Mori Satoko, Matsunami Masatoshi
Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University.
Graduate School of Medicine, University of the Ryukyus.
Genes Genet Syst. 2018 Sep 15;93(2):65-73. doi: 10.1266/ggs.17-00015. Epub 2018 Apr 10.
Acceleration of the amino acid substitution rate is a good indicator of positive selection in adaptive evolutionary changes of functional genes. Genomic information about mammals has become readily available in recent years, as many researchers have attempted to clarify the adaptive evolution of mammals by examining evolutionary rate change based on multiple loci. The order Cetartiodactyla (Artiodactyla and Cetacea) is one of the most diverse orders of mammals. Species in this order are found throughout all continents and seas, except Antarctica, and they exhibit wide variation in morphology and habitat. Here, we focused on the metabolism-related genes of mitochondrial DNA (mtDNA) in species of the order Cetartiodactyla using 191 mtDNA sequences available in databases. Based on comparisons of the dN/dS ratio (ω) in 12 protein-coding genes, ATP8 was shown to have a higher ω value (ω = 0.247) throughout Cetartiodactyla than the other 11 genes (ω < 0.05). In a branch-site analysis of ATP8 sequences, a markedly higher ω value of 0.801 was observed in the ancestral lineage of the clade of Cetacea, which is indicative of adaptive evolution. Through efforts to detect positively selected amino acids, codon positions 52 and 54 of ATP8 were shown to have experienced positive selective pressure during the course of evolution; multiple substitutions have occurred at these sites throughout the cetacean lineage. At position 52, glutamic acid was replaced with asparagine, and, at position 54, lysine was replaced with non-charged amino acids. These sites are conserved in most Artiodactyla. These results imply that the ancestor of cetaceans underwent accelerated amino acid changes in ATP8 and replacements at codons 52 and 54, which adjusted metabolism to adapt to the marine environment.
氨基酸替代率的加速是功能基因适应性进化变化中正向选择的良好指标。近年来，随着许多研究人员试图通过基于多个基因座研究进化速率变化来阐明哺乳动物的适应性进化，有关哺乳动物的基因组信息已变得 readily available。鲸偶蹄目（偶蹄目和鲸目）是哺乳动物中最多样化的目之一。该目中的物种遍布除南极洲以外的所有大陆和海洋，并且它们在形态和栖息地方面表现出广泛的差异。在这里，我们使用数据库中可用的191个线粒体DNA（mtDNA）序列，重点研究了鲸偶蹄目物种中线粒体DNA（mtDNA）的代谢相关基因。基于对12个蛋白质编码基因的dN/dS比率（ω）的比较，结果表明，在整个鲸偶蹄目中，ATP8的ω值（ω = 0.247）高于其他11个基因（ω < 0.05）。在对ATP8序列的分支位点分析中，在鲸目进化枝的祖先谱系中观察到明显更高的ω值0.801，这表明存在适应性进化。通过努力检测正选择的氨基酸，结果表明ATP8的第52和54密码子位置在进化过程中经历了正选择压力；在整个鲸类谱系的这些位点发生了多次替代。在第52位，谷氨酸被天冬酰胺取代，在第54位，赖氨酸被不带电荷的氨基酸取代。这些位点在大多数偶蹄目中是保守的。这些结果意味着鲸类的祖先在ATP8中经历了加速的氨基酸变化以及第52和54密码子的替代，从而调整了新陈代谢以适应海洋环境。
