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Table 6 Parameter estimations and likelihood ratio tests for the branch-site models

From: FoxO gene family evolution in vertebrates

 

df

Parameter estimatesa

lnLb

2⊿c

P value

Positive selected sites

FoxO1

      

MA Vs M1a (test 1)

2

p0 = 0.70592 p1 = 0.18493 (p2 = 0.10915) w0 = 0.07205 (w1 = 1.00000) w2 = 1.00000

-22667.231

81.89419

P < 0.01

213S** 216S* 219S* 252M* 276V** 285P* 296L** 306A** 340F* 360E*

FoxO3

      

MA Vs M1a (test 1)

2

p0 = 0.77299 p1 = 0.10453 (p2 = 0.12248) w0 = 0.06958 (w1 = 1.00000) w2 = 1.00000

-22646.766

122.8257

P < 0.01

5H** 25D* 26F** 33D** 34L**37N** 217A* 231G** 329G*

FoxO4

      

MA Vs M1a (test 1)

2

p0 = 0.67705 p1 = 0.18055 (p2 = 0.1424) w0 = 0.07468 (w1 = 1.00000) w2 = 1.00000

-22660.108

96.14052

P < 0.01

7V** 173R** 194T** 201I** 202L** 211F**223H* 225P** 242T* 254R** 314S**

FoxO6

      

MA Vs M1a (test 1)

2

p0 = 0.58516 p1 = 0.13030 (p2 = 0.28454) w0 = 0.06572 (w1 = 1.00000) w2 = 1.05311

-22527.632

361.0936

P < 0.01

42Q** 46K** 155I* 164T** 165N** 173R* 174E** 176E** 178L** 179F** 180C** 188I* 189V** 203L* 207R* 223H** 230I** 231G* 232Y** 233K** 234N** 237Y** 258S** 265N* 269T** 271E** 272N** 273E** 274V** 275H** 276V** 277S** 278Q* 279G** 280L** 281H** 282P** 283S** 286N* 314S** 316V** 320H** 330Y* 366T** 367G** 368T** 369P*

  1. Note: aThe number of free parameters;
  2. bLikelihood of the model;
  3. c2(l1-l0);
  4. * P > 0.95;
  5. ** P > 0.99;
  6. The bold amino acid residues were also found to be implicated in the functional divergence (implemented in Diverge 2.0) between FoxO