Evolutionary analysis of mitochondrially encoded proteins of toad-headed lizards, Phrynocephalus, along an altitudinal gradient

Convergent evolution in nuclear and mitochondrial OXPHOS subunits underlies the phylogenetic discordance in deep lineages of Squamata

The order Squamata is a good candidate for detecting unusual patterns of mitochondrial evolution. The lineages leading to the snake and agamid clades likely experienced convergent evolution in mitochondrial OXidative PHOSphorylation (OXPHOS) genes, which provides strong support for the sister relationship of these two groups. The OXPHOS subunits are encoded by both the nuclear and mitochondrial genomes, which are subject to distinct evolutionary pressures. Nevertheless, the cooperation between OXPHOS subunits is essential for proper OXPHOS function, as incompatibilities between subunits can be highly deleterious. In the present study, we annotated OXPHOS genes of 56 Squamata species. The nuclear OXPHOS subunits that physically interact with mitochondrial proteins also support the clade sister relationship between snakes and agamids. Additionally, we found a significant number of convergent amino acid changes between agamids and snakes, not only in mitochondrial OXPHOS genes, but also in nuclear ones, with a higher rate of convergence in the nuclear OXPHOS subunits that play central roles in the OXPHOS complexes, like COX4 and NDUFA4. Overall, the common selective pressures in two distinct lineages can lead two sets of genes, encoded by two different genomes, to exhibit similar patterns of convergent evolution, as well as similar evolutionary rates. As a consequence, the coevolution of interdependent subunits and their adaptation to specific evolutionary pressures can heavily influence the molecular structure of cytonuclear enzyme complexes and blur phylogenetic signals.

Stronger Evidence for Relaxed Selection Than Adaptive Evolution in High-elevation Animal mtDNA

Mitochondrial (mt) genes are the subject of many adaptive hypotheses due to the key role of mitochondria in energy production and metabolism. One widespread adaptive hypothesis is that selection imposed by life at high elevation leads to the rapid fixation of beneficial alleles in mtDNA, reflected in the increased rates of mtDNA evolution documented in many high-elevation species. However, the assumption that fast mtDNA evolution is caused by positive selection, rather than relaxed purifying selection, has rarely been tested. Here, we calculated the dN/dS ratio, a metric of nonsynonymous substitution bias, and explicitly tested for relaxed selection in the mtDNA of over 700 species of terrestrial vertebrates, freshwater fishes, and arthropods, with information on elevation and latitudinal range limits, range sizes, and body sizes. We confirmed that mitochondrial genomes of high-elevation taxa have slightly higher dN/dS ratios compared to low-elevation relatives. High-elevation species tend to have smaller ranges, which predict higher dN/dS ratios and more relaxed selection across species and clades, while absolute elevation and latitude do not predict higher dN/dS. We also find a positive relationship between body mass and dN/dS, supporting a role for small effective population size leading to relaxed selection. We conclude that higher mt dN/dS among high-elevation species is more likely to reflect relaxed selection due to smaller ranges and reduced effective population size than adaptation to the environment. Our results highlight the importance of rigorously testing adaptive stories against non-adaptive alternative hypotheses, especially in mt genomes.

The first complete mitochondrial genome of Sumatran striped rabbit Nesolagus netscheri (Schlegel, 1880), and its phylogenetic relationship with other Leporidae

Nesolagus netscheri, a Sumatran striped rabbit, is one of the rarest rabbits in the Leporidae family, and its genetic information is still limited. This study provides the first mitochondrial genome and molecular systematic characterization of the Sumatran striped rabbit, Nesolagus netscheri, Indonesia's rarest rabbit. It consists of a circular double-stranded DNA of 16,709 bp. It showed that the mitochondrial genome structure of N. netscheri is similar to that of N. timminsi. The mitochondrial genome of N. netscheri contained 22 transfer RNA (tRNA) genes, and all tRNA except for trnS1 showed a characteristic cloverleaf secondary structure. Evidence was found that the atp8 gene of N. netscheri is under positive selection pressure. The phylogenetic analysis shows Leporidae was monophyletic, with Nesolagus at the basal. The study indicates a split between N. netscheri and N. timminsi in the Late Pleistocene around 0.43 million years ago. This research is a fundamental reference for the conservation of the rarest lagomorph species and provides important information for future evolutionary studies in the Leporidae family.

