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. 2015 May 21;3:e976. doi: 10.7717/peerj.976

Table 2. Codon-based maximum likelihood and Bayesian analysis for positively selected sites in exon 4 and exons 1, 2, and 3 combined.

Statistics with significance level p < 0.05, posterior probability >0.9 and Bayes Factor >50 are boldfaced. Consensus column summarizes methods which found the codon positively selected with significance level p < 0.2. Analysis was made using the Datamonkey server www.datamonkey.org (Delport et al., 2010; Pond, Frost & Muse, 2005).

Codon SLAC SLAC FEL FEL REL REL MEME MEME FUBAR FUBAR Consensus
dNdS p-value dNdS p-value dNdS Bayes F ω + p-value dNdS Post.Pr. S F R M Fu
Positively selected sites in exon 4
24 3.97 0.63 9.15 0.20 1.60 2.00 >100 0.13 0.40 0.83 + +
28 4.79 0.49 10.80 0.15 1.63 2.14 >100 0.19 0.40 0.83 + +
30 6.63 0.46 9.98 0.31 1.46 1.41 >100 0.02 0.41 0.87 +
45 −3.49 0.92 −12.31 0.35 −0.45 0.01 >100 0.04 0.51 0.32 +
47 4.92 0.46 7.18 0.21 1.61 2.21 >100 0.046 0.37 0.83 +
48 4.61 0.52 8.18 0.30 1.46 1.58 >100 0.13 0.30 0.81 +
49 5.50 0.41 13.24 0.12 1.65 2.23 >100 0.16 0.55 0.86 + +
51 6.90 0.37 12.22 0.10 1.71 2.36 >100 0.11 0.84 0.94 + + +
55 4.79 0.48 10.78 0.13 1.68 2.45 >100 0.03 0.42 0.84 + +
57 7.27 0.32 12.63 0.11 1.68 2.21 >100 0.14 0.74 0.92 + + +
59 4.94 0.45 8.24 0.19 1.63 2.23 >100 0.22 0.29 0.81 +
62 0.43 0.72 4.43 0.72 −0.01 0.02 >100 0.01 0.40 0.66 +
Positively selected sites in exons 1, 2, and 3 combined
42 10.51 0.38 240.59 0.11 7.67 17.23 >100 0.14 4.37 0.97 + + +
89 8.90 0.61 189.86 0.29 7.25 10.16 >100 0.30 3.43 0.93 +