Table 1. Parameter estimates and log-likelihood values for Potamogeton rbcL under eight codon substitution models included in PAML.

Model	Log-likelihood	Parameters a
Site-specific models
M0 : one ω	−2182.1	ω = 0.129
M1A : nearly neutral	−2167.3	p0 a = 0.912, ω0 = 0.000
		p1 = 0.088, ω1 = 1.000
M2A : positive selection	−2163.1	p0 = 0.914, ω0 = 0.000
		p1 = 0.082, ω1 = 1.000
		p2 = 0.004, ω2 = 11.494
M7 : beta	−2167.4	p = 0.005, q = 0.0482
M8 : beta & ωs≥1	−2163.4	p0 = 0.963
		p = 0.010, q = 0.314
		p1 = 0.037, ω1 = 3.825
M8A : beta & ωs = 1	−2167.3	p0 = 0.912
		p = 0.005, q = 99.000
		p1 = 0.088, ω1 = 1.000
Branch-site models
Foreground: Heterophylly
Model A (ω2 = 1 fixed)	−2166.7	p0 = 0.871, ω0 = 0.000
		p1 = 0.064, ω1 = 1.000
		p2+p3 = 0.065 , ω2 = 1.000
Model A (ω2 estimated)	−2162.1	p0 = 0.920, ω0 = 0.000
		p1 = 0.066, ω1 = 1.000
		p2+p3 = 0.013 , ω2 = 26.150
Foreground: Homophylly
Model A (ω2 = 1 fixed)	−2166.0	p0 = 0.850, ω0 = 0.000
		p1 = 0.053, ω1 = 1.000
		p2+p3 = 0.097 , ω2 = 1.000
Model A (ω2 estimated)	−2165.8	p0 = 0.899, ω0 = 0.000
		p1 = 0.055, ω1 = 1.000
		p2+p3 = 0.046 , ω2 = 2.575

^athe proportion (p_i) of codon sites with ω_i. In models M7, M8 and M8A, ω was drawn from a beta distribution B(p, q) for a proportion (p₀) of sites.