Complete Mitochondrial DNA Sequences of Six Snakes: Phylogenetic Relationships and Molecular Evolution of Genomic Features

The Phylogenetic Relationships of Major Lizard Families Using Mitochondrial Genomes and Selection Pressure Analyses in Anguimorpha

Anguimorpha, within the order Squamata, represents a group with distinct morphological and behavioral characteristics in different ecological niches among lizards. Within Anguimorpha, there is a group characterized by limb loss, occupying lower ecological niches, concentrated within the subfamily Anguinae. Lizards with limbs and those without exhibit distinct locomotor abilities when adapting to their habitats, which in turn necessitate varying degrees of energy expenditure. Mitochondria, known as the metabolic powerhouses of cells, play a crucial role in providing approximately 95% of an organism's energy. Functionally, mitogenomes (mitochondrial genomes) can serve as a valuable tool for investigating potential adaptive evolutionary selection behind limb loss in reptiles. Due to the variation of mitogenome structures among each species, as well as its simple genetic structure, maternal inheritance, and high evolutionary rate, the mitogenome is increasingly utilized to reconstruct phylogenetic relationships of squamate animals. In this study, we sequenced the mitogenomes of two species within Anguimorpha as well as the mitogenomes of two species in Gekkota and four species in Scincoidea. We compared these data with the mitogenome content and evolutionary history of related species. Within Anguimorpha, between the mitogenomes of limbless and limbed lizards, a branch-site model analysis supported the presence of 10 positively selected sites: Cytb protein (at sites 183 and 187), ND2 protein (at sites 90, 155, and 198), ND3 protein (at site 21), ND5 protein (at sites 12 and 267), and ND6 protein (at sites 72 and 119). These findings suggested that positive selection of mitogenome in limbless lizards may be associated with the energy requirements for their locomotion. Additionally, we acquired data from 205 mitogenomes from the NCBI database. Bayesian inference (BI) and Maximum Likelihood (ML) trees were constructed using the 13 mitochondrial protein-coding genes (PCGs) and two rRNAs (12S rRNA and 16S rRNA) from 213 mitogenomes. Our phylogenetic tree and the divergence time estimates for Squamata based on mitogenome data are consistent with results from previous studies. Gekkota was placed at the root of Squamata in both BI and ML trees. However, within the Toxicofera clade, due to long-branch attraction, Anguimorpha and (Pleurodonta + (Serpentes + Acrodonta)) were closely related groupings, which might indicate errors and also demonstrate that mitogenome-based phylogenetic trees may not effectively resolve long-branch attraction issues. Additionally, we reviewed the origin and diversification of Squamata throughout the Mesozoic era, suggesting that Squamata originated in the Late Triassic (206.05 Mya), with the diversification of various superfamilies occurring during the Cretaceous period. Future improvements in constructing squamate phylogenetic relationships using mitogenomes will rely on identifying snake and acrodont species with slower evolutionary rates, ensuring comprehensive taxonomic coverage of squamate diversity, and increasing the number of genes analyzed.

A comparison of gene organisations and phylogenetic relationships of all 22 squamate species listed in South Korea using complete mitochondrial DNA

Studies using complete mitochondrial genome data have the potential to increase our understanding on gene organisations and evolutionary species relationships. In this study, we compared complete mitochondrial genomes between all 22 squamate species listed in South Korea. In addition, we constructed Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) phylogenetic trees using 13 mitochondrial protein-coding genes. The mitochondrial genes for all six species in the suborder Sauria followed the same organisation as the sequenced Testudines (turtle) outgroup. In contrast, 16 snake species in the suborder Serpentes contained some gene organisational variations. For example, all snake species contained a second control region (CR2), while three species in the family Viperidae had a translocated tRNA-Pro gene region. In addition, the snake species, Elapheschrenckii, carried a tRNA-Pro pseudogene. We were also able to identify a translocation of a tRNA-Asn gene within the five tRNA (WANCY gene region) gene clusters for two true sea snake species in the subfamily Hydrophiinae. Our BI phylogenetic tree was also well fitted against currently known Korean squamate phylogenetic trees, where each family and genus unit forms monophyletic clades and the suborder Sauria is paraphyletic to the suborder Serpentes. Our results may form the basis for future northeast Asian squamate phylogenetic studies.

Complete mitochondrial genomes of Boigakraepelini and Hebiuscraspedogaster (Reptilia, Squamata, Colubridae) and their phylogenetic implications

The complete sequence of the mitochondrial genome is a powerful tool for studying phylogenetic relationships and molecular evolution in various species. In this work, the mitogenomes of Boigakraepelini and Hebiuscraspedogaster were sequenced and characterized for the first time. The lengths of the B.kraepelini and H.craspedogaster mitogenomes were 17,124 bp and 17,120 bp, respectively, and both included 13 protein-coding genes, 22 tRNAs, two rRNAs and two control regions. The arrangements of these mitochondrial genes were the same in B.kraepelini and H.craspedogaster. In addition, both genome compositions showed A+T bias (59.03%, 60.93%) and had positive AT skews (0.179, 0.117) and negative GC skews (-0.397, -0.348). The phylogenetic results illustrated a close relationship between B.kraepelini and the genus Lycodon. Moreover, H.craspedogaster was clustered with other Hebius snakes and closely related to other Natricinae species. These results will provide references for further research on the phylogeny of Colubridae.