Amblyopinae Mitogenomes Provide Novel Insights into the Paraphyletic Origin of Their Adaptation to Mudflat Habitats

The water-to-land transition is one of the most important events in evolutionary history of vertebrates. However, the genetic basis underlying many of the adaptations during this transition remains unclear. Mud-dwelling gobies in the subfamily Amblyopinae are one of the teleosts lineages that show terrestriality and provide a useful system for clarifying the genetic changes underlying adaptations to terrestrial life. Here, we sequenced the mitogenome of six species in the subfamily Amblyopinae. Our results revealed a paraphyletic origin of Amblyopinae with respect to Oxudercinae, which are the most terrestrial fishes and lead an amphibious life in mudflats. This partly explains the terrestriality of Amblyopinae. We also detected unique tandemly repeated sequences in the mitochondrial control region in Amblyopinae, as well as in Oxudercinae, which mitigate oxidative DNA damage stemming from terrestrial environmental stress. Several genes, such as ND2, ND4, ND6 and COIII, have experienced positive selection, suggesting their important roles in enhancing the efficiency of ATP production to cope with the increased energy requirements for life in terrestrial environments. These results strongly suggest that the adaptive evolution of mitochondrial genes has played a key role in terrestrial adaptions in Amblyopinae, as well as in Oxudercinae, and provide new insights into the molecular mechanisms underlying the water-to-land transition in vertebrates.

Gut Virome of the World's Highest-Elevation Lizard Species (Phrynocephalus erythrurus and Phrynocephalus theobaldi) Reveals Versatile Commensal Viruses

The gut virome is a reservoir of diverse symbiotic and pathogenic viruses coevolving with their hosts, and yet limited research has explored the gut viromes of highland-dwelling rare species. Using viral metagenomic analysis, the viral communities of the Phrynocephalus lizards living in the Qinghai-Tibet Plateau were investigated. Phage-encoded functional genes and antibiotic resistance genes (ARGs) were analyzed. The viral communities of different lizard species were all predominated by bacteriophages, especially the Caudovirales order. The virome of Phrynocephalus erythrurus living around the Namtso Lake possessed a unique structure, with the greatest abundance of the Parvoviridae family and the highest number of exclusive viral species. Several vertebrate-infecting viruses were discovered, including caliciviruses, astroviruses, and parvoviruses. Phylogenetic analyses demonstrated that the virus hallmark genes of bacteriophages possessed high genetic diversity. After functional annotation, the majority of phage-associated functional genes were classified in the energy metabolism category. In addition, plenty of ARGs belonging to the multidrug category were discovered, and five ARGs were exclusive to the virome from Phrynocephalus theobaldi. This study provided the first insight into the structure and function of the virome in highland lizards, contributing to the protection of threatened lizard species. Also, our research is of exemplary significance for the gut virome research of lizard species and other cold-blooded and highland-dwelling animals, prompting a better understanding of the interspecific differences and transmission of commensal viruses. IMPORTANCE The Phrynocephalus lizards inhabiting the Qinghai-Tibet Plateau (QTP) are considered to be the highest-altitude lizard species in the world, and they have been added to the IUCN list of threatened species. Living in the QTP with hypoxic, arid, natural conditions, the lizards presented a unique pattern of gut virome, which could provide both positive and negative effects, such as the enrichment of functional genes and the dissemination of antibiotic resistance genes (ARGs). This work provides the foundation for further research on the gut virome in these endangered lizard species and other cold-blooded and highland-dwelling animals, contributing to the maintenance of ecological balance on the plateau.

