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Table 2 Parameters estimation and likelihood ratio tests of ARF genes for the branch-site models

From: Genome-wide identification, molecular evolution, and expression analysis of auxin response factor (ARF) gene family in Brachypodium distachyon L

Clade Model npa lnL 2lnL Positive selected sitesb
Ia Model A-null 365 −30,653.840481   Not allowed
  Model A 366 −30,653.840481 0 169D, 339 A, 340 G**, 355 T**, 356 T**, 358 P**, 360 Y
Ib Model A-null 365 −30,683.021342   Not allowed
  Model A 366 −30,683.021342 0 None
II Model A-null 365 −30,601.447106   Not allowed
  Model A 366 −30,601.447106 0 229 I, 230 M**, 231 P, 232 S*, 236 S,
238 D**, 239 S**, 240 M**, 241 H**,
243 G**, 244 L**, 246 A**, 247 A**,
250 H*, 252 A, 255 N**, 259 T*, 266 S,
273 I, 275 L**, 276 A**, 279 V**,
281 S, 282 V**, 283 Y, 287 V**,
289 V**, 291 M, 295 M**, 297 F,
308 M**, 310 T**, 312 T*, 314 I**,
337 S**, 338 T**, 340 G**, 343 Q*,
344 P**, 345 R*, 353 P*, 354 L**,
358 P**, 371 P**
III Model A-null 365 −30,624.183120   Not allowed
  Model A 366 −30,624.183120 0 193 V, 204 D**,213 N, 228 T, 230 M**, 231 P**, 232 S**, 233 S**, 236 S**, 237 S**, 241 H, 246 A**, 250 H,
698 A, 700 A*, 701 T*,745 Y,749 R*,
752 V, 832 G**
  1. Note: p < 0.05 and p < 0.01 were marked by* and **, respectively. All sites are located on reference amino acid sequence BdARF1 according to the multiple sequence alignment result. Sites are highlighted in red subjected to functional divergence and positive selection
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