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Table 2 Likelihood ratio test of positive selection in toxins

From: Venom gland transcriptomes of two elapid snakes (Bungarus multicinctus and Naja atra) and evolution of toxin genes

gene
group
n Lc S M0 M2a model
ω (p 1 )
M8 model
ω (p 1 )
M1a-M2a
2ΔlnL
M7-M8
2ΔlnL
     model     
orphan II 4 67 0.97 1.06 6.56 (0.102) 6.57(0.102) 4.98 2.54
long chain 4 72 2.43 2.41 8.56 (0.547) 8.55(0.551) 38.98** 19.47**
short chain 4 64 1.09 1.37 5.69 (0.309) 4.21(0.461) 7.77* 5.81
cytotoxin 4 64 1.53 2.66 19.5 (0.505) 19.5(0.505) 26.52** 17.25**
PLA2 (only) 4 125 1.66 0.82 3.16 (0.362) 3.01(0.391) 13.78** 6.91*
PLA2 6 125 2.43 0.95 4.40 (0.300) 4.34(0.306) 30.24** 15.74**
lectins 7 134 3.67 1.25 3.36 (0.341) 3.32(0.352) 27.26** 14.30**
Bbeta 4 61 1.73 0.80 10.8 (0.200) 10.8(0.200) 25.18** 12.73**
Kunitz 3 58 0.87 2.49 19.7 (0.312) 18.3(0.318) 18.98** 11.90**
LAO 5 493 0.60 1.18 3.67 (0.294) 3.67(0.293) 29.13** 14.58**
Metal 8 605 2.52 1.06 4.30 (0.227) 4.23(0.238) 179.63* 100.69**
CRISP 8 221 1.46 1.19 3.69 (0.308) 3.70(0.308) 36.62** 18.39**
NP 6 50 5.17 0.48 10.6 (0.122) 9.76(0.122) 11.91** 5.54
NGF 9 117 0.94 1.41 8.08 (0.151) 7.84(0.154) 39.94** 19.96**
vespryn 7 159 0.30 0.87 3.61 (0.273) 3.61(0.273) 6.66* 3.34
  1. Note: n represents number of sequences in a gene group. L c represents number of codons in the gene after alignment gaps are removed. S is the tree length, measured asqqqq the number of nucleotide substitutions per codon. ω is the estimate of the dN/dS ratio under the M0, M2a or M8 model [19]. The proportions of sites under positive selection (p 1 ) are given under the M2a or M8 model. The 2ΔlnL parameter in the tests of M1a versus M2a or M8 versus M7, indicating positive selection is marked with *. *: significant at 5% level; **: significant at 1% level. PLA2 (only) = Phospholipase A2, Bbeta = B chain of β bungarotoxin, Kunitz = Kunitz-type protease inhibitor, Metal = Metalloproteinase.