Table 4.

Low-temperature-induced genes under positive selection

Branch	Gene	Annotation	Putative function(s)	No selection (log likelihood)	Selection (log likelihood)	P-value (fdr)	Sites
BP	Bradi1 g13640.1	Chaperone J2	Co-chaperone activity	−2539.972	−2533.284	0.019	7, 231
	Bradi2 g38290.1	ku70-binding protein	Double strand break repair	−1855.013	−1849.220	0.028	116
	Bradi2 g55070.1	SOUL heme binding protein	Red/far-red light signaling	−1727.853	−1719.885	0.009	48, 183
	Bradi2 g58050.1	Fructose-bisphosphate aldolase	Glycolysis	−3248.868	−3242.741	0.022	82, 97, 285
	Bradi3 g17200.1	Tyrosyl-tRNA synthetase	Translation	−3324.640	−3316.783	0.009	21, 30, 157
	Bradi4 g09430.1	Acidic endochitinase	Disease response	−2495.464	−2486.970	0.009	38, 60, 167, 200, 205, 223, 226
	Bradi4 g34170.1	Ribosomal protein S16	Translation	−1177.237	−1170.983	0.022	101, 135
	Bradi4 g36800.1	Phospholipase D delta	Cell membrane lipid hydrolysis/signaling	−7418.390	−7411.998	0.022	87, 93, 150, 203, 250, 444, 819
	Bradi5 g25050.1	Naringenin 3-dioxygenase	Flavanoid biosynthesis	−2904.277	−2897.533	0.019	273, 293
CP	Bradi1 g35200.2	Novel plant SNARE 11	Membrane receptor/protein transport	−2251.089	−2241.895	0.007	72, 113, 137

Annotations of putative functions are based on Brachypodium distachyon gene homology to Arabidopsis thaliana proteins.

BP, basal Pooideae ancestral; CP, core Pooideae stem.

Sites refer to codons in the trimmed alignments with a Bayes empirical Bayes posterior probability ≥ 0.9. All point estimates for foreground omega values (ω2) were > 7.