Skip to main content

Table 4 Summary of codeml results

From: The venom-gland transcriptome of the eastern coral snake (Micrurus fulvius) reveals high venom complexity in the intragenomic evolution of venoms

Class n/Model M1: Nearly neutral −lnL M2: Positive selection −lnL M0:ω λ p-value
3FTx 26 p: 0.27 0.73 1,600.40 p: 0.13 0.31 0.56 1,576.50 1.48 47.8 4.17 ×10−11*
  F81+G ω: 0.11 1.00   ω: 0.00 1.00 3.79     
KUN 9 p: 0.32 0.68 965.08 p: 0.31 0.45 0.24 962.16 0.58 5.84 5.39 ×10−2
  GTR+G ω: 0.02 1.00   ω: 0.03 1.00 2.74     
LCN 9 p: 0.86 0.14 315.85 p: 0.84 0.00 0.16 305.84 999.00 20.02 4.49 ×10−5*
  JC+I ω: 1.00 1.00   ω: 0.00 1.00 999.00     
PLA2 52 p: 0.66 0.34 4,761.33 p: 0.49 0.28 0.23 4,359.71 3.32 443.24 0.00*
  SYM+G ω: 0.05 1.00   ω: 0.04 1.00 11.68     
  1. dN/dS ratios are represented by ω; λ represents our test statistic which is negative twice the difference in log likelihoods compared across models to a χ2 distribution with two degrees of freedom; and p corresponds to the proportion of codon sites falling into one of three rate classes which are purifying selection, neutral selection, and positive selection, respectively. The model selected by MrModelTest2.3 [50] for the estimation of the maximum-likelihood phylogeny is given and n corresponds to the number of sequences used in the analysis. Significant p-values are indicated by an asterisk.