Evolution of the Noncoding Features of Sea Snake Mitochondrial Genomes within Elapidae

Mitochondrial genomes of four elapid snakes (three marine species [Emydocephalus ijimae, Hydrophis ornatus, and Hydrophis melanocephalus], and one terrestrial species [Sinomicrurus japonicus]) were completely sequenced by a combination of Sanger sequencing, next-generation sequencing and Nanopore sequencing. Nanopore sequencing was especially effective in accurately reading through long tandem repeats in these genomes. This led us to show that major noncoding regions in the mitochondrial genomes of those three sea snakes contain considerably long tandem duplications, unlike the mitochondrial genomes previously reported for same and other sea snake species. We also found a transposition of the light-strand replication origin within a tRNA gene cluster for the three sea snakes. This change can be explained by the Tandem Duplication—Random Loss model, which was further supported by remnant intervening sequences between tRNA genes. Mitochondrial genomes of true snakes (Alethinophidia) have been shown to contain duplicate major noncoding regions, each of which includes the control region necessary for regulating the heavy-strand replication and transcription from both strands. However, the control region completely disappeared from one of the two major noncoding regions for two Hydrophis sea snakes, posing evolutionary questions on the roles of duplicate control regions in snake mitochondrial genomes. The timing and molecular mechanisms for these changes are discussed based on the elapid phylogeny.

Divergent Specialization of Simple Venom Gene Profiles among Rear-Fanged Snake Genera (Helicops and Leptodeira, Dipsadinae, Colubridae)

Many venomous animals express toxins that show extraordinary levels of variation both within and among species. In snakes, most studies of venom variation focus on front-fanged species in the families Viperidae and Elapidae, even though rear-fanged snakes in other families vary along the same ecological axes important to venom evolution. Here we characterized venom gland transcriptomes from 19 snakes across two dipsadine rear-fanged genera (Leptodeira and Helicops, Colubridae) and two front-fanged genera (Bothrops, Viperidae; Micrurus, Elapidae). We compared patterns of composition, variation, and diversity in venom transcripts within and among all four genera. Venom gland transcriptomes of rear-fanged Helicops and Leptodeira and front-fanged Micrurus are each dominated by expression of single toxin families (C-type lectins, snake venom metalloproteinase, and phospholipase A2, respectively), unlike highly diverse front-fanged Bothrops venoms. In addition, expression patterns of congeners are much more similar to each other than they are to species from other genera. These results illustrate the repeatability of simple venom profiles in rear-fanged snakes and the potential for relatively constrained venom composition within genera.

Mitochondrial genome of the critically Endangered silver boa (Chilabothrus argentum; Squamata: Boidae)

We present the complete mitochondrial genome of Chilabothrus argentum, which is 17,345 bp in length, has 22 transfer ribonucleic acids (tRNAs), 2 ribosomal subunits (rRNAs), 13 protein-coding genes, an origin of the light-strand replication (O_L), and two control regions (CR1, CR2). A maximum likelihood phylogenetic estimate using nine other snake mitochondrial genomes yields agreement with previous investigations into the evolutionary relationships of snakes.

Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward

DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.

A new record of odd-scaled snake (Serpentes, Xenodermidae) from Vietnam: expanded description of Parafimbrios vietnamensis based on integrative taxonomy

Based on the combination of molecular and morphological data, we herein report the second known finding of the xenodermid snake species Parafimbriosvietnamensis Ziegler, Ngo, Pham, Nguyen, Le & Nguyen, 2018. The male individual was found in the Yen Bai Province of northwestern Vietnam, more than 200 km from the type locality in Lai Chau Province. Genetic divergence between the newly-collected male and the holotype was low (1.7%), and is in agreement with morphological data that supports that they are conspecific. We give a detailed description of the morphological characters and coloration of the new record and provide an expanded diagnosis of P.vietnamensis. Parafimbrios is a poorly-understood genus, and our recent discovery brings the total number of known specimens of the genus to nine, 1/3 of them having been found in Vietnam (one specimen of P.lao and now two specimens of P.vietnamensis).

Insights into skull evolution in fossorial snakes, as revealed by the cranial morphology of Atractaspis irregularis (Serpentes: Colubroidea)

Comparative osteological analyses of extant organisms provide key insight into major evolutionary transitions and phylogenetic hypotheses. This is especially true for snakes, given their unique morphology relative to other squamates and the persistent controversy regarding their evolutionary origins. However, the osteology of several major snake groups remains undescribed, thus hindering efforts to accurately reconstruct the phylogeny of snakes. One such group is the Atractaspididae, a family of fossorial colubroids. We herein present the first detailed description of the atractaspidid skull, based on fully segmented micro-computed tomography (micro-CT) scans of Atractaspis irregularis. The skull of Atractaspis presents a highly unique morphology influenced by both fossoriality and paedomorphosis. This paedomorphosis is especially evident in the jaws, palate, and suspensorium, the major elements associated with macrostomy (large-gaped feeding in snakes). Comparison to scolecophidians-a group of blind, fossorial, miniaturized snakes-in turn sheds light on current hypotheses of snake phylogeny. Features of both the naso-frontal joint and the morphofunctional system related to macrostomy refute the traditional notion that scolecophidians are fundamentally different from alethinophidians (all other extant snakes). Instead, these features support the controversial hypothesis of scolecophidians as "regressed alethinophidians," in contrast to their traditional placement as the earliest-diverging snake lineage. We propose that Atractaspis and scolecophidians fall along a morphological continuum, characterized by differing degrees of paedomorphosis. Altogether, a combination of heterochrony and miniaturization provides a mechanism for the derivation of the scolecophidian skull from an ancestral fossorial alethinophidian morphotype, exemplified by the nonminiaturized and less extreme paedomorph Atractaspis.

