Table 2. Identification of positively selected sites in piscidins by maximum likelihood analysis using various models of evolution.

Method	Model	Parameter estimates	Ln Likelihood	Model comparison	Positively selected sites a
CODEML	M0: neutral	ω = 0.28	−809.60		None
	M1: nearly neutral	ω0 = 0.14, ω1 = 1.00p0 = 0.67, p1 = 0.33	−794.42		Not allowed
	M2: positive selection	ω0 = 0.15, ω1 = 1.00, ω2 = 13.76p0 = 0.66, p1 = 0.31, p2 = 0.03	−793.20	M2 vs M12ΔLnL = 2.44, df = 2, p = 0.29	29
	M3: discrete	ω0 = 0.05, ω1 = 0.29, ω2 = 2.25p0 = 0.22, p1 = 0.59, p2 = 0.19	−792.42	M3 vs M02ΔLnL = 34.36, df = 4, p = 0.00	25, 29, 43
	M7: β	p = 0.73, q = 1.27	−795.43		Not allowed
	M8: β + ωS>1	p = 0.73, q = 1.27ω = 2.31p0 = 0.83, p1 = 0.17	−792.29	M8 vs M72ΔLnL = 5.68, df = 2, p = 0.04	29
HYPHY	REL	ω = 1.14			25, 29

^aOnly positively selected sites with Bayesian posterior probabilities equal or greater than 95% are indicated. Sites with a posterior probability greater than 99% are highlighted in bold.