Biological and extrinsic correlates of extinction risk in Chinese lizards

China is a country with one of the most species-rich reptile faunas in the world. However, nearly a quarter of Chinese lizard species assessed by the China Biodiversity Red List are threatened. Nevertheless, to date, no study has explicitly examined the pattern and processes of extinction and threat in Chinese lizards. In this study, we conducted the first comparative phylogenetic analysis of extinction risk in Chinese lizards. We addressed the following 3 questions: (1) What is the pattern of extinction and threat in Chinese lizards? (2) Which species traits and extrinsic factors are related to their extinction risk? (3) How can we protect Chinese lizards based on our results? We collected data on 10 species traits (body size [BS], clutch size, geographic range size, activity time, reproductive mode, habitat specialization [HS], habitat use, leg development, maximum elevation, and elevation range) and 7 extrinsic factors (mean annual precipitation (MAP), mean annual temperature, mean annual solar insolation, normalized difference vegetation index (NDVI), human footprint, human population density, and human exploitation). After phylogenetic correction, these variables were used separately and in combination to assess their associations with extinction risk. We found that Chinese lizards with a small geographic range, large BS, high HS, and living in high MAP areas were vulnerable to extinction. Conservation priority should thus be given to species with the above extinction-prone traits so as to effectively protect Chinese lizards. Preventing future habitat destruction should also be a primary focus of management efforts because species with small range size and high HS are particularly vulnerable to habitat loss.

Mitochondria and the Frozen Frog

The wood frog, Rana sylvatica, is the best-studied of a small group of amphibian species that survive whole body freezing during the winter months. These frogs endure the freezing of 65-70% of their total body water in extracellular ice masses. They have implemented multiple adaptations that manage ice formation, deal with freeze-induced ischemia/reperfusion stress, limit cell volume reduction with the production of small molecule cryoprotectants (glucose, urea) and adjust a wide variety of metabolic pathways for prolonged life in a frozen state. All organs, tissues, cells and intracellular organelles are affected by freeze/thaw and its consequences. This article explores mitochondria in the frozen frog with a focus on both the consequences of freezing (e.g., anoxia/ischemia, cell volume reduction) and mitigating defenses (e.g., antioxidants, chaperone proteins, upregulation of mitochondria-encoded genes, enzyme regulation, etc.) in order to identify adaptive strategies that defend and adapt mitochondria in animals that can be frozen for six months or more every year. A particular focus is placed on freeze-responsive genes in wood frogs that are encoded on the mitochondrial genome including ATP6/8, ND4 and 16S RNA. These were strongly up-regulated during whole body freezing (24 h at -2.5 °C) in the liver and brain but showed opposing responses to two component stresses: strong upregulation in response to anoxia but no response to dehydration stress. This indicates that freeze-responsive upregulation of mitochondria-encoded genes is triggered by declining oxygen and likely has an adaptive function in supporting cellular energetics under indeterminate lengths of whole body freezing.

Complete mitochondrial genome sequence of Lepus yarkandensis Günther, 1875 (Lagomorpha, Leporidae): characterization and phylogenetic analysis

Lepusyarkandensis is a national second-class protected animal endemic to China and distributed only in the hot and arid Tarim Basin in Xinjiang. We sequenced and described the complete mitogenome of L.yarkandensis to analyze its characteristics and phylogeny. The species’ DNA is a 17,047 bp circular molecule that includes 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region. The overall base composition was as follows: A, 31.50%; T, 29.40%; G, 13.30% and C, 25.80%, with a high A+T bias of 60.9%. In the PCGs, ND6 had deviation ranges for AT skew (–0.303) and GC skew (0.636). The Ka/Ks values of ND1 (1.067) and ND6 (1.352) genes were >1, indicating positive selection, which might play an important role in the adaptation of L.yarkandensis to arid and hot environments. The conserved sequence block, the central conserved domain, and the extended termination-associated sequences of the control region and their features were identified and described. The phylogenetic tree based on the complete mitogenome showed that L.yarkandensis was closely related to the sympatric Lepustibetanuspamirensis. These novel datasets of L.yarkandensis can supply basic data for phylogenetic studies of Lepus spp., apart from providing essential and important resource for further genetic research and the protection of this species.