Phylogenomics, biogeography and taxonomic revision of New Guinean pythons (Pythonidae, Leiopython) harvested for international trade

The large and enigmatic New Guinean pythons in the genus Leiopython are harvested from the wild to supply the international trade in pets. Six species are currently recognized (albertisii, biakensis, fredparkeri, huonensis, meridionalis, montanus) but the taxonomy of this group has been controversial. We combined analysis of 421 nuclear loci and complete mitochondrial genomes with morphological data to construct a detailed phylogeny of this group, understand their biogeographic patterns and establish the systematic diversity of this genus. Our molecular genetic data support two major clades, corresponding to L. albertisii and L. fredparkeri, but offer no support for the other four species. Our morphological data also only support two species. We therefore recognize L. albertisii and L. fredparkeri as valid species and place L. biakensis, L. meridionalis, L. huonensis and L. montanus into synonymy. We found that L. albertisii and L. fredparkeri are sympatric in western New Guinea; an atypical pattern compared to other Papuan species complexes in which the distributions of sister taxa are partitioned to the north and south of the island's central mountain range. For the purpose of conservation management, overestimation of species diversity within Leiopython has resulted in the unnecessary allocation of resources that could have been expended elsewhere. We strongly caution against revising the taxonomy of geographically widespread species groups when little or no molecular genetic data and only small morphological samples are available.

Structural Variation of the Turtle Mitochondrial Control Region

The present study describes the most comprehensive comparison of turtle mtD-loop regions to date. The primary structure was compared from DNA sequences accessed from GenBank from 48 species in 13 families of extant turtles, and secondary structures of the mtD-loop region were inferred from thermal stabilities, using the program Mfold, for each superfamiliy of turtles. Both primary and secondary structures were found to be highly variable across the order. The Cryptodira showed conservation in the primary structure at conserved sequence blocks (CSBs), but the Pleurodira displayed limited conservation of primary structural characters, other than the coreTAS, a binding site for the helicase TWINKLE, which was highly conserved in the Central and Right Domains across the order. No secondary structure was associated with a TAS, but an AT-rich fold (secondary structure) near the 3' terminus of the mtD-loop region was detected in all turtle superfamilies. Mapping of character states of structural features of the mtD-loop region revealed that most character states were autapomorphies and inferred a number of homoplasies. The Left Domain of turtles, containing no highly conserved structural elements, likely does not serve a functional role; therefore, the Central Domain in turtles is likely equivalent to the Left Domain of mammals. The AT-rich secondary structural element near the 3' terminus of the mtD-loop region may be conserved across turtles because of a functional role, perhaps containing the Light Strand Promotor, or perhaps interacting with the TWINKLE-coreTAS complex in the Central and Right Domains to regulate mtDNA replication and transcription.

Six additional mitochondrial genomes for North American nightsnakes (Dipsadidae: Hypsiglena) and a novel gene feature for advanced snakes

The North American nightsnakes in the genus Hypsiglena is composed of nine named and at least two unnamed species. Here, we provide the first mt-genome of H. affinis, an additional mt-genome for H. sp. nov. 1, and four additional mt-genomes from the widespread H. jani. These mtDNA genomes were sequenced using both Illumina and Ion Torrent sequencing technologies. The resulting genomes contained the expected 13 protein coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions typical of colubroid snakes. Two of the H. jani samples had partial tRNA^Ile genes upstream of CR2 which has not been previously documented in colubroid snakes. A maximum likelihood gene-tree based on these data combined with previously published sequence data recovers a well-supported phylogeny and is in concordance with previous estimates of evolutionary relationships in this group.

Ketoh G, D’Cruze N. The first genetic assessment of wild and farmed ball pythons (Reptilia, Serpentes, Pythonidae) in southern Togo

The ball python (Python regius) is the world’s most commonly traded python species for the “exotic” pet industry. The majority of these live snakes are produced via a number of python farms in West Africa that have been in operation since the 1960s and involved with “ranching” operations since the 1990s. However, to date no thorough taxonomic review or genetic studies have been conducted within its range, despite the fact that the evaluation of a species’ genetic variability is generally considered mandatory for effective management. We used mtDNA sequence data and eight polymorphic microsatellite markers to assess the underlying population genetic structure and to test the potential of the nuclear markers to assign farm individuals to wild reference populations in southern Togo. Despite the relatively large distances between sample locations, no significant genetic population structure was found, either in mtDNA sequence data or in the microsatellite data. Instead, our data indicate considerable gene flow among the locations. The absence of a distinct population subdivision may have resulted from an anthropogenic driven admixture of populations associated with commercial wildlife trade activity in recent decades. Given the ongoing largely unregulated nature of the commercial ranching of ball pythons in West Africa, should a wild release component continue, as a first measure we recommend that the Management Authorities should develop an action plan with specific release protocols for python farms to minimise any potential negative conservation impacts resulting from admixture (genetic pollution) between farmed and wild individuals.

Next-generation sequencing yields a complete mitochondrial genome of the Tartar sand boa (Eryx tataricus) from Junggar Basin

The viviparous Tartar sand boa, Eryx tataricus, is a widespread species in arid Central Asia. A complete mitochondrial genome of one individual from Junggar Basin in Northwest China was determined by next-generation sequencing. The mitogenome is 17,537 bp in size, comprising 2 ribosomal RNA genes, 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 control regions. The order and structure of the genes are similar to those of other Henophidia snakes. Phylogenetic analysis based on 13 concatenated PCGs recovered the monophyly of Boidae and indicated that E. tataricus is closely related to Boa constrictor plus Eunectes notaeus.

