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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