GENETICS/2019/301974

<b>Supplementary Figure 1: Phylogeny of Anguilliformes used for the detection of positive selection. Deep-sea species were marked in red. </b><b>Supplementary Figure 2: Phylogeny of Beryciformes and Stephanoberyciformes used for detection of positive selection. Deep-sea species were marked in red. </b><b>Supplementary Figure 3: Phylogeny of Ophidiiformes used for detection of positive selection. Deep-sea species were marked in red.</b><b>Supplementary Figure 4: Phylogeny of Osmeriformes and Stomiiformes used for detection of positive selection. Deep-sea species were marked in red.</b><b>Supplementary Figure 5: Phylogeny of Perciformes used for detection of positive selection. Deep-sea species were marked in red.</b><b>Supplementary Figure 6: Phylogeny of Carangimorpha used for detection of positive selection. Deep-sea species were marked in red.</b><b>Supplementary Figure 7: Phylogeny of Scombriformes used for detection of positive selection. Deep-sea species were marked in red.</b><b>Supplementary Figure 8: Phylogeny of Pleuronectiformes used for detection of positive selection. Deep-sea species were marked in red.</b><b>Supplementary Figure 9: Phylogeny of Scorpaeniformes used for detection of positive selection. Deep-sea species were marked in red.</b><b>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. </b><b><br></b><b>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. </b><b><br></b><b>Supplementary Table 1: The depth-range of 115 species of 1,042 bony fishes.</b><b>Supplementary Table 2: Selection pressure analyses for the 13 genes in Anguilliformes.</b><b>Supplementary Table 3: Selection pressure analyses for the 13 genes in Beryciformes and Stephanoberyciformes.</b><b>Supplementary Table 4: Selection pressure analyses for the 13 genes in Ophidiiformes.</b><b>Supplementary Table 5: Selection pressure analyses for the 13 genes in Osmeriformes and Stomiiformes.</b><b>Supplementary Table 6: Selection pressure analyses for the 13 genes in Perciformes.</b><b>Supplementary Table 7: Selection pressure analyses for the 13 genes in Carangimorpha.</b><b>Supplementary Table 8: Selection pressure analyses for the 13 genes in Scombriformes.</b><b>Supplementary Table 9: Selection pressure analyses for the 13 genes in Pleuronectiformes.</b><b>Supplementary Table 10: Selection pressure analyses for the 13 genes in Scorpaeniformes.</b>

补充图1：用于正选择检测的鳗鲡目（Anguilliformes）系统发育树，深海物种以红色标注。
补充图2：用于正选择检测的金眼鲷目（Beryciformes）与刺金眼鲷目（Stephanoberyciformes）系统发育树，深海物种以红色标注。
补充图3：用于正选择检测的鼬鳚目（Ophidiiformes）系统发育树，深海物种以红色标注。
补充图4：用于正选择检测的胡瓜鱼目（Osmeriformes）与巨口鱼目（Stomiiformes）系统发育树，深海物种以红色标注。
补充图5：用于正选择检测的鲈形目（Perciformes）系统发育树，深海物种以红色标注。
补充图6：用于正选择检测的鲹形亚目（Carangimorpha）系统发育树，深海物种以红色标注。
补充图7：用于正选择检测的鲭形目（Scombriformes）系统发育树，深海物种以红色标注。
补充图8：用于正选择检测的鲽形目（Pleuronectiformes）系统发育树，深海物种以红色标注。
补充图9：用于正选择检测的鲉形目（Scorpaeniformes）系统发育树，深海物种以红色标注。
补充图10：深海鱼类NADH泛醌氧化还原酶链（NADH-ubiquinone oxidoreductase chain）1、2、3、4、4L、5及6的趋同/平行氨基酸位点三维可视化展示。NADH亚基内的趋同/平行氨基酸位点映射至牛源ND结构[PDB:5LDX]。ND1中存在平行氨基酸位点S250A与L251F；ND2中存在平行氨基酸位点F21L、L154I、T229S、T310I以及趋同氨基酸位点A/M261I与T/P322I。ND3存在1个平行氨基酸位点V94I。ND4中存在平行氨基酸位点A20T、I96L、G111S与I442V，ND6中存在平行氨基酸位点L94M。红色标注位于细胞内结构域的突变位点，黑色标注跨膜（TM）亚基位点，蓝色标注细胞外结构域位点。MM：线粒体基质；IM：膜间隙。
补充图11：深海鱼类细胞色素c氧化酶亚基I、II及III的平行氨基酸位点三维可视化展示。10个平行氨基酸位点映射至牛源COX结构[PDB:1V54]。CoxI中存在位点M92I、I97M、V155I、V416I与V460I；CoxII中存在位点S47T、I97V、M100I与S155T；CoxIII中存在位点T119A。细胞内结构域的突变位点以红色标注，跨膜（TM）亚基位点以黑色标注。MM：线粒体基质；IM：膜间隙。
补充表1：1042种硬骨鱼中115个物种的栖息深度范围。
补充表2：鳗鲡目13个基因的选择压力分析。
补充表3：金眼鲷目与刺金眼鲷目13个基因的选择压力分析。
补充表4：鼬鳚目13个基因的选择压力分析。
补充表5：胡瓜鱼目与巨口鱼目13个基因的选择压力分析。
补充表6：鲈形目13个基因的选择压力分析。
补充表7：鲹形亚目13个基因的选择压力分析。
补充表8：鲭形目13个基因的选择压力分析。
补充表9：鲽形目13个基因的选择压力分析。
补充表10：鲉形目13个基因的选择压力分析。