Table 2. Likelihood parameter estimates under site-specific models of Hh vertebrate paralogs, branch calculated with PAML v4.3 [51].

Gene	Model	Parameters	Lnl	Models Compared	LRT (2Δl)	p-value	df
Dhh	M0	ω0 = 0.08479	−7360.011	M0 vs M3*	190.185	0.000	4
	M3	ω0 = 0.00492 ω1 = 0.08337 ω2 = 0.31612	−7162.160
		p0 = 0.39785 p1 = 0.34084 p2 = 0.26131
	M7	p = 0.41513 q = 3.11107	−7163.063	M7* vs M8	0.006	0.997	2
		ω = 0.114
	M8	p0 = 0.99999 p = 0.41486 q = 3.10767	−7163.066
		(p1 = 0.00001) ω1 = 2.90725
Ihh	M0	ω0 = 0.06236	−8206.454	M0 vs M3*	740.516	0.000	4
	M3	ω0 = 0.00520 ω1 = 0.11825 ω2 = 0.34903	−7836.196
		p0 = 0.59836 p1 = 0.27289 p2 = 0.12874
	M7	p = 0.25686 q = 2.77341	−7838.824	M7* vs M8	0.002	0.999
		ω = 0.080
	M8	p0 = 0.99999 p = 0.25687 q = 2.77361	−7838.825
		(p1 = 0.00001) ω1 = 1.00000
Shh	M0	ω0 = 0.04658	−7648.861	M0 vs M3*	612.130	0.000	4
	M3	ω0 = 0.00188 ω1 = 0.06952 ω2 = 0.26493	−7342.796
		p0 = 0.60204 p1 = 0.25287 p2 = 0.14509
	M7	p = 0.20836 q = 3.15101	−7342.669	M7* vs M8	0.007	0.996	2
		ω = 0.058
	M8	p0 = 0.99999 p = 0.20836 q = 3.15102	−7342.672
		(p1 = 0.00001) ω1 = 5.18630

An asterisk (*) marks the accepted model.