The revised complete mitogenome sequence of the tree frog Polypedatesmegacephalus (Anura, Rhacophoridae) by next-generation sequencing and phylogenetic analysis

The mitochondrial genome (mitogenome) sequence of the tree frog Polypedates megacephalus (16,473 bp) was previously reported as having the unusual characteristic of lacking the ND5 gene. In this study, a new mitogenome of P. megacephalus (19,952 bp) was resequenced using the next-generation sequencing (NGS) and standard Sanger sequencing technologies. It was discovered that the ND5 gene was not lost but translocated to the control region (CR) from its canonical location between the ND4 and ND6 genes. In addition, a duplicated control region was found in the new mitogenome of this species. Conservative region identification of the ND5 gene and phylogenetic analysis confirmed that the ND5 gene was located between two control regions. The phylogenetic relationship among 20 related species of anura revealed a rearrangement of the ND5 gene during the evolutionary process. These results also highlighted the advantages of next-generation sequencing. It will not only decrease the time and cost of sequencing, but also will eliminate the errors in published mitogenome databases.

Characterization of five complete Cyrtodactylus mitogenome structures reveals low structural diversity and conservation of repeated sequences in the lineage

Mitochondrial genomes (mitogenomes) of five Cyrtodactylus were determined. Their compositions and structures were similar to most of the available gecko lizard mitogenomes as 13 protein-coding, two rRNA and 22 tRNA genes. The non-coding control region (CR) of almost all Cyrtodactylus mitogenome structures contained a repeated sequence named the 75-bp box family, except for C. auribalteatus which contained the 225-bp box. Sequence similarities indicated that the 225-bp box resulted from the duplication event of 75-bp boxes, followed by homogenization and fixation in C. auribalteatus. The 75-bp box family was found in most gecko lizards with high conservation (55-75% similarities) and could form secondary structures, suggesting that this repeated sequence family played an important role under selective pressure and might involve mitogenome replication and the likelihood of rearrangements in CR. The 75-bp box family was acquired in the common ancestral genome of the gecko lizard, evolving gradually through each lineage by independent nucleotide mutation. Comparison of gecko lizard mitogenomes revealed low structural diversity with at least six types of mitochondrial gene rearrangements. Cyrtodactylus mitogenome structure showed the same gene rearrangement as found in most gecko lizards. Advanced mitogenome information will enable a better understanding of structure evolution mechanisms.

Cytonuclear discordance in the Florida Everglades invasive Burmese python (Python bivittatus) population reveals possible hybridization with the Indian python (P. molurus)

The invasive Burmese python (Python bivittatus) has been reproducing in the Florida Everglades since the 1980s. These giant constrictor snakes have caused a precipitous decline in small mammal populations in southern Florida following escapes or releases from the commercial pet trade. To better understand the invasion pathway and genetic composition of the population, two mitochondrial (mtDNA) loci across 1,398 base pairs were sequenced on 426 snakes and 22 microsatellites were assessed on 389 snakes. Concatenated mtDNA sequences produced six haplotypes with an average nucleotide and haplotype diversity of π = 0.002 and h = 0.097, respectively. Samples collected in Florida from morphologically identified P. bivittatus snakes were similar to published cytochrome oxidase 1 and cytochrome b sequences from both P. bivittatus and Python molurus and were highly divergent (genetic distances of 5.4% and 4.3%, respectively). The average number of microsatellite alleles and expected heterozygosity were N A = 5.50 and H E = 0.60, respectively. Nuclear Bayesian assignment tests supported two genetically distinct groups and an admixed group, not geographically differentiated. The effective population size (N E = 315.1) was lower than expected for a population this large, but reflected the low genetic diversity overall. The patterns of genetic diversity between mtDNA and microsatellites were disparate, indicating nuclear introgression of separate mtDNA lineages corresponding to cytonuclear discordance. The introgression likely occurred prior to the invasion, but genetic information on the native range and commercial trade is needed for verification. Our finding that the Florida python population is comprised of distinct lineages suggests greater standing variation for adaptation and the potential for broader areas of suitable habitat in the invaded range.

The complete mitochondrial genomes of Tarsiger cyanurus and Phoenicurus auroreus: a phylogenetic analysis of Passeriformes

Passeriformes is the largest group within aves and the phylogenetic relationships between Passeriformes have caused major disagreement in ornithology. Particularly, the phylogenetic relationships between muscicapoidea and sylvioidea are complex, and their taxonomic boundaries have not been clearly defined. Our aim was to study the status of two bird species: Tarsiger cyanurus and Phoenicurus auroreus. Furthermore, we analyzed the phylogenetic relationships of Passeriformes. Complete mitochondrial DNA (mtDNA) sequences of both species were determined and the lengths were 16,803 (T. cyanurus) and 16,772 bp (P. auroreus), respectively. Thirteen protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region were identified in these mtDNAs. The contents of A and T at the base compositions was significantly higher than the content of G and C, and this AT skew was positive, while the GC skew was negative. The monophyly of Passeriformes is divided into four major clades: Corvoidea, Sylvioidea, Passeroidea, and Musicicapoidea. Paridae should be separated from the superfamily Sylvioidea and placed within the superfamily Muscicapoidea. The family Muscicapidae and Corvida were paraphyly, while Carduelis and Emberiza were grouped as a sister taxon. The relationships between some species of the order passeriformes may remain difficult to resolve despite an effort to collect additional characters for phylogenetic analysis. Current research of avian phylogeny should focus on adding characters and taxa and use both effectively to obtain a better resolution for deeper and shallow nodes.

Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

BACKGROUND

Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake's mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes.

RESULTS

In total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B, III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the O_L was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNA^Leu gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome.

CONCLUSIONS

The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity.

