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Table 3 Gene symbol, differences of substitution rate and selection test of each gene

From: The molecular evolutionary dynamics of oxidative phosphorylation (OXPHOS) genes in Hymenoptera

Gene Symbol Complex Median Amino acid Substitution
Rate differences
PAML
Branch Model
PAML Branch-site Model MEME TreeSAAP Sites shared between methods
Hymenoptera
-
Coleoptera
Hymenoptera
-
Lepidoptera
Hymenoptera
-
Diptera
mt:ND1 1 −0.37 −0.01 0.14   0 1 0 0
mt:ND2 1 1.91 2.34 2.28   0 2 2 0
mt:ND3 1 −0.13 −0.18 0.25 Lower 0 0 1 0
mt:ND4 1 0.76 0.71 0.81 Higher 0 0 0 0
mt:ND4L 1 1.09 0.59 1.15   0 1 0 0
mt:ND5 1 0.13 0.30 0.33 Lower 0 1 4 0
mt:ND6 1 1.87 3.33 3.81   0 0 0 0
mt:Cyt-b 3 0.60 0.58 0.51   0 1 3 0
mt:CoI 4 0.27 0.31 0.21 Higher 0 1 0 0
mt:CoII 4 0.12 0.22 0.05   0 0 0 0
mt:CoIII 4 −0.60 −0.07 −0.37 Lower 0 0 1 0
mt:ATP6 5 0.16 0.12 0.30   0 2 1 0
mt:ATP8 5 2.38 2.14 2.37   0 0 0 0
ND-42 1 0.97 1.31 1.10 Higher 14 2 14 5
ND-39 1 0.15 0.08 0.31 Higher 11 2 2 2
ND-24 1 0.52 0.24 0.35 Higher 12 0 3 1
ND-75 1 0.14 0.01 0.06   4 1 0 0
ND-B22 1 0.35 0.22 0.74 Higher 0 0 2 0
ND-SGDH 1 0.24 0.07 0.14 Higher 2 1 0 1
ND-B17.2 1 0.33 0.68 0.12 Higher 4 0 0 0
ND-MLRQ 1 0.38 0.78 0.37 Higher 0 1 0 0
ND-23 1 0.12 0.06 0.10 Higher 0 0 0 0
ND-B12 1 −0.13 −0.43 0.00 Higher 0 0 0 0
ND-B16.6 1 0.80 0.55 0.58 Higher 5 1 1 0
ND-B14.5B 1 1.12 2.09 1.33   0 0 0 0
ND-B18 1 0.61 0.17 1.20 Higher 0 0 1 0
ND-PDSW 1 0.48 0.32 0.64 Higher 1 0 0 0
ND-18 1 0.68 0.70 0.66 Higher 0 0 6 0
ND-30 1 0.20 0.06 0.05 Higher 0 0 0 0
UQCR-Q 3 0.19 0.36 0.48 Higher 0 1 1 1
COX5B 4 −0.20 −0.18 −0.08   2 0 0 0
ATPsynF 5 0.45 0.42 0.49 Higher 0 0 0 0
ATPsynγ 5 0.12 0.11 0.30   0 2 0 0
blw 5 −0.04 −0.04 −0.04   0 2 0 0
ATPsynG 5 1.14 0.12 0.90 Higher 0 0 0 0
ATPsynC 5 0.02 −0.02 0.02   0 0 0 0
  1. Gene symbol is the name of the gene in Drosophila melanogaster. Complex indicates the location of the gene product in the OXPHOS complex. The median of amino acid substitution rate differences is the differences between the median substitution rate of Hymenoptera compared to the other three orders. Positive or negative values indicate the amino acid substitution rate of a gene is higher or lower in Hymenoptera than in the other insect orders. For PAML branch model, “Higher” or “Lower” means the gene has a significant higher or lower dN/dS ratio in Hymenoptera than in the other three orders based on PAML branch model test. For PAML branch-site model and MEME, the number indicates the number of codons under positive selection with dN/dS > 1. For TreeSAAP, the number indicates the number of amino acids under positive selection. The last column indicates the number of codon sites or amino acids found by at least two methods in PAML branch-site model, MEME, or TreeSAAP