Table 2.

Parameter estimates for the evolutionary analysis of the schizothoracine EPO

Models	Estimate of parameters	ℓ	Positively selected sites	P value
Branch model
free-ratio	(see Fig. 3 for ω values for each node)	−2272.00	None
Branch-site models (LRT for branch-site: 0.20)
Model Null	p0 = 0.19, p1 = 0.08 (p2 + p3 = 0.73), ω0 = 0.14, ω1 = 1.00, ω3 = 1.00	−2267.82	None
Model A	p0 = 0.48, p1 = 0.21(p2 + p3 = 0.31), ω0 = 0.14, ω1 = 1.00, ω3 = 2.45	−2267.72	117 L (p = 0.727), 131H (p = 0.621)	0.6547
			133 T (p = 0.719), 138S (p = 0.797)	(df = 1)
			153 L (p = 0.571)

The branch-site model in codeml program divides all the sites into four classes, class 0, 1, 2, and 3. Class 0 is for the sites under purifying selection. Class 1 is for the sites under neutral selection. Class 2 and 3 are for the sites that have positive selection in foreground branches. In this table, p ₀ and ω₀ stand for the percentage and averaged omega value of class 0 sites in the alignment. P ₁ and ω₁ stand for the percentage and averaged omega value of class 1 sites. P ₂ + p ₃ and ω₂ + ω₃ are for the percentage and averaged omega value of the sites in class 2 and 3