The complete mitochondrial genome of the parthenogenetic Caucasian rock lizard Darevskia unisexualis (Squamata: lacertidae) contains long tandem repeat formed by 59 bp monomer

The first complete mitochondrial genome sequence of parthenogenetic Caucasian rock lizard Darevskia unisexualis (Lacertidae family) is determined by hybrid assembly with Illumina HiSeq and PacBio RS II platforms. The circular 21.4 kbp mitogenome contains 13 protein-coding genes, 12S and 16S rRNA genes, 20 tRNAs, two pseudogenized tRNAs, and one long tandem repeats with 4.1 kbp length formed by 59 bp monomer repeated x70.6 times located before control region. This finding represents a new example of mitogenome variation in lizards of hybrid origin, providing fundamental data for following study of a unique hybridization system formed by parthenogenetic and bisexual species in the mountain steppe of central Armenia.

The complete mitochondrial genome of Bothrops jararaca (Reptilia, Serpentes, Viperidae)

The complete mitochondrial genome, containing 17,526 bp, was determined from the pitviper Bothrops jararaca. It is the first mitogenome for the most medically important genus of snake in Latin America. This mitogenome has common snake mitochondrial features such as a duplicated control region that has nearly identical sequences at two different locations of the mitogenome and a translocation of tRNA-Leu (UUR). Besides, we found a translocation of the tRNA-Pro compared to Colubridae snakes. Finally, an unusual possible duplication containing a tRNA-Phe was observed for the first time and may represent a marker of the genus.

Sequencing and analysis of the mitochondrial genome of Pituophis catenifer sayi (Squamata: Colubridae)

The complete DNA sequence of the mitochondrial genome of the bullsnake (Pituophis catenifer sayi) is presented and analyzed in this study. The genome is 17,193 bp in length, and contains 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 2 control regions. The overall base composition of the H-strand is A (34.5%), T (26.2%), C (25.8%) and G (12.7%). The gene order and orientation of the mitogenome is consistent with other sequenced genomes from colubrid snakes. Phylogenetic analyses using the ML, NJ and MP methods for a set of colubrids, including every sequenced genus within the sub-family Colubrinae, produced identical trees. We show that Pituophis is most closely related to the American ratsnake genus Pantherophis.

The complete mitochondrial genomes of sixteen ardeid birds revealing the evolutionary process of the gene rearrangements

BACKGROUND

The animal mitochondrial genome is generally considered to be under selection for both compactness and gene order conservation. As more mitochondrial genomes are sequenced, mitochondrial duplications and gene rearrangements have been frequently identified among diverse animal groups. Although several mechanisms of gene rearrangement have been proposed thus far, more observational evidence from major taxa is needed to validate specific mechanisms. In the current study, the complete mitochondrial DNA of sixteen bird species from the family Ardeidae was sequenced and the evolution of mitochondrial gene rearrangements was investigated. The mitochondrial genomes were then used to review the phylogenies of these ardeid birds.

RESULTS

The complete mitochondrial genome sequences of the sixteen ardeid birds exhibited four distinct mitochondrial gene orders in which two of them, named as "duplicate tRNA(Glu)-CR" and "duplicate tRNAThr-tRNA(Pro) and CR", were newly discovered. These gene rearrangements arose from an evolutionary process consistent with the tandem duplication--random loss model (TDRL). Additionally, duplications in these gene orders were near identical in nucleotide sequences within each individual, suggesting that they evolved in concert. Phylogenetic analyses of the sixteen ardeid species supported the idea that Ardea ibis, Ardea modesta and Ardea intermedia should be classified as genus Ardea, and Ixobrychus flavicollis as genus Ixobrychus, and indicated that within the subfamily Ardeinae, Nycticorax nycticorax is closely related to genus Egretta and that Ardeola bacchus and Butorides striatus are closely related to the genus Ardea.

CONCLUSIONS

The duplicate tRNAThr-CR gene order is found in most ardeid lineages, suggesting this gene order is the ancestral pattern within these birds and persisted in most lineages via concerted evolution. In two independent lineages, when the concerted evolution stopped in some subsections due to the accumulation of numerous substitutions and deletions, the duplicate tRNAThr-CR gene order was transformed into three other gene orders. The phylogenetic trees produced from concatenated rRNA and protein coding genes have high support values in most nodes, indicating that the mitochondrial genome sequences are promising markers for resolving the phylogenetic issues of ardeid birds when more taxa are added.

The complete mitochondrial genome of the Elaphe perlacea (Squamata: Colubridae)

The Pearl-banded rat-snake Elaphe perlacea (recently renamed Euprepiophis perlacea) belongs to the family Colubridae, and is only distributed in western Sichuan Province, China. In this study, the whole mitochondrial genome of E. perlacea was first sequenced. It was determined to be 17,160 bp and included 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 control regions (D-loop). Except for eight tRNAs and nd6 genes, all other mitochondrial genes were encoded on the heavy strand (H strand). Molecular data presented here provide a useful tool for helping set the stage for further studies and the molecular evolution of the mitochondrial genome.

Mitochondrial genome sequence of Sibynophis chinensis (Squamata, Colubridae)

The complete mitochondrial (mt) genome of the Chinese many-toothed snake, Sibynophis chinensis, was sequenced and found to be 17,163 bp in length. The arrangement of 13 protein-coding genes, tRNAs and rRNAs was identical to that of other common snake mt genomes. The mt protein-coding genes of S. chinensis utilized ATA, ATG, ATA and GTG as initiation codons and AGA, AGG, TAA, TAG and T as termination codons. Among three tRNA clusters (LQM, WANCY and HSL), LQM was found instead of IQM, which is common in other vertebrates. We also identified two control regions that contained several conserved elements known as conserved sequence blocks and termination-associated sequences related to mt replication and transcription.

