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Table 3 Parameter estimates and LRT of M3 vs MD and M1a vs MC in DEF-like genes from Orchidaceae-specific clades 3 and 41.

From: Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses

Model Estimate of parameters L
M3 discrete
k = 2
ω0 = 0.02182, f0 = 0.76519
ω1 = 0.23442, f1 = 0.23481
-3729.728309
M3 discrete
k = 3
ω0 = 0.02182, f0 = 0.09116
ω1 = 0.02182, f1= 0.67403
ω2 = 0.23442, f2 = 0.23481
-3729.728309
Model D
k = 2
ω0 = 0.02175, f0= 0.76410
ω1C4 = 0.24611, ω1C3 = 0.22536, f1= 0.23590
-3729.649245
Model D
k = 3
ω0 = 0.23556, f0 = 0.23301
ω1 = 0.01603, f1 = 0.00000
ω2C4 = 0.02665, ω2C3 = 0.01863, f2 = 0.76699
-3729.138799
Model 1a ω0 = 0.05538, f0 = 0.95421
ω1 = 1.00000, f1 = 0.04579
-3764.994659
Model C ω 0 = 0.21797, f 0 = 0.23733
ω 1 = 1.00000, f 1 = 0.00687
ω 2C4 = 0.02599, ω 2C3 = 0.01796, f 2 = 0.75580
-3728.737317
  1. LRTs of variable ω's among sites
  2. M3(k = 2) vs M3 (k = 3) 2δ = 0 df = 2 P = 1
  3. LRTs of variable ω's among sites and branches
  4. M3 (k = 2) vs MD (k = 2) 2δ = 0.158128 df = 2 P = 0.9240
  5. M3 (k = 3) vs MD (k = 3) 2δ = 1.17902 df = 2 P = 0.5546
  6. M3 (k = 2) vs MD (k = 3) 2δ = 1.17902 df = 4 P = 0.8815
  7. M1a vs MC 2δ = 72.514684 df = 2 P < 0.0001
  8. 1. Bonferroni correction for the 6 tests applied to each pair of clades: 0.008333