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.

Chen et al.

Chen et al. BMC Evolutionary Biology 2013 13:34   doi:10.1186/1471-2148-13-34

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