The complete mitochondrial DNA sequence of Crotalus horridus (timber rattlesnake)

The complete mitogenome of the timber rattlesnake (Crotalus horridus) was completed using Sanger sequencing. It is 17,260 bp with 13 protein-coding genes, 21 tRNAs, two rRNAs and two control regions. Gene synteny is consistent with other snakes with the exception of a missing redundant tRNA (Ser) . This mitogenome should prove to be a useful addition of a well-known member of the Viperidae snake family.

Rates of molecular evolution vary in vertebrates for insulin-like growth factor-1 (IGF-1), a pleiotropic locus that regulates life history traits

Insulin-like growth factor-1 (IGF-1) is a member of the vertebrate insulin/insulin-like growth factor/relaxin gene family necessary for growth, reproduction, and survival at both the cellular and organismal level. Its sequence, protein structure, and function have been characterized in mammals, birds, and fish; however, a notable gap in our current knowledge of the function of IGF-1 and its molecular evolution is information in ectothermic reptiles. To address this disparity, we sequenced the coding region of IGF-1 in 11 reptile species-one crocodilian, three turtles, three lizards, and four snakes. Complete sequencing of the full mRNA transcript of a snake revealed the Ea-isoform, the predominant isoform of IGF-1 also reported in other vertebrate groups. A gene tree of the IGF-1 protein-coding region that incorporated sequences from diverse vertebrate groups showed similarity to the species phylogeny, with the exception of the placement of Testudines as sister group to Aves, due to their high nucleotide sequence similarity. In contrast, long-branch lengths indicate more rapid divergence in IGF-1 among lizards and snakes. Additionally, lepidosaurs (i.e., lizards and snakes) had higher rates of non-synonymous:synonymous substitutions (dN/dS) relative to archosaurs (i.e., birds and crocodilians) and turtles. Tests for positive selection on specific codons within branches and evaluation of the changes in the amino acid properties, suggested positive selection in lepidosaurs on the C domain of IGF-1, which is involved in binding affinity to the IGF-1 receptor. Predicted structural changes suggest that major alterations in protein structure and function may have occurred in reptiles. These data propose new insights into the molecular co-evolution of IGF-1 and its receptors, and ultimately the evolution of IGF-1's role in regulating life-history traits across vertebrates.

Complete mitochondrial genome sequence from an endangered Indian snake, Python molurus molurus (Serpentes, Pythonidae)

This paper reports the complete mitochondrial genome sequence of an endangered Indian snake, Python molurus molurus (Indian Rock Python). A typical snake mitochondrial (mt) genome of 17258 bp length comprising of 37 genes including the 13 protein coding genes, 22 tRNA genes, and 2 ribosomal RNA genes along with duplicate control regions is described herein. The P. molurus molurus mt. genome is relatively similar to other snake mt. genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases. The nucleotide composition of the genome shows that there are more A-C % than T-G% on the positive strand as revealed by positive AT and CG skews. Comparison of individual protein coding genes, with other snake genomes suggests that ATP8 and NADH3 genes have high divergence rates. Codon usage analysis reveals a preference of NNC codons over NNG codons in the mt. genome of P. molurus. Also, the synonymous and non-synonymous substitution rates (ka/ks) suggest that most of the protein coding genes are under purifying selection pressure. The phylogenetic analyses involving the concatenated 13 protein coding genes of P. molurus molurus conformed to the previously established snake phylogeny.

DNA barcoding amphibians and reptiles

Only a few major research programs are currently targeting COI barcoding of amphibians and reptiles (including chelonians and crocodiles), two major groups of tetrapods. Amphibian and reptile species are typically old, strongly divergent, and contain deep conspecific lineages which might lead to problems in species assignment with incomplete reference databases. As far as known, there is no single pair of COI primers that will guarantee a sufficient rate of success across all amphibian and reptile taxa, or within major subclades of amphibians and reptiles, which means that the PCR amplification strategy needs to be adjusted depending on the specific research question. In general, many more amphibian and reptile taxa have been sequenced for 16S rDNA, which for some purposes may be a suitable complementary marker, at least until a more comprehensive COI reference database becomes available. DNA barcoding has successfully been used to identify amphibian larval stages (tadpoles) in species-rich tropical assemblages. Tissue sampling, DNA extraction, and amplification of COI is straightforward in amphibians and reptiles. Single primer pairs are likely to have a failure rate between 5 and 50% if taxa of a wide taxonomic range are targeted; in such cases the use of primer cocktails or subsequent hierarchical usage of different primer pairs is necessary. If the target group is taxonomically limited, many studies have followed a strategy of designing specific primers which then allow an easy and reliable amplification of all samples.

Crocodilian phylogeny inferred from twelve mitochondrial protein-coding genes, with new complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae

We report complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae, whose gene orders match those of other crocodilians. Phylogenetic analyses based on the sequences of 12 mitochondrial protein-coding genes support monophyly of two crocodilian taxonomic families, Alligatoridae (genera Alligator, Caiman, and Paleosuchus) and Crocodylidae (genera Crocodylus, Gavialis, Mecistops, Osteolaemus, and Tomistoma). Our results are consistent with monophyly of all crocodilian genera. Within Alligatoridae, genus Alligator is the sister taxon of a clade comprising Caiman and Paleosuchus. Within Crocodylidae, the basal phylogenetic split separates a clade comprising Gavialis and Tomistoma from a clade comprising Crocodylus, Mecistops, and Osteolaemus. Mecistops and Osteolaemus form the sister taxon to Crocodylus. Within Crocodylus, we sampled five Indopacific species, whose phylogenetic ordering is ((C. mindorensis, C. novaeguineae), (C. porosus, (C. siamensis, C. palustris))). The African species C. niloticus and New World species C. acutus form the sister taxon to the Indopacific species, although our sampling lacks three other New World species and an Australian species of Crocodylus.

