GENETICS/2019/301974

Supplementary Figure 1: Phylogeny of Anguilliformes used for the detection of positive selection. Deep-sea species were marked in red.

Supplementary Figure 2: Phylogeny of Beryciformes and Stephanoberyciformes used for detection of positive selection. Deep-sea species were marked in red.

Supplementary Figure 3: Phylogeny of Ophidiiformes used for detection of positive selection. Deep-sea species were marked in red.

Supplementary Figure 4: Phylogeny of Osmeriformes and Stomiiformes used for detection of positive selection. Deep-sea species were marked in red.

Supplementary Figure 5: Phylogeny of Perciformes used for detection of positive selection. Deep-sea species were marked in red.

Supplementary Figure 6: Phylogeny of Carangimorpha used for detection of positive selection. Deep-sea species were marked in red.

Supplementary Figure 7: Phylogeny of Scombriformes used for detection of positive selection. Deep-sea species were marked in red.

Supplementary Figure 8: Phylogeny of Pleuronectiformes used for detection of positive selection. Deep-sea species were marked in red.

Supplementary Figure 9: Phylogeny of Scorpaeniformes used for detection of positive selection. Deep-sea species were marked in red.

Supplementary Figure 10: Three-dimensional representation of convergent/parallel amino acid sites in deep-sea fishes in the NADH-ubiquinone oxidoreductase chain 1, 2, 3, 4, 4L, 5 and 6. Convergent/parallel amino acid sites within NADH subunits are mapped to the bovine ND structure [PDB:5LDX]. Parallel amino acid sites S250A and L251F occur in ND1; Parallel amino acid sites F21L, L154I, T229S and T310I and convergent amino acid sites A/M261I and T/P322I occur in ND2. ND3 has one parallel amino acid site V94I. Parallel amino acid sites A20T, I96L, G111S and I442V occur in ND4 and parallel amino acid site L94M is in ND6. Red indicates mutations located in intracellular domain, TM subunit sites are in black, and blue shows extracellular domain sites. MM: mitochondrial matrix; IM: intermembrane space.

Supplementary Figure 11: Three-dimensional representation of parallel amino acid sites in deep-sea fishes in cytochrome c oxidase subunits I, II and III. Ten parallel amino acid sites map to the bovine COX structure [PDB:1V54]. Sites M92I, I97M, V155I, V416I and V460I occur in CoxI, sites S47T, I97V, M100I and S155T are in CoxII, and site T119A is in CoxIII. Mutation sites located in the intracellular domain are shown in red while TM subunit sites are shown in black. MM: mitochondria matrix; IM: intermembrane space.

Supplementary Table 1: The depth-range of 115 species of 1,042 bony fishes.

Supplementary Table 2: Selection pressure analyses for the 13 genes in Anguilliformes.

Supplementary Table 3: Selection pressure analyses for the 13 genes in Beryciformes and Stephanoberyciformes.

Supplementary Table 4: Selection pressure analyses for the 13 genes in Ophidiiformes.

Supplementary Table 5: Selection pressure analyses for the 13 genes in Osmeriformes and Stomiiformes.

Supplementary Table 6: Selection pressure analyses for the 13 genes in Perciformes.

Supplementary Table 7: Selection pressure analyses for the 13 genes in Carangimorpha.

Supplementary Table 8: Selection pressure analyses for the 13 genes in Scombriformes.

Supplementary Table 9: Selection pressure analyses for the 13 genes in Pleuronectiformes.

Supplementary Table 10: Selection pressure analyses for the 13 genes in Scorpaeniformes.