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Table 2 Branches or group of branches tested by branch selection models

From: Evolutionary mechanisms driving the evolution of a large polydnavirus gene family coding for protein tyrosine phosphatases

Hypothesis Test MA/MAnull Likelihood values χ2 value df LRT p-value
Clade 1       
Clade Cα MA 7035.70 27.77 1 1.36E-07 <0.001
  MAnull 7049.58     
Branch Cα MA 7058.20 0 1 1 NS
  MAnull 7058.20     
Branch I MA 7058.08 0 1 1 NS
  MAnull 7058.08     
Clade Z MA 7050.24 5.25 1 0.022 <0.05
  MAnull 7052.87     
Branch IZ MA 7055.64 3.58 1 0.049 <0.05
  MAnull 7057.58     
Clade 2       
Clade ε MA 2591.88 0 1 1 NS
  MAnull 2593.91     
Branch ε MA 2601.60 0 1 1 NS
  MAnull 2601.60     
Clade RΔ MA 2026.57 7.45 1 0.006 <0.01
  MAnull 2030.29     
Branch RΔ MA 2601.78 0.03 1 0.86 NS
  MAnull 2601.80     
Clade 3       
Clade S MA 5205.54 3.15 1 0.076 NS
  MAnull 5207.11     
Branch H MA 5211.87 0.05 1 0.816 NS
  MAnull 5211.90     
Branch HS MA 5211.93 0 1 1 NS
  MAnull 5211.93     
Branch M MA 5211.93 0 1 1 NS
  MAnull 5211.93     
Clade EX MA 5193.81 13.47 1 2.42E-04 <0.001
  MAnull 5200.55     
Clade 4       
Branch Q MA 6960.59 0 1 1 NS
  MAnull 6960.59     
Branch K MA 6956.33 0 1 1 NS
  MAnull 6956.33     
Branch P MA 6958.79 5.14 1 0.023 <0.05
  MAnull 6961.36     
Clade Y MA 6960.24 2.75 1 0.097 NS
  MAnull 6961.61     
  1. *Model comparisons were performed using Likelihood Ratio Test (LRT) between nested models.
  2. Model MA defines four classes of sites, where the two last classes have ω > 1 on the lineage of interest and ω < 1 for the rest of branches. This model is compared with MAnull which imposes ω=1 for the latter two classes.