Table 3.

Branch comparisons of dN/dS, dN, and dS for gene groups

Gene groups	Branch comparisons	dN/dS	dN	dS
All 73 genes	Branch leading to Poaceae vs. all other branches	0.0984	<0.0001**	<0.0001**
	Branch leading to Poaceae vs. internal Poaceae	0.0872	<0.0001**	<0.0001**
	Branch leading to Poaceae vs. non-Poaceae monocots	0.0904	<0.0001**	<0.0001**
	Branch leading to Poaceae vs. other angiosperms	0.1103	<0.0001**	<0.0001**
	Internal Poaceae vs. non-Poaceae monocots	na	<0.0001**	<0.0001**
	Internal Poaceae vs. other angiosperms	0.6577	<0.0001**	<0.0001**
	Non-Poaceae monocots vs. other angiosperms	0.7123	0.8426	0.6613
Photosynthetic apparatus (psa-, psb-, and pet-genes)	Branch leading to Poaceae vs. all other branches	0.0001**	0.2746	<0.0001**
	Branch leading to Poaceae vs. internal Poaceae	0.0001**	0.0053*	<0.0001**
	Branch leading to Poaceae vs. non-Poaceae monocots	0.0001**	0.6835	<0.0001**
	Branch leading to Poaceae vs. other angiosperms	0.0001**	0.4589	<0.0001**
	Internal Poaceae vs. non-Poaceae monocots	na	<0.0001**	<0.0001**
	Internal Poaceae vs. other angiosperms	0.0116	<0.0001**	<0.0001**
	Non-Poaceae monocots vs. other angiosperms	0.0223	0.2702	0.9622
Genes expression (rpl-, rps, and rpo-genes)	Branch leading to Poaceae vs. all other branches	<0.0001**	<0.0001**	<0.0001**
	Branch leading to Poaceae vs. internal Poaceae	<0.0001**	<0.0001**	<0.0001**
	Branch leading to Poaceae vs. non-Poaceae monocots	<0.0001**	<0.0001**	<0.0001**
	Branch leading to Poaceae vs. other angiosperms	<0.0001**	<0.0001**	<0.0001**
	Internal Poaceae vs. non-Poaceae monocots	na	<0.0001**	<0.0001**
	Internal Poaceae vs. other angiosperms	<0.0001**	<0.0001**	<0.0001**
	Non-Poaceae monocots vs. other angiosperms	<0.0001**	0.1513	0.5967
Photosynthetic metabolism (atp- and ndh-genes)	Branch leading to Poaceae vs. all other branches	0.0123	<0.0001**	<0.0001**
	Branch leading to Poaceae vs. internal Poaceae	0.0411	<0.0001**	<0.0001**
	Branch leading to Poaceae vs. non-Poaceae monocots	0.0427	<0.0001**	<0.0001**
	Branch leading to Poaceae vs. other angiosperms	0.0065	<0.0001**	<0.0001**
	Internal Poaceae vs. non-Poaceae monocots	na	<0.0001**	<0.0001**
	Internal Poaceae vs. other angiosperms	0.1186	<0.0001**	<0.0001**
	Non-Poaceae monocots vs. other angiosperms	0.1574	0.7511	0.8547

P-values were generated using Wilcoxon rank sums tests and asterisks show significant values after correction for multiple comparisons using Holm’s method, i.e., sequential Bonferroni correction (** α = 0.01, * α = 0.05). The value ‘na’ is due to model parameters in PAML analyses