Mitochondrial genome evolution in fire ants (Hymenoptera: Formicidae)

Background

Complete mitochondrial genome sequences have become important tools for the study of genome architecture, phylogeny, and molecular evolution. Despite the rapid increase in available mitogenomes, the taxonomic sampling often poorly reflects phylogenetic diversity and is often also biased to represent deeper (family-level) evolutionary relationships.

Results

We present the first fully sequenced ant (Hymenoptera: Formicidae) mitochondrial genomes. We sampled four mitogenomes from three species of fire ants, genus Solenopsis, which represent various evolutionary depths. Overall, ant mitogenomes appear to be typical of hymenopteran mitogenomes, displaying a general A+T-bias. The Solenopsis mitogenomes are slightly more compact than other hymentoperan mitogenomes (~15.5 kb), retaining all protein coding genes, ribosomal, and transfer RNAs. We also present evidence of recombination between the mitogenomes of the two conspecific Solenopsis mitogenomes. Finally, we discuss potential ways to improve the estimation of phylogenies using complete mitochondrial genome sequences.

Conclusions

The ant mitogenome presents an important addition to the continued efforts in studying hymenopteran mitogenome architecture, evolution, and phylogenetics. We provide further evidence that the sampling across many taxonomic levels (including conspecifics and congeners) is useful and important to gain detailed insights into mitogenome evolution. We also discuss ways that may help improve the use of mitogenomes in phylogenetic analyses by accounting for non-stationary and non-homogeneous evolution among branches.

Molecular basis of infrared detection by snakes

Snakes possess a unique sensory system for detecting infrared radiation, enabling them to generate a 'thermal image' of predators or prey. Infrared signals are initially received by the pit organ, a highly specialized facial structure that is innervated by nerve fibres of the somatosensory system. How this organ detects and transduces infrared signals into nerve impulses is not known. Here we use an unbiased transcriptional profiling approach to identify TRPA1 channels as infrared receptors on sensory nerve fibres that innervate the pit organ. TRPA1 orthologues from pit-bearing snakes (vipers, pythons and boas) are the most heat-sensitive vertebrate ion channels thus far identified, consistent with their role as primary transducers of infrared stimuli. Thus, snakes detect infrared signals through a mechanism involving radiant heating of the pit organ, rather than photochemical transduction. These findings illustrate the broad evolutionary tuning of transient receptor potential (TRP) channels as thermosensors in the vertebrate nervous system.

The structure of the Australian and South American marsupial mitochondrial control region

BACKGROUND AND AIMS

The mitochondrial control region (CR) was studied across five marsupialian orders, in order to give a detailed overview of its features.

RESULTS

The CR is organised into three domains similar to the CR of placental mammals. However, the conservation of different features among the marsupial orders is in general more strict. In the first domain, two conserved blocks extended termination-associated sequences (ETAS 1 and ETAS 2) are present in all marsupial orders. In the third domain, the three conserved sequence blocks (CSB 1, CSB 2 and CSB 3) are present and complete, with CSB 1 being duplicated in four of five marsupial orders.

CONCLUSIONS

The nucleotide frequency and secondary structures of the repeats were typical for marsupial species. The repeats are generally AT-rich except in Dasyuridae and Paucituberculata, which show a significant increase in GC content.

Mitochondrial DNA variation reveals recent evolutionary history of main Boa constrictor clades

We sequenced a 1114-bp fragment of cytochrome b gene in six subspecies (115 samples) of Boa constrictor and detected 67 haplotypes. Our analyses revealed the presence of two distinct clades, one from Central America (CA) including the neighboring part of South America west of the Andes, and the other covering the rest of South America (SA). Sequence divergence between CA and SA clades is about 5-7%, which roughly corresponds to a separation at the time of uplift of the Colombian Andes following formation of the Panama Isthmus before 3.5 Myr Sequence divergence within the SA and CA clades is only 2-3%, suggesting a fairly recent spread of these clades Into their current geographic ranges. Thus, we may not be dealing with taxa with a markedly old evolutionary history. Because juveniles of B. constrictor feed mostly on small rodents, we hypothesized that spread of this species was allowed by a new food source represented by murold rodents that appeared after closure of the Panama portal. With respect to the taxonomy, B. c. imperator may be elevated to full species rank. Within the SA clade, a haplotype of Argentinian B. c. occidentalis is markedly distinct, while the remaining haplotype groups analyzed are distributed throughout large ranges and may all belong to a single nominotypic subspecies.

Snake mitochondrial genomes: phylogenetic relationships and implications of extended taxon sampling for interpretations of mitogenomic evolution

Background

Snake mitochondrial genomes are of great interest in understanding mitogenomic evolution because of gene duplications and rearrangements and the fast evolutionary rate of their genes compared to other vertebrates. Mitochondrial gene sequences have also played an important role in attempts to resolve the contentious phylogenetic relationships of especially the early divergences among alethinophidian snakes. Two recent innovative studies found dramatic gene- and branch-specific relative acceleration in snake protein-coding gene evolution, particularly along internal branches leading to Serpentes and Alethinophidia. It has been hypothesized that some of these rate shifts are temporally (and possibly causally) associated with control region duplication and/or major changes in ecology and anatomy.

