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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
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BMC Ecology and Evolution

ISSN: 2730-7182

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