The Complete Mitochondrial Genomes of Three Sphenomorphinae Species (Squamata: Scincidae) and the Selective Pressure Analysis on Mitochondrial Genomes of Limbless Isopachys gyldenstolpei

Abstract

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. Isopachys gyldenstolpei is a typical limbless skink. Here, we report the complete mitochondrial genomes of I. gyldenstolpei, Sphenomorphus indicus, and Tropidophorus hainanus. The latter two species were included as limbed comparator species to the limbless I. gyldenstolpei. The results showed that the full lengths of the mitochondrial genomes of I. gyldenstolpei, S. indicus, and T. hainanus 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. gyldenstolpei and limbed skinks (S. indicus and T. hainanus) is discussed. Through BI and ML trees, Sphenomorphinae and Mabuyinae were monophyletic, while the paraphyly of Scincinae was also recovered. The limbless skink I. gyldenstolpei is closer to the species of Tropidophorus, which has formed a sister group with (T. hainanus + T. hangman). In the mitochondrial genome adaptations between limbless I. gyldenstolpei 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.

Mitochondrial Protein-Coding Gene Expression in the Lizard Sphenomorphus incognitus (Squamata:Scincidae) Responding to Different Temperature Stresses

“…In previous studies examining mitochondrial gene expression and positive selection analysis in relation to low temperatures, particularly in insects [ 49 ], amphibians [ 50 ], and reptiles [ 51 ], the majority of identified genes were found to be components of mitochondrial Complex I. Within mitochondria, the proteins that these genes encode play crucial roles in the tricarboxylic acid cycle (TCA cycle) and the NADH generated from beta-oxidation.…”

Complete Mitochondrial Genome and Phylogenetic Analysis of Tarsiger indicus (Aves: Passeriformes: Muscicapidae)

“…Vertebrate mitochondrial genomes (mitogenomes) are circular, typically 14,000-20,000 bp, and contain 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA genes (tRNAs), and one large non-coding D-loop region [10,11]. The mitogenome has been extensively used in population genetics, population dynamics, and adaptive evolution studies of various animal groups [12][13][14][15][16], particularly in phylogenetic reconstruction among animal species [14,[16][17][18][19]. It is worth emphasizing that mitochondrial genomes are more reliable in phylogenetic reconstruction than a single mitochondrial gene [20][21][22].…”

Structure and Phylogenetic Relationships of Scolopacidae Mitogenomes (Charadriiformes: Scolopacidae)

“…However, the current research on Scolopacidae still fails to provide a clear explanation for their evolutionary mechanisms. Molecular-level studies of Scolopacidae are not only helpful in clarifying their phylogenetic relationships but also offer new insights into the evolution of Scolopacidae [ 17 , 18 ].…”