Mitochondrial genome data alone are not enough to unambiguously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Arthropoda)

The First Complete Mitochondrial Genome of the Genus Pachycondyla (Formicidae, Ponerinae) and Insights into the Phylogeny of Ants

Ants are the standout group among eusocial insects in terms of their exceptional species richness and ecological dominance. The phylogenetic relationships among the group remain elusive. Mitochondrial genome sequences, as a kind of molecular marker, have been widely utilized in the phylogenetic analysis of insects. However, the number of ant mitogenomes published is still very limited. In this study, we utilized next-generation sequencing to determine the complete mitogenome of Pachycondyla annamita (Formicidae, Ponerinae). This is the first mitogenome from the genus Pachycondyla. Two gene rearrangements were identified in the mitogenome, the transposition of trnQ and trnM and the transposition of trnV and rrnS. The secondary structures of tRNAs were predicted. The tRNA genes trnR and trnS1 lacked the dihydrouridine (DHU) arm, and the trnE lacked the TΨC (T) arm. Phylogenetic analyses of the mitochondrial protein-coding genes under maximum likelihood (ML) and Bayesian inference (BI) criteria resulted in conflicting hypotheses. BI analysis using amino acid data with the site-heterogeneous mixture model produced a tree topology congruent with previous studies. The Formicidae was subdivided into two main clades, namely the "poneroid" clade and the "formicoid" clade. A sister group relationship between Myrmicinae and Formicinae was recovered within the "formicoid" clade.

Mitogenomic phylogenetic analyses provide novel insights into the taxonomic problems of several hesperiid taxa (Lepidoptera: Hesperiidae)

Here, we present new molecular and morphological evidence that contributes towards clarifying the phylogenetic relations within the family Hesperiidae, and overcomes taxonomic problems regarding this family. First, nine new complete mitogenomes, comprising seven newly sequenced species and two samples of previously sequenced species collected from different localities, were obtained and assembled to analyze characteristics. The length of the mitogenomes ranges from 15,284 to 15,853 bp and encodes 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. Two model-based methods (maximum likelihood and Bayesian inference) were used to infer the phylogenetic relationships. Based on the mitogenomic phylogenetic analyses and morphological evidence, we claim that the lineage that comprises two Asian genera, Apostictopterus Leech and Barca de Nicéville, should be a tribe Barcini stat. nov. of the subfamily Trapezitinae, Pseudocoladenia dea (Leech, 1894), P. festa (Evans, 1949), and Abraximorpha esta Evans, 1949 are considered distinct species. Finally, we suggest that Lotongus saralus chinensis Evans, 1932 should belong to the genus Acerbas de Nicéville, 1895, namely Acerbas saralus chinensis (Evans, 1932) comb. nov..

Conflicts in Mitochondrial Phylogenomics of Branchiopoda, with the First Complete Mitogenome of Laevicaudata (Crustacea: Branchiopoda)

Conflicting phylogenetic signals are pervasive across genomes. The potential impact of such systematic biases may be reduced by phylogenetic approaches accommodating for heterogeneity or by the exclusive use of homoplastic sites in the datasets. Here, we present the complete mitogenome of Lynceus grossipedia as the first representative of the suborder Laevicaudata. We employed a phylogenomic approach on the mitogenomic datasets representing all major branchiopod groups to identify the presence of conflicts and concordance across the phylogeny. We found pervasive phylogenetic conflicts at the base of Diplostraca. The homogeneity of the substitution pattern tests and posterior predictive tests revealed a high degree of compositional heterogeneity among branchiopod mitogenomes at both the nucleotide and amino acid levels, which biased the phylogenetic inference. Our results suggest that Laevicaudata as the basal clade of Phyllopoda was most likely an artifact caused by compositional heterogeneity and conflicting phylogenetic signal. We demonstrated that the exclusive use of homoplastic site methods combining the application of site-heterogeneous models produced correct phylogenetic estimates of the higher-level relationships among branchiopods.

