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Table 3 Natural selection tests of plant SDH

From: New insights into the evolutionary history of plant sorbitol dehydrogenase

Model

np

l= ln L

Estimates of parameters

Positively selected sites

M0: one-ratio

w(mono)=w (Aer)=w(sdhC1)=w(sdhC2)

1

-30147.4

w(mono)=w(Aer)=w(sdhC1)=w(sdhC2)=0.10492

Not Allowed (NA)

Branch-specific models

w(mono)=w(Aer)=w(sdhC1)≠w(sdhC2) (two ratios)

2

-30141.1

w(mono)=w(Aer)=w(sdhC1)=0.10415, w(sdhC2)=859.33956

NA

w(mono)≠w(Aer)≠w(sdhC1)=w(sdhC2) (three ratios)

3

-30147.3

w(mono)=0.10510, w(Aer)=0.10821, w(sdhC1)=w(sdhC2)=0.06935

NA

w(mono)≠w(Aer)≠w(sdhC1)≠w(sdhC2) (four ratios)

4

-30140.8

w(mono)=0.10428, w(Aer)=0.09731, w(sdhC1)=0.0001, w(sdhC2)=999

NA

w(mono)=w(Aer)=w(sdhC1)≠w(sdhC2) (two ratios with w(sdhC2) fixed to 1)

1

-30141.4

w(mono)=w(Aer)=w(sdhC1)=0.10424 (w(sdhC2)=1)

NA

Site-specific models

M1:Neutral (2 site classes)

2

-29650.0

p0=0.87775 (p1=1-p0=0.12225); w0=0.07628 (w1=1)

NA

M2:Selection (3 site classes)

3

-29650.0

p0=0.87775, p1=0.07499 (p2=1-p0-p1=0.04726); w0=0.07628 (w1=1), w2=1

None

Branch-site models (SDH Class II as foreground lineage)

Model A Null (4 site classes)

3

-29643.2

p0=0.33951, p1=0.04783 (p2+p3=0.61266); w0=0.07544

NA

Model A (4 site classes)

4

-29640.9

p0=0.82864, p1=0.11666 (p2+p3=0.0547), w0=0.07544 (w1=1), w2=132.6226

Sites for foreground lineage: 42H,43F,112G, 113S,116T, 270Q (p > 0.99);

  1. All calculations were implemented using codeml at PAML4.7. Different models were specified according to the software instruction. “np” refers to the number of parameters, “l = (ln L)” refers to the log value of the likelihood. The estimated parameters w and p refer to the Ka/Ks ratio and the percentage of the corresponding site classes respectively. In the one-ratio model M0 and the Branch-specific models, w(mono), w(Aer), w(sdhC1) and w(sdhC2) stand for the w ratios for the monocot, A. coerulea, SDH Class I and SDH Class II branches respectively. In the Site-specific models and the Branch-site models, w0, w1 and w2 represent the w ratios for the specific site classes in respective models (see the Methods section for more details). For the Branch-site models, the SDH Class II branch was specified as the foreground branch. Amino acid site numbering is according to LIDH (Uniprot No: Q1PSI9) without the first 20 amino acids.