The Complete Mitochondrial Genomes of Three Sphenomorphinae Species (Squamata: Scincidae) and the Selective Pressure Analysis on Mitochondrial Genomes of Limbless <i>Isopachys gyldenstolpei</i>
In order to adapt to diverse habitats, organisms often evolve corresponding adaptive mechanisms to cope with their survival needs. The species-rich family of Scincidae contains both limbed and limbless species, which differ fundamentally in their locomotor demands, such as relying on the movement of...
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MDPI AG
2022-08-01
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| author | Lian Wu Yao Tong Sam Pedro Galilee Ayivi Kenneth B. Storey Jia-Yong Zhang Dan-Na Yu |
| author_facet | Lian Wu Yao Tong Sam Pedro Galilee Ayivi Kenneth B. Storey Jia-Yong Zhang Dan-Na Yu |
| author_sort | Lian Wu |
| collection | DOAJ |
| description | In order to adapt to diverse habitats, organisms often evolve corresponding adaptive mechanisms to cope with their survival needs. The species-rich family of Scincidae contains both limbed and limbless species, which differ fundamentally in their locomotor demands, such as relying on the movement of limbs or only body swing to move. Locomotion requires energy, and different types of locomotion have their own energy requirements. Mitochondria are the energy factories of living things, which provide a lot of energy for various physiological activities of organisms. Therefore, mitochondrial genomes could be tools to explore whether the limb loss of skinks are selected by adaptive evolution. <i>Isopachys gyldenstolpei</i> is a typical limbless skink. Here, we report the complete mitochondrial genomes of <i>I</i>. <i>gyldenstolpei</i>, <i>Sphenomorphus indicus,</i> and <i>Tropidophorus hainanus</i>. The latter two species were included as limbed comparator species to the limbless <i>I. gyldenstolpei</i>. The results showed that the full lengths of the mitochondrial genomes of <i>I</i>. <i>gyldenstolpei</i>, <i>S</i>. <i>indicus</i>, and <i>T. hainanus</i> were 17,210, 16,944, and 17,001 bp, respectively. Three mitochondrial genomes have typical circular double-stranded structures similar to other reptiles, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and the control region. Three mitochondrial genomes obtained in this study were combined with fifteen mitochondrially complete genomes of Scincidae in the NCBI database; the phylogenetic relationship between limbless <i>I</i>. <i>gyldenstolpei</i> and limbed skinks (<i>S</i>. <i>indicus</i> and <i>T</i>. <i>hainanus</i>) is discussed. Through BI and ML trees, Sphenomorphinae and Mabuyinae were monophyletic, while the paraphyly of Scincinae was also recovered. The limbless skink <i>I</i>. <i>gyldenstolpei</i> is closer to the species of <i>Tropidophorus,</i> which has formed a sister group with (<i>T</i>. <i>hainanus + T</i>. <i>hangman)</i>. In the mitochondrial genome adaptations between limbless <i>I. gyldenstolpei</i> and limbed skinks, one positively selected site was found in the branch-site model analysis, which was located in ND2 (at position 28, BEB value = 0.907). Through analyzing the protein structure and function of the selected site, we found it was distributed in mitochondrial protein complex I. Positive selection of some mitochondrial genes in limbless skinks may be related to the requirement of energy to fit in their locomotion. Further research is still needed to confirm this conclusion though. |
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| spelling | doaj.art-e659eb2504af40e78a8a7ae0ef0aaf502023-12-03T13:12:56ZengMDPI AGAnimals2076-26152022-08-011216201510.3390/ani12162015The Complete Mitochondrial Genomes of Three Sphenomorphinae Species (Squamata: Scincidae) and the Selective Pressure Analysis on Mitochondrial Genomes of Limbless <i>Isopachys gyldenstolpei</i>Lian Wu0Yao Tong1Sam Pedro Galilee Ayivi2Kenneth B. Storey3Jia-Yong Zhang4Dan-Na Yu5College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, ChinaCollege of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, ChinaCollege of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, ChinaDepartment of Biology, Carleton University, Ottawa, ON K1S5B6, CanadaCollege of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, ChinaCollege of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, ChinaIn order to adapt to diverse habitats, organisms often evolve corresponding adaptive mechanisms to cope with