A Re-Assessment of Positive Selection on Mitochondrial Genomes of High-Elevation Phrynocephalus Lizards

Due to their integral roles in oxidative phosphorylation, mitochondrially encoded proteins represent common targets of selection in response to altitudinal hypoxia across high-altitude taxa. While previous studies revealed evidence of positive selection on mitochondrial genomes of high-altitude Phrynocephalus lizards, their conclusions were restricted by out-of-date phylogenies and limited taxonomic sampling. Using topologies derived from both nuclear and mitochondrial DNA phylogenies, we re-assessed the evidence of positive selection on the mitochondrial genomes of high-altitude Phrynocephalus. We sampled representative species from all four main lineages and sequenced the mitochondrial genome of P. maculatus, a putative sister taxon to the high-altitude group. Positive selection was assessed through two widely used branch-site tests: the branch-site model in PAML and BUSTED in HyPhy. No evidence of positive selection on mitochondrial genes was detected on branches leading to two most recent common ancestors of high-altitude species; however, we recovered evidence of positive selection on COX1 on the P. forsythii branch, which represents a reversal from high- to low-elevation environments. A positively selected site therein marked a threonine to valine substitution at position 419. We suggest this bout of selection occurred as the ancestors of P. forsythii re-colonized lower altitude environments north of the Tibetan Plateau. Despite their role in oxidative phosphorylation, we posit that mitochondrial genes are unlikely to have represented historical targets of selection for high-altitude adaptation in Phrynocephalus. Consequently, future studies should address the roles of nuclear genes and differential gene expression.

Convergent Evolution of Himalayan Marmot with Some High-Altitude Animals through ND3 Protein

The Himalayan marmot (Marmota himalayana) mainly lives on the Qinghai-Tibet Plateau and it adopts multiple strategies to adapt to high-altitude environments. According to the principle of convergent evolution as expressed in genes and traits, the Himalayan marmot might display similar changes to other local species at the molecular level. In this study, we obtained high-quality sequences of the CYTB gene, CYTB protein, ND3 gene, and ND3 protein of representative species (n = 20) from NCBI, and divided them into the marmot group (n = 11), the plateau group (n = 8), and the Himalayan marmot (n = 1). To explore whether plateau species have convergent evolution on the microscale level, we built a phylogenetic tree, calculated genetic distance, and analyzed the conservation and space structure of Himalayan marmot ND3 protein. The marmot group and Himalayan marmots were in the same branch of the phylogenetic tree for the CYTB gene and CYTB protein, and mean genetic distance was 0.106 and 0.055, respectively, which was significantly lower than the plateau group. However, the plateau group and the Himalayan marmot were in the same branch of the phylogenetic tree, and the genetic distance was only 10% of the marmot group for the ND3 protein, except Marmota flaviventris. In addition, some sites of the ND3 amino acid sequence of Himalayan marmots were conserved from the plateau group, but not the marmot group. This could lead to different structures and functional diversifications. These findings indicate that Himalayan marmots have adapted to the plateau environment partly through convergent evolution of the ND3 protein with other plateau animals, however, this protein is not the only strategy to adapt to high altitudes, as there may have other methods to adapt to this environment.

Mitogenomics of the endemic Ethiopian rats: looking for footprints of adaptive evolution in sky islands

Organisms living in high altitude must adapt to environmental conditions with hypoxia and low temperature, e.g. by changes in the structure and function of proteins associated with oxidative phosphorylation in mitochondria. Here we analysed the signs of adaptive evolution in 27 mitogenomes of endemic Ethiopian rats (Stenocephalemys), where individual species adapted to different elevation. Significant signals of positive selection were detected in 10 of the 13 mitochondrial protein-coding genes, with a majority of functional substitutions in the NADH dehydrogenase complex. Higher frequency of positively selected sites was found in phylogenetic lineages corresponding to Afroalpine specialists.