Comparative mitochondrial genome analysis and phylogenetic relationship among lepidopteran species

Lepidoptera has rich species including many agricultural pests and economical insects around the world. The mitochondrial genomes (mitogenomes) were utilized to explore the phylogenetic relationships between difference taxonomic levels in Lepidoptera. However, the knowledge of mitogenomic characteristics and phylogenetic position about superfamily-level in this order is unresolved. In this study, we integrated 794 mitogenomes consisting of 37 genes and a noncoding control region, which covered 26 lepidopteran superfamilies from newly sequenced and publicly available genomes for comparative genomic and phylogenetic analysis. In primitive taxon, putative start codon of cox1 gene was ATA or ATT instead of CGA, but stop codon of that showed four types, namely TAA, TAG, TA and T. The 7-bp overlap between atp8 and atp6 presented as "ATGATAA". Moreover, the most frequently utilized amino acids were leucine (UUA) in 13 PCGs. Phylogenetic analysis showed that the main backbone relationship in Lepidoptera was (Hepialoidea + (Nepticuloidea + (Adeloidea + (Tischerioidea + (Tineoidea + (Yponomeutoidea + (Gracillarioidea + (Papilionoidea + ((Zygaenoidea + Tortricoidea) + (Gelechioidea + (Pyraloidea + ((Geometroidea + Noctuoidea) + (Lasiocampoidea + Bombycoidea))))))))))))).

Morphological characterization and mt DNA barcode of a tiger moth species, Asota ficus (Fabricius, 1775) (Lepidoptera: Noctuoidea: Erebidae: Aganainae) from India

The members of the genus Asota are widely distributed from Africa, India, Sri Lanka, Myanmar, and Malayan regions to the Australian region containing 55 described species. Asota ficus (Fabricius, 1775) is one among the nine species of the genus described from India having a wide range of distribution. The present study includes the first mitochondrial DNA barcode generated from India for A. ficus with a valid voucher describing external morphological characters together with the male and female genitalia. Discussions pertain to the utility of DNA barcodes for studies on moths in India with a comment on the identity of other sequences showing shallow genetic divergence with our sequences.

Whole-genome single nucleotide polymorphism and mating compatibility studies reveal the presence of distinct species in sub-Saharan Africa Bemisia tabaci whiteflies

In sub-Saharan Africa cassava growing areas, two members of the Bemisia tabaci species complex termed sub-Saharan Africa 1 (SSA1) and SSA2 have been reported as the prevalent whiteflies associated with the spread of viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) pandemics. At the peak of CMD pandemic in the late 1990s, SSA2 was the prevalent whitefly, although its numbers have diminished over the last two decades with the resurgence of SSA1 whiteflies. Three SSA1 subgroups (SG1 to SG3) are the predominant whiteflies in East Africa and vary in distribution and biological properties. Mating compatibility between SSA1 subgroups and SSA2 whiteflies was reported as the possible driver for the resurgence of SSA1 whiteflies. In this study, a combination of both phylogenomic methods and reciprocal crossing experiments were applied to determine species status of SSA1 subgroups and SSA2 whitefly populations. Phylogenomic analyses conducted with 26 548 205 bp whole genome single nucleotide polymorphisms (SNPs) and the full mitogenomes clustered SSA1 subgroups together and separate from SSA2 species. Mating incompatibility between SSA1 subgroups and SSA2 further demonstrated their distinctiveness from each other. Phylogenomic analyses conducted with SNPs and mitogenomes also revealed different genetic relationships among SSA1 subgroups. The former clustered SSA1-SG1 and SSA1-SG2 together but separate from SSA1-SG3, while the latter clustered SSA1-SG2 and SSA1-SG3 together but separate from SSA1-SG1. Mating compatibility was observed between SSA1-SG1 and SSA1-SG2, while incompatibility occurred between SSA1-SG1 and SSA1-SG3, and SSA1-SG2 and SSA1-SG3. Mating results among SSA1 subgroups were coherent with phylogenomics results based on SNPs but not the full mitogenomes. Furthermore, this study revealed that the secondary endosymbiont-Wolbachia-did not mediate reproductive success in the crossing assays carried out. Overall, using genome wide SNPs together with reciprocal crossings assays, this study established accurate genetic relationships among cassava-colonizing populations, illustrating that SSA1 and SSA2 are distinct species while at least two species occur within SSA1 species.

