Differential strengths of selection on S-RNases from Physalis and Solanum(Solanaceae)

Table 4 Clade model likelihood ratio tests comparing Physalis Clade A (subtree) and its subtending branch to all other S-RNases^a

Model
1) Global dN/dS rate (whole tree)
Shared Parameters	lnL	AIC
dNdS Clade A = dNdS All^a	-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 + All^a = 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 All^a
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 + All^a
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 All^a = 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 All^a 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.

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