Environmental and geological changes in the Tarim Basin promoted the phylogeographic formation of Phrynocephalus forsythii (Squamata: Agamidae)

Environmental factors can promote genetic divergence among populations. The Tarim Basin has experienced a series of environmental and geological changes since the late Pliocene. Phrynocephalus forsythii (Agamidae) has a continuous and circular distribution around the Tarim Basin, and the evolutionary history of this species remains unclear. In the present study, mitochondrial DNA and single nucleotide polymorphism sequences were obtained from 195 P. forsythii samples in the Tarim Basin to examine the phylogeographic structure and evolutionary history of this species. All populations of P. forsythii formed three distinct clusters: the Minfeng, low-elevation, and high-elevation groups. The Minfeng group was the first to separate from all other groups at 4.26 Ma after the original desert environment emerged in the Tarim Basin. The uplift of the Kunlun Mountains created a new high-altitude environment along the southwestern edge of the basin and promoted the divergence of low-elevation and high-elevation groups at 3.67 Ma. Subsequently, the gradual development of deserts and rivers in the Tarim Basin accelerated the dispersal of P. forsythii, eventually forming the current distribution pattern. Our results indicate that ecological separation caused by environmental and geological changes in the Tarim Basin was the main cause for the genetic divergence of P. forsythii.

The role of selection in the evolution of marine turtles mitogenomes

Sea turtles are the only extant chelonian representatives that inhabit the marine environment. One key to successful colonization of this habitat is the adaptation to different energetic demands. Such energetic requirement is intrinsically related to the mitochondrial ability to generate energy through oxidative phosphorylation (OXPHOS) process. Here, we estimated Testudines phylogenetic relationships from 90 complete chelonian mitochondrial genomes and tested the adaptive evolution of 13 mitochondrial protein-coding genes of sea turtles to determine how natural selection shaped mitochondrial genes of the Chelonioidea clade. Complete mitogenomes showed strong support and resolution, differing at the position of the Chelonioidea clade in comparison to the turtle phylogeny based on nuclear genomic data. Codon models retrieved a relatively increased dN/dS (ω) on three OXPHOS genes for sea turtle lineages. Also, we found evidence of positive selection on at least three codon positions, encoded by NADH dehydrogenase genes (ND4 and ND5). The accelerated evolutionary rates found for sea turtles on COX2, ND1 and CYTB and the molecular footprints of positive selection found on ND4 and ND5 genes may be related to mitochondrial molecular adaptation to stress likely resulted from a more active lifestyle in sea turtles. Our study provides insight into the adaptive evolution of the mtDNA genome in sea turtles and its implications for the molecular mechanism of oxidative phosphorylation.

Elevation as a selective force on mitochondrial respiratory chain complexes of the Phrynocephalus lizards in the Tibetan plateau

Animals living in extremely high elevations have to adapt to low temperatures and low oxygen availability (hypoxia), but the underlying genetic mechanisms associated with these adaptations are still unclear. The mitochondrial respiratory chain can provide >95% of the ATP in animal cells, and its efficiency is influenced by temperature and oxygen availability. Therefore, the respiratory chain complexes (RCCs) could be important molecular targets for positive selection associated with respiratory adaptation in high-altitude environments. Here, we investigated positive selection in 5 RCCs and their assembly factors by analyzing sequences of 106 genes obtained through RNA-seq of all 15 Chinese Phrynocephalus lizard species, which are distributed from lowlands to the Tibetan plateau (average elevation >4,500 m). Our results indicate that evidence of positive selection on RCC genes is not significantly different from assembly factors, and we found no difference in selective pressures among the 5 complexes. We specifically looked for positive selection in lineages where changes in habitat elevation happened. The group of lineages evolving from low to high altitude show stronger signals of positive selection than lineages evolving from high to low elevations. Lineages evolving from low to high elevation also have more shared codons under positive selection, though the changes are not equivalent at the amino acid level. This study advances our understanding of the genetic basis of animal respiratory metabolism evolution in extreme high environments and provides candidate genes for further confirmation with functional analyses.

