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Table 2 Results of PAML analysis

From: Selection on the mitochondrial ATP synthase 6 and the NADH dehydrogenase 2 genes in hares (Lepus capensis L., 1758) from a steep ecological gradient in North Africa

.Model

ln L

ATP6

ND2

ATP6-ND2

 

ND2

ATP6

ATP6-ND2

Parameters

Sites a

p (ΔLRT)

Parameters

Sites a

p (ΔLRT)

Parameters

Sites a

p (ΔLRT)

M0 (one ratio)

−1661.369

−1268.911

−4331.728

ω = 0.032

  

ω = 0.033

  

ω = 0.034

  

M1a (nearly neutral)

−1581.564

−1229.647

−4130.457

p0 = 0.983,

p1 = 0.017

 

<0.001

(M0)

p0 = 0.965,

p1 = 0.035

 

<0.001

(M0)

p0 = 0.975,

p1 = 0.024

 

<0.001

(M0)

M2a (positive selection)

−1578.949

−1219.011

−4107.380

p0 = 0.984,

p1 = 0.009,

p2 = 0.007,

ω2 = 11.336

72

<0.001

(M1a)

p0 = 0.965,

p1 = 0.009,

p2 = 0.026,

ω2 = 2.146

16, 22, 25

>0.05

(M1a)

p0 = 0.976,

p1 = 0.013,

p2 = 0.012,

ω2 = 5.092

72, 16, 22

<0.001

(M1a)

M3 (discrete)

−1579.601

−1218.993

−4104.053

p0 = 0.984,

p1 = 0.009,

p2 = 0.007,

ω0 = 0.000,

ω1 = 0.89,

ω2 = 11.402

 

<0.001

(M0)

p0 = 0.891,

p1 = 0.075,

p2 = 0.035,

ω0 = 0.000,

ω1 = 0.000,

ω2 = 1.708

 

<0.001

(M0)

p0 = 0.932,

p1 = 0.056,

p2 = 0.012,

ω0 = 0.000,

ω1 = 0.000,

ω2 = 0.356

 

<0.001

(M0)

M7 (beta)

−1586.014

−1255.405

−4146.712

p = 0.005,

q = 0.016

  

p = 0.005,

q = 0.050

  

p = 0.005,

q = 0.039

  

M8 (beta and omega)

−1579.100

−1230.106

−4149.305

p0 = 0.985,

p1 = 0.015,

p = 0.005,

q = 61.89,

ω = 3.406

72

<0.001

(M7)

p0 = 0.965,

p1 = 0.035,

p = 0.005,

q = 99.000,

ω = 1.708

16, 22, 25

<0.001

(M7)

p0 = 0.976,

p1 = 0.024,

p = 0.005,

q = 61.397,

ω = 2.392

72, 16, 22, 25

>0.05

(M7)

  1. Model = name of the model; ln L = the natural logarithm of the likelihood obtained for every model; Parameters = estimates of ω values and proportion of codons that belong to each ω class; Sites: position in the corresponding gene of each site under positive selection; p(ΔLRT) = P-values of the log likelihood ratio test for model comparisons, null models are shown in brackets.
  2. a: BEB: P(ω > 1) > 0.50; P(ω > 1) > 0.95 is shown in bold