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Table 3 Parameter estimates under different site models and statistics of the likelihood ratio (2Δl) hypothesis tests in PAML

From: Adaptive evolution in the toxicity of a spider’s venom enzymes

Model Estimates of parameters - l LRT (pairs) df 2Δl P Positively selected sites
BEB (%)
M0: one ratio ω = 0.25443 28843.35 M0/M3 4 1666.50 1.11 x 10−359 N.A.
M3: discrete ω0 = 0.03317;
ω1 = 0.22423;
ω2 = 0.62748;
p0 = 0.26344;
p1 = 0.47946;
p2 = 0.2571
28010.09      None
M1a: neutral ω0 = 0.18188;
ω1 = 1.00000;
p0 = 0.73346;
p1 = 0.26654
28338.75 M1/M2 2 14.56 6.87 x 10−04 NA
M2a: selection ω0 = 0.184690;
ω1 = 1.000000;
ω2 = 1.879270;
p0 = 0.72964;
p1 = 0.25444;
p2 = 0.01592
28331.46      58I (99.1 %);
204L (94.0 %);
208A (75.4 %);
236S (80.0 %)
M7: beta p = 0.70821;
q = 1.65979
27977.46 M7/M8 2 35.54 1.92 x 10−08 NA
M8: beta & w p0 = 0.96464;
p = 0.85258;
q = 2.56188;
p1 = 0.03536;
ω = 1.262270
27959.69      18K (67.8 %);
38K (53.0 %),
58I (99.9 %);
151K (52.3 %)
204L (98.2 %);
208A (92.3 %);
236S (95.5 %)
Model A (null) p0 = 0.52400;
p1 = 0.18218;
p2a = 0.21802;
p2b = 0.07580;
ω0 = 0.16817;
ω1 = 1.00000;
background: ω2a = 0.16817;
ω2b = 1.00000;
foreground: ω2a = 1.00000;
ω2b = 1.00000
28279.91 Null/
Alt.
1 13.89 1.94 x 10−04 21P (95.7 %);
22T (100.0 %);
40S (99.0 %);
53F (98.7 %);
84G (97.2 %);
144G (99.8 %);
179T (98.5 %);
201F (98.2 %)
205G (99.8 %);
214I (95.3 %);
231S (100.0 %);
239R (95.9 %);
240K (97.2 %);
243E (100.0 %);
253Y (99.6 %);
265G (99.8 %)
Model A
(alternative)
p0 = 0.58498;
p1 = 0.20363;
p2a = 0.15681;
p2b = 0.05458;
ω0 = 0.17009;
ω1 = 1.00000;
background:
ω2a = 0.17009;
ω2b = 1.00000;
foreground:
ω2a = 1.97553;
ω2b = 1.97553
28272.97      NA
  1. l = lnL = log likelihood; LRT: likelihood ratio test; df: degrees of freedom; 2Δl: twice the log-likelihood difference of the models compared. P: p-value; BEB: Bayes Empirical Bayes (BEB) probabilities