Evolutionary dynamic analyses on monocot flavonoid 3′-hydroxylase gene family reveal evidence of plant-environment interaction

Table 2 Natural selection tests on plant F3’Hs. “np” stands for the number of parameters. ln(Likelihood) refers the log value of the likelihood

Model	np	ln(Likelihood)	Estimates of parameters^a (ω = d_N: d_S; P – percentage of site)	Positively selected sites^b
One-ratio
ω_[eudi] = ω_[mono1] = ω_[mono2]	1	−29,872.87	ω_[eudi] = ω_[mono1] = ω_[mono2] = 0.12094	Not Allowed (NA)
Branch-specific models
ω_[eudi] = ω_[mono1] ≠ ω_[mono2]	2	−29,862.42	ω_[eudi] = ω_[mono1] = 0.11857, ω_[mono2] = 0.82808	NA
ω_[eudi] = ω_[mono2] ≠ ω_[mono1]	2	−29,870.85	ω_[eudi] = ω_[mono2] = 0.11990, ω_[mono1] = 0.43835	NA
ω_[eudi] ≠ ω_[mono1] ≠ ω_[mono2]	3	− 29,862.42	ω_[eudi] = 0.11853, ω_[mono2] = 0.78501, ω_[mono1] = 0.12479	NA
Site-specific models
Neutral M1 (2 site classes)	2	−29,413.91	P₀ = 0.87805 (P₁ = 1-P₀ = 0.12195); ω₀ = 0.09334 (ω₁ = 1- ω₀ = 1.0)	NA
Selection M1 (3 site classes	3	−29,413.91	P₀ = 0.87805, P₁ = 0.01421, P₂ = 1-P₀-P₁ = 0.10774; ω₀ = 0.09334 (ω₁ = 1.0), ω₂ = 1.0	NA
Branch-site models
Model A Null (Class I F3’H)	3	−29,408.41	P₀ = 0, P₁ = 0.0, P₂ + P₃ = 1; ω₀ = 0.09152, ω₁ = 1.0, ω₂ = 1.0
Model A (Class I F3’H)	4	−29,408.41	P₀ = 0.00005, P₁ = 0.00001, P₂ + P₃ = 0.99994; ω₀ = 0.09152, ω₁ = 1.0, ω₂ = 1.0	None
Model A Null (Class II F3’H)	3	−29,394.83	P₀ = 0.51238, P₁ = 0.07209, P₂ + P₃ = 0.41553; ω₀ = 0.09046, ω₁ = 1.0, ω₂ = 1.0	NA
Model A (Class II F3’H)	4	−29,392.04	P₀ = 0.68799, P₁ = 0.09608, P₂ + P₃ = 0.21593; ω₀ = 0.09035, ω₁ = 1.0, ω₂ = 8.19737	108R,222A, 265 V, 274 T, 355Q, 447S, 449 L (p < 0.05)

^aIn the site-specific model M1, two site classes were specified: highly conserved sites (ω₀) and neutral sites (ω₁ = 1). For the site-specific model M2, there were three site classes: highly conserved sites (ω₀), neutral sites (ω₁ = 1) and positively selected sites (ω₂). In Model A, four site classes were specified. The first two classes had ω ratios of ω₀ and ω₁ respectively, corresponding to highly conserved sites and neutral sites across all lineages. In the other two site classes, the background lineages had ω₀ or ω₁ while the foreground lineages had ω₂. ^bPositively selected amino acids at P-value ≤0.05 are numbered according to HORVU6Hr1G002400.1, excluding the first 34 amino acids predicted as membrane targeting signal

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