Table 2. Results of branch-site model analysis and the likelihood ratio test for the foreground branches of Scutellaria DFR duplicates.

	Foreground branch	np	lnL	2ΔL	P	Proportion	Background ω	Foreground ω	PS site (Pr ω > 1)
#1	Dup1 fixed ω = 1	136	−2629.741	0.4763	0.4556	p0 = 0	ω0 = 0.0355	ω0 = 0.0355	None
						p1 = 0	ω1 = 1	ω1 = 1
						p2a = 0.8073	ω2a = 0.0355	ω2a = 1
						p2b = 0.1927	ω2b = 1	ω2b = 1
#1	Dup1	137	−2629.503			p0 = 0	ω0 = 0.0358	ω0 = 0.0358
						p1 = 0	ω1 = 1	ω1 = 1
						p2a = 0.8081	ω2a = 0.0358	ω2a = 64.0267
						p2b = 0.1919	ω2b = 1	ω2b = 64.0267
#1	Dup2 fixed ω = 1	136	−2629.61	−0.2294	#NUM!	p0 = 0.0165	ω0 = 0.0356	ω0 = 0.0356	None
						p1 = 0.0039	ω1 = 1	ω1 = 1
						p2a = 0.7907	ω2a = 0.0356	ω2a = 1
						p2b = 0.1889	ω2b = 1	ω2b = 1
#1	Dup2	137	−2629.725			p0 = 0	ω0 = 0.0359	ω0 = 0.0359
						p1 = 0	ω1 = 1	ω1 = 1
						p2a = 0.8079	ω2a = 0.0359	ω2a = 48.6756
						p2b = 0.1921	ω2b = 1	ω2b = 48.6756
$1	Dup1 fixed ω = 1	136	−2628.349	18.0661	1.12E–05	p0 = 0.7837	ω0 = 0.0337	ω0 = 0.0337
						p1 = 0.1114	ω1 = 1	ω1 = 1
						p2a = 0.0919	ω2a = 0.0337	ω2a = 1
						p2b = 0.0131	ω2b = 1	ω2b = 1
$1	Dup1	137	−2619.314			p0 = 0.7921	ω0 = 0.0412	ω0 = 0.0412	253D (1.000)
						p1 = 0.1929	ω1 = 1	ω1 = 1
						p2a = 0.0121	ω2a = 0.0412	ω2a = 6.4153
						p2b = 0.0029	ω2b = 1	ω2b = 6.4153
$1	Dup2 fixed ω = 1	136	−2629.786	8.845	0.0016	p0 = 0.7754	ω0 = 0.0327	ω0 = 0.0327
						p1 = 0.1800	ω1 = 1	ω1 = 1
						p2a = 0.0362	ω2a = 0.0327	ω2a = 1
						p2b = 0.0084	ω2b = 1	ω2b = 1
$1	Dup2	137	−2625.364			p0 = 0.7966	ω0 = 0.0396	ω0 = 0.0396	253 H (0.978)
						p1 = 0.1954	ω1 = 1	ω1 = 1
						p2a = 0.0064	ω2a = 0.0396	ω2a = 11.6666
						p2b = 0.0016	ω2b = 1	ω2b = 11.6666

Designations #1 and $1 indicate that the foreground branch is the lineage of entire clades or all lineages of the clade, respectively.