Table 3.

Likelihood values and parameter estimates for the FGF5 gene

Models	ln La	Estimate of parameters	2ΔLb(P-value)	Positively selected sites
M0:one-ratio	−4450.77242	ω = 0.16615
Branch-specific models
Branch a (ancestral Cetacea)
Two-ratio	−4450.74677	ω0 = 0.16656, ω1 = 0.14336	0.0513
			(P = 0.8208)
Branch b (ancestral Odontoceti)
Two-ratio	−4447.80276	ω0 = 0.16253, ω1 = 1.04812	5.93932
			(P= 0.0148)
Branch c (ancestral Mysticeti)
Two-ratio	−4449.912614	ω0 = 0.16491, ω1= 0.93251	1.719612
			(P = 0.189743)
Branch d (ancestral Cetartiodactyla)
Two-ratio	−4449.692636	ω0 = 0.16802, ω1 = 0.0001	2.159568
			(P = 0.1416845)
Branch e (ancestral Carnivora)
Two-ratio	−4450.028289	ω0 = 0.16284, ω1 = 0.28977	1.488262
			(P = 0.2224863)
Branch f (ancestral Chiroptera)
Two-ratio	−4450.762558	ω0 = 0.16637, ω1 = 0.14605	0.019724
			(P = 0.8883106)
Branch g (ancestral Rodentia)
Two-ratio	−4450.367662	ω0 = 0.16377, ω1 = 0.33139	0.809516
			(P = 0.3682634)
Branch h (ancestral Primates)
Two-ratio	−4450.765224	ω0 = 0.16585, ω1 = 0.17607	0.014396
			(P = 0.9044964)
Branch-site models
Null	−4370.04122	p0 = 0.80258, p1 = 0.19742, ω0 = 0.05816, ω1 = 1
Branch a (ancestral Cetacea)
Alternative	−4370.04122	p0 = 0.80258, p1 = 0.19742, p2a = 0, p2b = 0, ω0 = 0.05816, ω1 = 1, ω2 = 1	0 (P = 1)	None
Branch b (ancestral Odontoceti)
Alternative	−4365.28771	p0 = 0.46391, p1 = 0.12028, p2a = 0.33019, p2b = 0.08561, ω0 = 0.05123, ω1 = 1, ω2 = 2.03039	9.50702	K24E(0.945);P34Q(0.914);S68P(0.535);S74N(0.947);S84T(0.94)
			(P= 0.0086)
Branch c (ancestral Mysticeti)
Alternative	−4368.231030	p0 = 0, p1 = 0, p2a = 0.80784, p2b = 0.19216, ω0 = 0.05877, ω1 = 1, ω2 = 1	3.62038	M119T(0.777);V235A(0.937)
			(P = 0.163623)
Branch d (ancestral Cetartiodactyla)
Alternative	−4370.041222	p0 = 0.80258, p1 = 0.19742, p2a = 0, p2b = 0,	0 (P = 1)	None
		ω0 = 0.05816, ω1 = 1, ω2 = 1
Branch e (ancestral Carnivora)
Alternative	−4370.041222	p0 = 0.80258, p1 = 0.19742, p2a = 0, p2b = 0,	0 (P = 1)	186T(0.571)
		ω0 = 0.05816, ω1 = 1, ω2 = 1
Branch f (ancestral Chiroptera)
Alternative	−4369.925398	p0 = 0.75669, p1 = 0.18750, p2a = 0.04473, p2b = 0.01108, ω0 = 0.05728, ω1 =1, ω2 =1	0.231644	84T(0.736)
			(P = 0.8906337)
Branch g (ancestral Rodentia)
Alternative	−4370.041222	p0 = 0.80258, p1 = 0.19742, p2a =0, p2b =0,	0 (P = 1)	43G(0.621)
		ω0 = 0.05816, ω1 = 1, ω2 = 1
Branch h (ancestral Primates)
Alternative	−4370.041222	p0 = 0.80258, p1 = 0.19742, p2a = 0, p2b = 0,	0 (P = 1)	None
		ω0 = 0.05817, ω1 = 1, ω2 = 1

Note: a, ln L is the log-likelihood score; b, likelihood ratio test (LRT) to detect positive selection.