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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

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

Model np ln(Likelihood) Estimates of parametersa
(ω = dN: dS; P – percentage of site)
Positively selected sitesb
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)
  1. 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