Results

The near-complete mitochondrial (mt) genomes of three henophidian snakes were sequenced: Anilius scytale, Rhinophis philippinus, and Charina trivirgata. All three genomes share a duplicated control region and translocated tRNA^LEU, derived features found in all alethinophidian snakes studied to date. The new sequence data were aligned with mt genome data for 21 other species of snakes and used in phylogenetic analyses. Phylogenetic results agreed with many other studies in recovering several robust clades, including Colubroidea, Caenophidia, and Cylindrophiidae+Uropeltidae. Nodes within Henophidia that have been difficult to resolve robustly in previous analyses remained uncompellingly resolved here. Comparisons of relative rates of evolution of rRNA vs. protein-coding genes were conducted by estimating branch lengths across the tree. Our expanded sampling revealed dramatic acceleration along the branch leading to Typhlopidae, particularly long rRNA terminal branches within Scolecophidia, and that most of the dramatic acceleration in protein-coding gene rate along Serpentes and Alethinophidia branches occurred before Anilius diverged from other alethinophidians.

Conclusions

Mitochondrial gene sequence data alone may not be able to robustly resolve basal divergences among alethinophidian snakes. Taxon sampling plays an important role in identifying mitogenomic evolutionary events within snakes, and in testing hypotheses explaining their origin. Dramatic rate shifts in mitogenomic evolution occur within Scolecophidia as well as Alethinophidia, thus falsifying the hypothesis that these shifts in snakes are associated exclusively with evolution of a non-burrowing lifestyle, macrostomatan feeding ecology and/or duplication of the control region, both restricted to alethinophidians among living snakes.

Conservation phylogenetics of helodermatid lizards using multiple molecular markers and a supertree approach

We analyzed both mitochondrial (mt-) and nuclear (n) DNAs in a conservation phylogenetic framework to examine deep and shallow histories of the Beaded Lizard (Heloderma horridum) and Gila Monster (H. suspectum) throughout their geographic ranges in North and Central America. Both mtDNA and intron markers clearly partitioned each species. One intron and mtDNA further subdivided H. horridum into its four recognized subspecies (H. n. alvarezi, charlesbogerti,exasperatum, and horridum). However, the two subspecies of H. suspectum (H. s. suspectum and H. s. cinctum) were undefined. A supertree approach sustained these relationships. Overall, the Helodermatidae is reaffirmed as an ancient and conserved group. Its most recent common ancestor (MRCA) was Lower Eocene [35.4 million years ago (mya)], with a approximately 25 my period of stasis before the MRCA of H. horridum diversified in Lower Miocene. Another approximately 5 my passed before H. h. exasperatum and H. h. horridum diverged, followed by approximately 1.5 my before H. h. alvarezi and H. h. charlesbogerti separated. Heloderma suspectum reflects an even longer period of stasis (approximately 30 my) before diversifying from its MRCA. Both H. suspectum (México) and H. h. alvarezi also revealed evidence of historic range expansion following a recent bottleneck. Our conservation phylogenetic approach emphasizes the origin and diversification of this group, yields information on the manner by which past environmental variance may have impacted its populations and, in turn, allows us to disentangle historic from contemporary impacts that might threaten its long-term persistence. The value of helodermatid conservation resides in natural services and medicinal products, particularly venom constituents, and these are only now being realized.

Shedding light on serpent sight: the visual pigments of henophidian snakes

The biologist Gordon Walls proposed his "transmutation" theory through the 1930s and the 1940s to explain cone-like morphology of rods (and vice versa) in the duplex retinas of modern-day reptiles, with snakes regarded as the epitome of his hypothesis. Despite Walls' interest, the visual system of reptiles, and in particular snakes, has been widely neglected in favor of studies of fishes and mammals. By analyzing the visual pigments of two henophidian snakes, Xenopeltis unicolor and Python regius, we show that both species express two cone opsins, an ultraviolet-sensitive short-wavelength-sensitive 1 (SWS1) (lambda(max) = 361 nm) pigment and a long-wavelength-sensitive (LWS) (lambda(max) = 550 nm) pigment, providing the potential for dichromatic color vision. They also possess rod photoreceptors which express the usual rod opsin (Rh1) pigment with a lambda(max) at 497 nm. This is the first molecular study of the visual pigments expressed in the photoreceptors of any snake species. The presence of a duplex retina and the characterization of LWS, SWS1, and Rh1 visual pigments in henophidian snakes implies that "lower" snakes do not provide support for Walls' transmutation theory, unlike some "higher" (caenophidian) snakes and other reptiles, such as geckos. More data from other snake lineages will be required to test this hypothesis further.

Mitochondrial ND3 as the novel causative gene for Leber hereditary optic neuropathy and dystonia

Leber hereditary optic neuropathy and dystonia (LDYT) is a mitochondrial disorder associated with variable combinations of vision loss and progressive generalized dystonia. LDYT is a unique oxidative phosphorylation disorder caused by mutations in mitochondrial ND6 or ND4 gene. In this paper, we describe a Chinese family with 18 LDYT patients. The comprehensive nucleotide sequence analysis of the entire mitochondrial genome using resequencing microarray revealed a mutation (mtND3*10197A (m.10197G>A)) substituting a threonine for a highly conserved alanine at codon 47 of MTND3 on the background of haplogroup D4b. Quantitative analysis of the heteroplasmy of the mutation revealed a homoplasmy in the leukocytes of all the affected individuals on the maternal side. This is the first description of the ND3 mutation causing LDYT. The mtND3*10197A (m.10197G>A) mutation has recently been described in French and Korean patients with Leigh syndrome. These findings suggest that the clinical presentations associated with the mtND3*10197A (m.10197G>A) mutation (ND3) are much wider, encompassing those of LDYT and Leigh syndrome.