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

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

Gene Symbol	Complex	Median Amino acid Substitution Rate differences			PAML Branch Model	PAML Branch-site Model	MEME	TreeSAAP	Sites shared between methods
Gene Symbol	Complex	Hymenoptera - Coleoptera	Hymenoptera - Lepidoptera	Hymenoptera - Diptera	PAML Branch Model	PAML Branch-site Model	MEME	TreeSAAP	Sites shared between methods
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

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

ISSN: 2730-7182