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Table 2 Parameter estimates and LRT of M3 vs. MD and M1a vs. MC in DEF-like genes from Orchidaceae-specific clades 1 and 21.

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 = 0.04544, f0 = 0.63768
ω1 = 0.42599, f1 = 0.36232
-3516.356560
M3 discrete
k = 3
ω0 = 0.04544, f0 = 0.63768
ω1 = 0.42599, f1 = 0.36232
ω2 = 38.73814, f2 = 0.00000
-3516.356560
Model D
k = 2
ω0 = 0.04102, f0 = 0.60628
ω1C1 = 0.26333, ω1C2 = 0.59513, f1= 0.39372
-3508.313165
Model D
k = 3
ω 0 = 1.28841, f 0 = 0.02038
ω 1 = 0.03309, f 1 = 0.55669
ω 2C1 = 0.21766, ω 2C2 = 0.50952, f 2 = 0.42294
-3506.393271
Model 1a ω0= 0.09066, f0 = 0.75319
ω1 = 1.00000, f1 = 0.24681
-3540.435701
Model C ω 0 = 0.03251, f 0 = 0.55437
ω 1 = 1.00000, f 1 = 0.02680
ω 2C1 = 0.21104, ω 2C2 = 0.50104, f 2 = 0.41883
-3506.594944
  1. LRTs of variable ω's among sites
  2. M3(k = 2) vs M3 (k = 3) 2δ = 3.617532 df = 2 P = 0.1639
  3. LRTs of variable ω's among sites and branches
  4. M3 (k = 2) vs MD (k = 2) 2δ = 16.08679 df = 2 P = 0.0003
  5. M3 (k = 3) vs MD (k = 3) 2δ = 16.309046 df = 2 P = 0.0003
  6. M3 (k = 2) vs MD (k = 3) 2δ = 19.926578 df = 4 P = 0.0005
  7. M1a vs MC 2δ = 67.681514 df = 2 P < 0.0001
  8. 1. Bonferroni correction for the 5 tests applied to each pair of clades: 0.008333