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

The order Microcoryphia, commonly known as bristletails, is considered as the most primitive one among living insects. Within this order, two species, Coreamachilis coreanus and C. songi (Machilidae: Machilinae), display the following contrasting reproductive strategies: parthenogenesis occurs in C. coreanus, whereas sexual reproduction is found in C. songi. In the present study, the complete mitogenomes of C. coreanus and C. songi were sequenced to compare their mitogenome structure, analyze relationships within the Microcoryphia, and assess adaptive evolution. The length of the mitogenomes of C. coreanus and C. songi were 15,578 bp and 15,570 bp, respectively, and the gene orders were those of typical insects. A long hairpin structure was found between the ND1 and 16S rRNA genes of both species that seem to be characteristic of Machilinae and Petrobiinae species. Phylogenetic assessment of Coreamachilis was conducted using BI and ML analyses with concatenated nucleotide sequences of the 13 protein-coding genes. The results showed that the monophyly of Machilidae, Machilinae, and Petrobiinae was not supported. The genus Coreamachilis (C. coreanus and C. songi) was a sister clade to Allopsontus helanensis, and then the clade of ((C. coreanus + C. songi) + A. helanensis) was a sister clade to A. baii, which suggests that the monophyly of Allopsontus was not supported. Positive selection analysis of the 13 protein-coding genes failed to reveal any positive selection in C. coreanus or C. songi. The long hairpin structures found in Machilinae and Petrobiinae were highly consistent with the phylogenetic results and could potentially be used as an additional molecular characteristic to further discuss relationships within the Microcoryphia.

Three Complete Mitochondrial Genomes of Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis (Insecta: Phasmatodea) and Their Phylogeny

Insects of the order Phasmatodea are mainly distributed in the tropics and subtropics and are best known for their remarkable camouflage as plants. In this study, we sequenced three complete mitochondrial genomes from three different families: Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis. The lengths of the three mitochondrial genomes were 15,896 bp, 16,869 bp, and 17,005 bp, respectively, and the gene composition and structure of the three stick insects were identical to those of the most recent common ancestor of insects. The phylogenetic relationships among stick insects have been chaotic for a long time. In order to discuss the intra- and inter-ordinal relationship of Phasmatodea, we used the 13 protein-coding genes (PCGs) of 85 species for maximum likelihood (ML) and Bayesian inference (BI) analyses. Results showed that the internal topological structure of Phasmatodea had a few differences in both ML and BI trees and long-branch attraction (LBA) appeared between Embioptera and Zoraptera, which led to a non-monophyletic Phasmatodea. Consequently, after removal of the Embioptera and Zoraptera species, we re-performed ML and BI analyses with the remaining 81 species, which showed identical topology except for the position of Tectarchus ovobessus (Phasmatodea). We recovered the monophyly of Phasmatodea and the sister-group relationship between Phasmatodea and Mantophasmatodea. Our analyses also recovered the monophyly of Heteropterygidae and the paraphyly of Diapheromeridae, Phasmatidae, Lonchodidae, Lonchodinae, and Clitumninae. In this study, Peruphasma schultei (Pseudophasmatidae), Phraortes sp. YW-2014 (Lonchodidae), and species of Diapheromeridae clustered into the clade of Phasmatidae. Within Heteropterygidae, O. guangxiensis was the sister clade to O. mouhotii belonging to Dataminae, and the relationship of (Heteropteryginae + (Dataminae + Obriminae)) was recovered.