their survival needs. The species-rich family of Scincidae contains both limbed and limbless species, which differ fundamentally in their locomotor demands, such as relying on the movement of limbs or only body swing to move. Locomotion requires energy, and different types of locomotion have their own energy requirements. Mitochondria are the energy factories of living things, which provide a lot of energy for various physiological activities of organisms. Therefore, mitochondrial genomes could be tools to explore whether the limb loss of skinks are selected by adaptive evolution. <i>Isopachys gyldenstolpei</i> is a typical limbless skink. Here, we report the complete mitochondrial genomes of <i>I</i>. <i>gyldenstolpei</i>, <i>Sphenomorphus indicus,</i> and <i>Tropidophorus hainanus</i>. The latter two species were included as limbed comparator species to the limbless <i>I. gyldenstolpei</i>. The results showed that the full lengths of the mitochondrial genomes of <i>I</i>. <i>gyldenstolpei</i>, <i>S</i>. <i>indicus</i>, and <i>T. hainanus</i> were 17,210, 16,944, and 17,001 bp, respectively. Three mitochondrial genomes have typical circular double-stranded structures similar to other reptiles, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and the control region. Three mitochondrial genomes obtained in this study were combined with fifteen mitochondrially complete genomes of Scincidae in the NCBI database; the phylogenetic relationship between limbless <i>I</i>. <i>gyldenstolpei</i> and limbed skinks (<i>S</i>. <i>indicus</i> and <i>T</i>. <i>hainanus</i>) is discussed. Through BI and ML trees, Sphenomorphinae and Mabuyinae were monophyletic, while the paraphyly of Scincinae was also recovered. The limbless skink <i>I</i>. <i>gyldenstolpei</i> is closer to the species of <i>Tropidophorus,</i> which has formed a sister group with (<i>T</i>. <i>hainanus + T</i>. <i>hangman)</i>. In the mitochondrial genome adaptations between limbless <i>I. gyldenstolpei</i> and limbed skinks, one positively selected site was found in the branch-site model analysis, which was located in ND2 (at position 28, BEB value = 0.907). Through analyzing the protein structure and function of the selected site, we found it was distributed in mitochondrial protein complex I. Positive selection of some mitochondrial genes in limbless skinks may be related to the requirement of energy to fit in their locomotion. Further research is still needed to confirm this conclusion though.https://www.mdpi.com/2076-2615/12/16/2015positive selectionmitochondrial genomes<i>Isopachys gyldenstolpei</i>limbless skinks |
| spellingShingle | Lian Wu Yao Tong Sam Pedro Galilee Ayivi Kenneth B. Storey Jia-Yong Zhang Dan-Na Yu The Complete Mitochondrial Genomes of Three Sphenomorphinae Species (Squamata: Scincidae) and the Selective Pressure Analysis on Mitochondrial Genomes of Limbless <i>Isopachys gyldenstolpei</i> Animals positive selection mitochondrial genomes <i>Isopachys gyldenstolpei</i> limbless skinks |
| title | The Complete Mitochondrial Genomes of Three Sphenomorphinae Species (Squamata: Scincidae) and the Selective Pressure Analysis on Mitochondrial Genomes of Limbless <i>Isopachys gyldenstolpei</i> |
| title_full | The Complete Mitochondrial Genomes of Three Sphenomorphinae Species (Squamata: Scincidae) and the Selective Pressure Analysis on Mitochondrial Genomes of Limbless <i>Isopachys gyldenstolpei</i> |
| title_fullStr | The Complete Mitochondrial Genomes of Three Sphenomorphinae Species (Squamata: Scincidae) and the Selective Pressure Analysis on Mitochondrial Genomes of Limbless <i>Isopachys gyldenstolpei</i> |
| title_full_unstemmed | The Complete Mitochondrial Genomes of Three Sphenomorphinae Species (Squamata: Scincidae) and the Selective Pressure Analysis on Mitochondrial Genomes of Limbless <i>Isopachys gyldenstolpei</i> |
| title_short | The Complete Mitochondrial Genomes of Three Sphenomorphinae Species (Squamata: Scincidae) and the Selective Pressure Analysis on Mitochondrial Genomes of Limbless <i>Isopachys gyldenstolpei</i> |
| title_sort | complete mitochondrial genomes of three sphenomorphinae species squamata scincidae and the selective pressure analysis on mitochondrial genomes of limbless i isopachys gyldenstolpei i |
| topic | positive selection mitochondrial genomes <i>Isopachys gyldenstolpei</i> limbless skinks |
| url | https://www.mdpi.com/2076-2615/12/16/2015 |
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