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

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

Clade	Model	np^a	lnL	2△lnL	Positive selected sites^b
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*

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

ISSN: 1471-2229