Increasing 28 mitogenomes of Ephemeroptera, Odonata and Plecoptera support the Chiastomyaria hypothesis with three different outgroup combinations

BACKGROUND

The phylogenetic relationships of Odonata (dragonflies and damselflies) and Ephemeroptera (mayflies) remain unresolved. Different researchers have supported one of three hypotheses (Palaeoptera, Chiastomyaria or Metapterygota) based on data from different morphological characters and molecular markers, sometimes even re-assessing the same transcriptomes or mitochondrial genomes. The appropriate choice of outgroups and more taxon sampling is thought to eliminate artificial phylogenetic relationships and obtain an accurate phylogeny. Hence, in the current study, we sequenced 28 mt genomes from Ephemeroptera, Odonata and Plecoptera to further investigate phylogenetic relationships, the probability of each of the three hypotheses, and to examine mt gene arrangements in these species. We selected three different combinations of outgroups to analyze how outgroup choice affected the phylogenetic relationships of Odonata and Ephemeroptera.

METHODS

Mitochondrial genomes from 28 species of mayflies, dragonflies, damselflies and stoneflies were sequenced. We used Bayesian inference (BI) and Maximum likelihood (ML) analyses for each dataset to reconstruct an accurate phylogeny of these winged insect orders. The effect of outgroup choice was assessed by separate analyses using three outgroups combinations: (a) four bristletails and three silverfish as outgroups, (b) five bristletails and three silverfish as outgroups, or (c) five diplurans as outgroups.

RESULTS

Among these sequenced mitogenomes we found the gene arrangement IMQM in Heptageniidae (Ephemeroptera), and an inverted and translocated tRNA-Ile between the 12S RNA gene and the control region in Ephemerellidae (Ephemeroptera). The IMQM gene arrangement in Heptageniidae (Ephemeroptera) can be explained via the tandem-duplication and random loss model, and the transposition and inversion of tRNA-Ile genes in Ephemerellidae can be explained through the recombination and tandem duplication-random loss (TDRL) model. Our phylogenetic analysis strongly supported the Chiastomyaria hypothesis in three different outgroup combinations in BI analyses. The results also show that suitable outgroups are very important to determining phylogenetic relationships in the rapid evolution of insects especially among Ephemeroptera and Odonata. The mt genome is a suitable marker to investigate the phylogeny of inter-order and inter-family relationships of insects but outgroup choice is very important for deriving these relationships among winged insects. Hence, we must carefully choose the correct outgroup in order to discuss the relationships of Ephemeroptera and Odonata.

Complete mitochondrial genomes of Epeorus carinatus and E. dayongensis (Ephemeroptera: Heptageniidae): Genomic comparison and phylogenetic inference

The current research on Ephemeroptera is mainly based on its morphology, since only small numbers of mitogenomes have been reported. In this study, the mitogenomes of Epeorus carinatus (15,338 bp) and E. dayongensis (15,609 bp) were sequenced, annotated and compared to genome data from congeners. Both mitogenomes had 23 tRNA genes including standard 22 and one extra tRNA^Met. The duplicated tRNA^Met gene had been found in other heptageniid species except Paegniodes cupulatus, suggesting it could be used as a molecular synapomorphy for partial Heptageniidae. The phylogenetic analyses based on Bayesian Inference (BI) and Maximum Likelihood (ML) showed that Heptageniidae was monophyletic and the relationships among known Epeorus species were ((E. carinatus + E. herklotsi) + (E. dayongensis + E. sp. 1)), which implied the focal species E. carinatus and E. dayongensis should be grouped into different subgenera.

The complete mitochondrial genome of Pedetontus zhejiangensis (Microcoryphia: Machilidae) and its phylogeny

The complete mitochondrial genome of Pedetontus zhejiangensis (Microcoryphia: Machilidae) was successfully sequenced. The mitochondrial genome of P. zhejiangensis was a circular molecule of 15,602 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and the control region, which showed the typical insect mitochondrial genome arrangement. The AT content of the whole genome was 73.8% and the length of the control region was 671 bp with 82.5% AT content. In BI and ML phylogenetic trees, P. zhejiangensis was a sister group to Pedetontus silvestrii, and the monophyly of Pedetontus was strongly supported. The genus Pedetontinus was a sister group to Pedetontus.

