Table 4.

Likelihood paramater estimates under the branch-site models.

Model	ℓ	Parameters	Positive Sites	Sig.
Hox1
M1a	-707.37	p0 = 0.982, p1 = 0.018; ω0 = 0.0017, ω1 = 1	Not Allowed
MA	-697.04	P0+1 = 0.935, p2 = 0.065; ω0/1 = 0.0034/1, ω2 = 999	3 (PP > 0.99)	P << 0.001
Hox2
M1a	-800.91	p0 = 0.985, p1 = 0.015; ω0 = 0.0059, ω1 = 1	Not Allowed
MA	-794.72	p0+1 = 0.981, p2 = 0.019; ω0/1 = 0.0062/1, ω2 = 17.98	1 (PP > 0.95)	P < 0.005
Hox3
M1a	-1684.44	p0 = 0.979, p1 = 0.021; ω0 = 0.0223, ω1 = 1	Not Allowed
MA	-1647.20	p0+1 = 0.833, p2 = 0.167; ω0/1 = 0.0116/1, ω2 = 170.6	12 (PP > 0.95)	P << 0.001
Hox4
M1a	-1547.08	p0 = 0.987, p1 = 0.013; ω0 = 0.0057, ω1 = 1	Not Allowed
MA	-1538.64	p0+1 = 0.987, p2 = 0.013; ω0/1 = 0.0046/1, ω2 = 3.70	1 (PP > 0.99)	P << 0.001
Hox5
M1a	-1280.06	p0 = 1.0, p1 = 0.0; ω0 = 0.0119, ω1 = 1	Not Allowed
MA-A	-1272.42	p0+1 = 0.897, p2 = 0.103; ω0/1 = 0.008/1, ω2 = 1.11	1 (PP > 0.95)	P << 0.001
MA-B	-1273.35	p0+1 = 0.925, p2 = 0.075; ω0/1 = 0.0085/1, ω2 = 477.6	None Identified	P << 0.001
MA-C	-1269.82	p0+1 = 0.903, p2 = 0.097; ω0/1 = 0.0106/1, ω2 = 76.7	4 (PP > 0.90)	P << 0.001
Hox6
M1a	-1309.19	p0 = 1.0, p1 = 0.0; ω0 = 0.0155, ω1 = 1	Not Allowed
MA	-1295.24	p0+1 = 0.754, p2 = 0.246; ω0/1 = 0.0108/1, ω2 = 999	10 (PP > 0.90)	P << 0.001
Hox7
M1a	-698.86	p0 = 1.0, p1 = 0.0; ω0 = 0.0029, ω1 = 1	Not Allowed
MA	-969.89	No Reliable Results		n.a.
Hox8
M1a	-1889.89	p0 = 0.985, p1 = 0.015; ω0 = 0.011, ω1 = 1	Not Allowed
MA	-1086.37	p0+1 = 0.949, p2 = 0.051; ω0/1 = 0.011/1, ω2 = 1.0	1 (PP > 0.95)	P < 0.05
Hox9
M1a	-1389.70	p0 = 1.0, p1 = 0.0; ω0 = 0.0101, ω1 = 1	Not Allowed
MA-A	-1386.83	p0+1 = 0.878, p2 = 0.122; ω0/1 = 0.0089/1, ω2 = 1.0	None Identified	P = 0.057
MA-B	-1380.29	No Reliable Results		n.a.
MA-C	-1269.82	p0+1 = 0.903, p2 = 0.097; ω0/1 = 0.0106/1, ω2 = 76.7	4 (PP > 0.90)	P << 0.001
MA-D	-1389.19	p0+1 = 0.9, p2 = 0.1; ω0/1 = 0.0095/1, ω2 = 1.0	1 (PP < 0.90)	n.s.
Hox10
M1a	-1747.75	p0 = 0.895, p1 = 0.105; ω0 = 0.0139, ω1 = 1	Not Allowed
MA	-1747.20	p0+1 = 0.853, p2 = 0.47 ω0/1 = 0.0123/1, ω2 = 1.0	1 (PP < 0.90)	n.s.
Hox11
M1a	-1210.27	p0 = 0.982, p1 = 0.018; ω0 = 0.0017, ω1 = 1	Not Allowed
MA	-1208.15	p0+1 = 0.973, p2 = 0.029; ω0/1 = 0.0092/1, ω2 = 1.0	None Identified	n.s.
Hox12
M1a	-1092.80	p0 = 1.0, p1 = 0.0; ω0 = 0.0229, ω1 = 1	Not Allowed
MA	1092.52	p0+1 = 0.973, p2 = 0.027; ω0/1 = 0.0226/1, ω2 = 1.0	None Identified	n.s.
Hox13
M1a	-1747.34	p0 = 1.0, p1 = 0.0; ω0 = 0.023, ω1 = 1	Not Allowed
MA	-1731.97	p0+1 = 0.918, p2 = 0.082; ω0/1 = 0.022/1, ω2 = 6.96	3 (PP > 0.90)	P << 0.001

Parameters that indicate positive selection are in bold. ℓ, likelihood of the model. Sig., significance of the model. Positive sites were identified using the Bayes empirical Bayes (BEB) method