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Table 3 Parameter estimates and likelihood values for branch-site models among sites and lineages of PEBP

From: Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume

Branch-site model Foreground branch Estimate of parameters Model comparison 2*|lnL1 − lnL2| df pLRT Selected sites
Model A FT proportion P = 0.54412, 0.44507, 0.00595, 0.00486 Model A
vs
Model Aa
3.816 1 0.05 19,106
background ω = 0.13622, 1.00000, 0.13622, 1.00000
foreground ω1 = 0.13622, 1.00000, 26.81509, 26.81509
TFL1 proportion P = 0.16400, 0.49980, 0.08306, 0.25314 Model A
vs
Model Aa
10.381 1 0.0013** 11,18
background ω = 0.14566, 1.00000, 0.14566, 1.00000
foreground ω = 0.14566, 1.00000, 999.00000, 999.00000
CEN proportion P = 0.23775, 0.76225, 0.00000, 0.00000 Model A
vs
Model Aa
2E-06 1 P > 0.05
background ω = 0.14634, 1.00000, 0.14634, 1.00000
foreground ω = 0.14634, 1.00000, 1.00000, 1.00000
BFT proportion P = 0.20425, 0.66599, 0.03046, 0.09930 Model A
vs
Model Aa
2.878 1 P > 0.05
background ω = 0.12885, 1.00000, 0.12885, 1.00000
foreground ω = 0.12885, 1.00000, 7.38132, 7.38132
(FT, TFL1, CEN, BFT) proportion P = 0.23291, 0.72041, 0.01140, 0.03528 Model A
vs
Model Aa
0.521 1 P > 0.05
background ω = 0.15263, 1.00000, 0.15263, 1.00000
foreground ω = 0.15263, 1.00000, 10.76576, 10.76576
  1. Significant chi-squared comparisons are indicated with * (pLRT < 0.05), ** (pLRT < 0.01), and *** (pLRT < 0.001). Positively selected sites in the foreground lineages were detected by Bayes Empirical Bayes analysis with a probability ≥ 0.7