Table 4

Clade model likelihood ratio tests comparing Physalis Clade A (subtree) and its subtending branch to all other S-RNasesa

Model

1) Global dN/dS rate (whole tree)

Shared Parameters

lnL

AIC


dNdS Clade A = dNdS Alla

-17167.25

34716.51

Global dN/dS = 0.90; CI = (0.87, 0.94)

2) Separating Branch Versus Two Clades

Shared Parameters

lnL

AIC


dNdSdNdS Shared Clades A + Alla = 0.90;

CI = (0.86, 0.94)

-17166.63

34717.27

Phys dNdS Branch A = 5.18; CI = (1.64, 10.49)

LRT p-value vs the single rate model = 0.266

3) Clade A + Branch vs Alla

Shared Parameters

lnL

AIC


dNdS Branch A = Clade A = 2.19; CI = (2.03, 2.36)

-17118.27

34620.54*

dNdS Clade S = 0.70; CI = (0.73, 0.77)

LRT p-value vs the single rate model < 0.001

4) Clade A (subtree) vs Branch + Alla

Shared Parameters

lnL

AIC


Phys dNdS Clade A = 2.04; CI = (2.20, 2.37)

-17118.80

34621.60

Phys dNdS Branch A = dNdS; Clade Alla = 0.70;

CI = (0.73, 0.77)

LRT p-value vs the single rate model < 0.001

5) Clade A, Solanum, and Branch

Shared Parameters

lnL

AIC


Phys dNdS Clade A = 2.04; CI = (2.20, 2.37)

-17118.25

34622.51

dNdS Clade Alla 0.70; CI = (0.73, 0.77)

Phys dNdS Branch A = 2.96; CI = (0.83, 6.17)

LRT p-value vs the single rate model < 0.001


a) Background branches include all Solanum alleles and Physalis alleles outside of sub-Clade A

Alternative models (2-5) were tested using likelihood ratio tests (LRTs) against the null model 1 where dN and dS rates are shared among all branches on the phylogeny. Significance of p ≤ 0.05 was determined using χ2 with degrees of freedom (DF) equal to the number different parameters between models.

*Model 3 showing a common dN/dS for Clade A AND the subtending branch has the best fit AIC score sharing a distinct dN/dS.

Paape and Kohn BMC Evolutionary Biology 2011 11:243   doi:10.1186/1471-2148-11-243

Open Data