Table 2

Branches or group of branches tested by branch selection models
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

*Model comparisons were performed using Likelihood Ratio Test (LRT) between nested models.

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.

Serbielle et al.

Serbielle et al. BMC Evolutionary Biology 2012 12:253   doi:10.1186/1471-2148-12-253

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