Fixation of genetic variation and optimization of gene expression: The speed of evolution in isolated lizard populations undergoing Reverse Island Syndrome

The ecological theory of island biogeography suggests that mainland populations should be more genetically divergent from those on large and distant islands rather than from those on small and close islets. Some island populations do not evolve in a linear way, but the process of divergence occurs more rapidly because they undergo a series of phenotypic changes, jointly known as the Island Syndrome. A special case is Reversed Island Syndrome (RIS), in which populations show drastic phenotypic changes both in body shape, skin colouration, age of sexual maturity, aggressiveness, and food intake rates. The populations showing the RIS were observed on islets nearby mainland and recently raised, and for this they are useful models to study the occurrence of rapid evolutionary change. We investigated the timing and mode of evolution of lizard populations adapted through selection on small islets. For our analyses, we used an ad hoc model system of three populations: wild-type lizards from the mainland and insular lizards from a big island (Capri, Italy), both Podarcis siculus siculus not affected by the syndrome, and a lizard population from islet (Scopolo) undergoing the RIS (called P. s. coerulea because of their melanism). The split time of the big (Capri) and small (Scopolo) islands was determined using geological events, like sea-level rises. To infer molecular evolution, we compared five complete mitochondrial genomes for each population to reconstruct the phylogeography and estimate the divergence time between island and mainland lizards. We found a lower mitochondrial mutation rate in Scopolo lizards despite the phenotypic changes achieved in approximately 8,000 years. Furthermore, transcriptome analyses showed significant differential gene expression between islet and mainland lizard populations, suggesting the key role of plasticity in these unpredictable environments.

Trans-Species Polymorphism in Mitochondrial Genome of Camarodont Sea Urchins

Mitochondrial (mt) genomes of the sea urchins Strongylocentrotus intermedius and Mesocentrotus nudus demonstrate the identical patterns of intraspecific length variability of the ND6 gene, consisting of 489 bp (S variant) and 498 bp (L variant), respectively. For both species, the ND6 length difference is due to the 488A>G substitution, which changes the stop codon TAG in S variant for a tryptophan codon TGG in L variant and elongates the corresponding ND6 protein by three additional amino acids, Trp-Leu-Trp. The phylogenetic analysis based on mt genomes of sea urchins and related echinoderm groups from GenBank has shown the S and L ND6 variants as shared among the camarodont sea urchins; the rest of the echinoderms demonstrate the S variant only. The data suggest that the ND6 488A>G substitution can be the first example of the trans-species polymorphism in sea urchins, persisting at least since the time of the Odontophora diversification at the Eocene/Oligocene boundary (approximately 34 million years ago), which was characterized by an abrupt climate change and significant global ocean cooling. Alternative hypotheses, including the convergent RNA editing and/or codon reassignment, are not supported by direct comparisons of the ND6 gene sequences with the corresponding transcripts using the basic local alignment search tool (BLAST) of full sea urchin transcriptomes.

Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection, and climate

Nuclear and mitochondrial genomes coexist within cells but are subject to different tempos and modes of evolution. Evolutionary forces such as drift, mutation, selection, and migration are expected to play fundamental roles in the origin and maintenance of diverged populations; however, divergence may lag between genomes subject to different modes of inheritance and functional specialization. Herein, we explore whole mitochondrial genome data and thousands of nuclear single nucleotide polymorphisms to evidence extreme mito-nuclear discordance in the small black-tailed brush lizard, Urosaurus nigricaudus, of the Peninsula of Baja California, Mexico and southern California, USA, and discuss potential drivers. Results show three deeply divergent mitochondrial lineages dating back to the later Miocene (ca. 5.5 Ma) and Pliocene (ca. 2.8 Ma) that likely followed geographic isolation due to trans-peninsular seaways. This contrasts with very low levels of genetic differentiation in nuclear loci (F_ST < 0.028) between mtDNA lineages. Analyses of protein-coding genes reveal substantial fixed variation between mitochondrial lineages, of which a significant portion comes from non-synonymous mutations. A mixture of drift and selection is likely responsible for the rise of these mtDNA groups, albeit with little evidence of marked differences in climatic niche space between them. Finally, future investigations can look further into the role that mito-nuclear incompatibilities and mating systems play in explaining contrasting nuclear gene flow.