.594	1	0.406					−6888.83
VEcad	M2	11	0	0.456	0.12	1	0.424	0.25			−6839.86
VEcad	M3	13	0.028	0.626	0.469	0.348	2.01	0.026			−6839.47	185.3	p<0.01
VEcad	M7	10							0.25	0.873	−6840.74
VEcad	M8	12		0.988			2.653	0.012	0.285	1.087	−6839.52	2.44	N.S.
Hcad	M0	9	0.083	1							−5730.47
Hcad	M1	9	0	0.691	1	0.309					−5784.28
Hcad	M2	11	0	0.522	1	0.014	0.183	0.464			−5704.58
Hcad	M3	13	0.023	0.103	0.023	0.623	0.293	0.274			−5704.38
Hcad	M7	10							0.372	3.288	−5704.47
Hcad	M8	12		0.736			0.297	0.264	2.631	99	−5704.39