Characterization of the mitochondrial genomes of two toads, Anaxyrus americanus (Anura: Bufonidae) and Bufotes pewzowi (Anura: Bufonidae), with phylogenetic and selection pressure analyses

Abstract

Mitogenomes are useful in analyzing phylogenetic relationships and also appear to influence energy metabolism, thermoregulation and osmoregulation. Much evidence has accumulated for positive selection acting on mitochondrial genes associated with environmental adaptation. Hence, the mitogenome is a likely target for environmental selection. The family Bufonidae (true toads) has only nine complete and four partial mitogenomes published compared to the 610 known species of this family. More mitogenomes are needed in order to obtain a clearer understanding of the phylogenetic relationships within Bufonidae that are currently controversial. To date, no mitogenomes have been reported from the genera Anaxyrus and Bufotes. Anaxyrus americanus can live in low temperature environments and Bufotes pewzowi can live in high salinity environments. We sequenced the mitogenomes of these two species to discuss the phylogenetic relationships within Bufonidae and the selection pressures experienced by specimens living in low temperature or saline environments. Like other toads, the circular mitogenomes of both species contained the typical 37 genes. Anaxyrus americanus had the highest A+T content of the complete mitogenome among the Bufonidae. In addition, A. americanus showed a negative AT-skew in the control region, whereas Bufotes pewzowi showed a positive AT-skew. Additionally, both toad species had unique molecular features in common: an ND1 gene that uses TTG as the start codon, an extra unpaired adenine (A) in the anticodon arm of trnS (AGY), and the loss of the DHU loop in trnC. The monophyly of Bufonidae was corroborated by both BI and ML trees. An analysis of selective pressure based on the 13 protein coding genes was conducted using the EasyCodeML program. In the branch model analysis, we found two branches of A. americanus and Bufotes pewzowi that were under negative selection. Additionally, we found two positively selected sites (at positions 115 and 119, BEB value > 0.90) in the ND6 protein in the site model analysis. The residue D (119) was located only in A. americanus and may be related to adaptive evolution in low temperature environments. However, there was no evidence of a positively selected site in Bufotes pewzowi in this study.

Insight into the Phylogenetic Relationships among Three Subfamilies within Heptageniidae (Insecta: Ephemeroptera) along with Low-Temperature Selection Pressure Analyses Using Mitogenomes

“…Adaptive evolution of mitochondrial genes under environmental pressure is supported by several studies [ 43 , 44 , 45 ]. Environmental temperature significantly influences energy requirements and metabolic adaptation, which is essential to mayflies as aquatic insects [ 46 , 47 ].…”

“…Despite the fact that mitogenomes are generally considered to be under neutral or nearly neutral selection [ 42 ], several studies have pointed out that positive selection acted on mitochondrial PCGs linked to environmental adaptations [ 43 , 44 , 45 ]. In this way, as a potential target associated with energy metabolism under environmental selection pressure, the mitogenome may be suitable for studying positive selection or natural selection.…”

Characterization of Two Mitogenomes of Hyla sanchiangensis (Anura: Hylidae), with Phylogenetic Relationships and Selection Pressure Analyses of Hylidae

“…Mitogenomes are currently used as an efficient tool for species identification and the analysis of phylogenetic relationships [16,17]. The length of frog mitogenomes is about 15-23 kb [18][19][20][21] and encodes 22 transfer RNAs (tRNAs), two ribosomal RNAs (12S and 16S RNAs), 13 protein-coding genes (PCGs), and the control region (CR) or Dloop region.…”

Comparative Mitogenomes of Two Coreamachilis Species (Microcoryphia: Machilidae) along with Phylogenetic Analyses of Microcoryphia

“…It is well known that the mitogenome is often assumed to be an important neutral marker [ 27 ]. However, recent research has shown that the evaluation of selective pressures acting on mitogenome proteins can provide key insights into the adaptive evolution of the mitogenome [ 28 , 29 , 30 , 31 , 32 , 33 ]. To date, various studies of mammalian [ 34 , 35 ], avian [ 36 ], frog [ 33 ], fish [ 37 ], and insect mitogenomes have indicated that adaptive evolution has occurred.…”

“…However, recent research has shown that the evaluation of selective pressures acting on mitogenome proteins can provide key insights into the adaptive evolution of the mitogenome [ 28 , 29 , 30 , 31 , 32 , 33 ]. To date, various studies of mammalian [ 34 , 35 ], avian [ 36 ], frog [ 33 ], fish [ 37 ], and insect mitogenomes have indicated that adaptive evolution has occurred. Among insects, this has included studies of Hymenoptera [ 38 ], Orthoptera [ 39 ], Ephemeroptera [ 40 ], Diptera [ 41 ], and Lepidoptera [ 42 ].…”