Table 5. LRT of 1ω-model vs reverted 2ω-model for individual genes.

Gene	Ancestral Poaceae	Other branches	(reverted 2ω)	(1ω)		P
rpoB*	0.3469	0.1013	−8546.12	−8574.82	57.41	3.53E-14
rps11*	0.7406	0.0538	−1126.87	−1144.90	36.06	1.91E-09
clpP*	0.5943	0.1374	−1767.99	−1778.73	21.47	3.95E-06
atpE*	0.9642	0.1309	−1132.80	−1143.33	21.05	4.48E-06
rps3*	0.5767	0.1273	−1958.45	−1968.07	19.24	1.15E-05
cemA*	1.4337	0.3047	−2214.75	−2224.29	19.09	1.25E-05
rpl22*	0.6319	0.1139	−1067.47	−1075.53	16.11	5.97E-05
rpoC1	0.2385	0.1294	−5702.89	−5708.31	10.85	0.000989
atpA	0.2296	0.1102	−4201.36	−4206.20	9.68	0.001860
PS13#	0.0540	0.1663	−3542.69	−3547.23	9.08	0.002578
rps2	0.3623	0.1288	−1886.14	−1890.56	8.83	0.002960
rpoC2	0.3364	0.2179	−10553.23	−10557.46	8.45	0.003642
psaC#	0.0001	0.0780	−603.22	−607.35	8.26	0.004047
rbcL#	0.0344	0.0937	−3805.48	−3809.48	8.00	0.004669
ndhH	0.1405	0.0592	−3144.67	−3148.58	7.81	0.005202
rps7	1.2673	0.2151	−865.87	−869.76	7.78	0.005297
rps12	0.6567	0.1220	−697.24	−700.69	6.91	0.008589
rps19	0.6328	0.1836	−727.58	−730.62	6.08	0.013646
rpl16#	0.0268	0.1060	−1131.04	−1134.08	6.07	0.013739
rpl14	0.2858	0.0995	−972.76	−975.00	4.47	0.034457

and refer to the estimates of non-synonymous/synonymous rate ratios based on the reverted 2ω-model. Only 20 genes rejecting the 1ω-model with P<0.05 are listed. In this analysis, 11 monocot species (6 Poacea species, Typha, Musa, Elaeis, Phalaenopsis, and Yucca) were used. 75 genes were analyzed, but genes with related functions were concatenated if the lengths are shorter than 180 nucleotides, and therefore the number of tests was 61. PS13 refers to the concatenated sequences of petG+petL+petN+psaI+psaJ+psbF+psbI+psbJ+psbK+psbL+psbM+psbN+psbΤ.

^*refers to a gene which remains significant after the Bonferroni correction.

^#refers to a gene with ω₁<ω₀.