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Table 1 CODEML analyses of selective pattern on the TAS1R2 in catarrhine primates

From: Differentiated adaptive evolution, episodic relaxation of selective constraints, and pseudogenization of umami and sweet taste genes TAS1Rs in catarrhine primates

Models

lnL

Compared

2ΔLnL

P-value

Parameter estimates

Branch model

     

M0:one-ratio

−7258.8072

   

ω = 0.1608

M1:free-ratio

−7211.2267

M0 vs. M1

95.1610

p < 0.05

 

Foreground branch: ancestral Colobinae

   

H1: ω0, ω1

−7256.0276

M0 vs. H1

5.5592

p < 0.05

ω0 = 0.1548, ω1 = 0.5583

H0: ω0, ω1 = 1

−7256.4033

H0 vs. H1

0.7514

p > 0.05

ω0 = 0.1543, ω1 = 1.0000

Foreground branch: ancestral Hylobates

H1: ω0, ω1

−7256.8606

M0 vs. H1

3.8932

p < 0.05

ω0 = 0.1570, ω1 = 0.5554

H0: ω0, ω1 = 1

–7257.1816

H0 vs. H1

0.6420

p > 0.05

ω0 = 0.1570, ω1 = 1.0000

Site model

     

M1a

–7149.5623

   

p0 = 0.8609, p1 = 0.1391,ω0 = 0.0451, ω1 = 1.0000

M2a

–7145.1097

M1a vs. M2a

8.9052

p < 0.05

p0 = 0.8669, p1 = 0.1198, p2 = 0.0133, ω0 = 0.0499, ω1 = 1.0000, ω2 = 3.6223

M8a

–7149.3577

   

p0 = 0.8725( p1 = 0.1275), p = 0.4874, q = 7.5964, ω = 1.0000

M8

–7143.4448

M8a vs. M8

11.8258

p < 0.01

p0 = 0.9744( p1 = 0.0257), p = 0.1750, q = 1.1154, ω = 2.8718

Branch-site model

    

Lineages of Cercopithecidae

    

Null

−7146.1093

   

p0 = 0.8463, p1 = 0.0953, p2a = 0.0525 p2b = 0.0059,ω0 = 0.0407, ω1 = 1.0000 ω2 = 1.0000

Alternative

−7144.2553

 

3.7080

p < 0.05

p0 = 0.8683, p1 = 0.0924, p2a = 0.0354 p2b = 0.0038,ω0 = 0.0481, ω1 = 1.000 ω2 = 2.0345

Lineages of Colobinae

    

Null

–7145.5063

   

p0 = 0.8299, p1 = 0.1176, p2a = 0.0460 p2b = 0.0065,ω0 = 0.0396, ω1 = 1.0000,ω2 = 1.0000

Alternative

–7143.7154

 

3.5818

p < 0.05

p0 = 0.8542, p1 = 0.1162, p2a = 0.0261 p2b = 0.0036,ω0 = 0.0428, ω1 = 1.0000 ω2 = 2.4997,

Lineages of Cercopithecinae

    

Null

−7148.7133

   

p0 = 0.8512, p1 = 0.1292, p2a = 0.0170 p2b = 0.0026,ω0 = 0.0440, ω1 = 1.0000,ω2 = 1.0000

Alternative

–7143.4285

 

10.5696

p < 0.01

p0 = 0.8639, p1 = 0.1228, p2a = 0.0116 p2b = 0.0017,ω0 = 0.0466, ω1 = 1.0000 ω2 = 5.8766

Lineages of Hylobatidae

    

Null

–7149.1766

   

p0 = 0.8489, p1 = 0.1326, p2a = 0.0161 p2b = 0.0025,ω0 = 0.0442, ω1 = 1.000 ω2 = 1.0000

Alternative

–7143.6646

 

11.0240

p0.01

p0 = 0.8612, p1 = 0.1297, p2a = 0.0079, p2b = 0.0012,ω0 = 0.0462, ω1 = 1.000 ω2 = 11.8832