Description of soybean aphid (Aphis glycines Matsumura) mitochondrial genome and comparative mitogenomics of Aphididae (Hemiptera: Sternorrhyncha)

The complete mitochondrial genome of the soybean aphid (Aphis glycines Matsumura), a major agricultural pest in the world, is described for the first time, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, as well as a large repeat region between tRNA-Glu and tRNA-Phe, and an AT-rich control region. The 17,954 bp mtgenome is the largest reported from the family Aphididae, and its gene order follows the ancestral insect mtgenome except for the repeat region, which contains a 195 bp unit repeated 11.9 times, representing the highest reported repeats among the known aphid mtgenomes to date. A new molecular phylogeny of Aphidae is reconstructed based on all available aphid mtgenomes, and it is shown that the mtgenome data can robustly resolve relationships at the subfamily level, but do not have sufficient phylogenetic information to resolve deep relationships. A phylogeny-based comparative analysis of mtgenomes has been performed to investigate the evolution of the repeat region between tRNA-Glu and tRNA-Phe. So far, among aphids, 13 species are known to have this repeat region of variable lengths, and a phylogenetic analysis of the repeat region shows that a large proportion of the sequences are conserved across the phylogeny, suggesting that the repeat region evolved in the most recent common ancestor of Aphidinae and Eriosomatinae, and that it has gone through numerous episodes of lineage-specific losses and expansions. Combined together, this study provides novel insights into how the repeat regions have evolved within aphids.

Complete mitochondrial genome of bamboo grasshopper, Ceracris fasciata, and the phylogenetic analyses and divergence time estimation of Caelifera (Orthoptera)

The bamboo grasshopper Ceracris fasciata is regarded as a major pest species because of the damage it causes to bamboo, and its classification within the families and subfamilies of the suborder Caelifera remains unclear. Thus, we attempted to resolve these questions using molecular biology methods and analyses. Our results are as follows: (1) the complete mitochondrial genome of C. fasciata is 15,569 bp in length. The mitochondrial genome contains a standard set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and an A + T-rich region in the same order as those of the other analysed Caeliferan species. The putative start codon for the COX1 gene in C. fasciata is ACC, although it is not defined in other genes. The presence of tandem repeats of different sizes in the A + T-rich region may lead to size differences in other mitochondrial genomes. The mitochondrial genome of C. fasciata harbours the typical 37 genes and an A + T-rich region, and it shows similar characteristics to those of other grasshopper species. Characterization of the mitochondrial genome has enriched our knowledge of the mitochondrial genomes of Orthoptera around the world. Therefore, the phylogenetic relationships in Orthoptera can be re-examined. (2) In phylogenetic analyses, the monophyly of Orthoptera and its two suborders (Caelifera and Ensifera) has been consistently recovered based on most of the datasets selected, regardless of the optimal criteria. Our results do not support the monophyly of the subfamily Oedipodinae of Caelifera. We found that Phlaeoba albonema of the Acridinae is sorted into a clade with Ceracris in all our phylogenetic trees, and field experiments show that Phlaeoba always lives with Ceracris in the same ecotopes. Therefore, we suggest that Phlaeoba should be classified as a member of the Oedipodinae. We found that C. fasciata always clustered with Ceracris kiangsu, and both were sisters to Ceracris versicolor. Therefore, the genetic relationship between C. fasciata and C. kiangsu is closer than that between C. fasciata and C. versicolor. (3) The oldest estimated time of divergence of Ensifera in this context was determined to be 146.16 million years ago (Mya), or around the late Jurassic or early Cretaceous. We estimated that katydids (Grylloidea) likely diverged from other groups in the early Cretaceous. According to our divergence time analyses, we concluded that the ancestral Acrididae probably originated in the early Paleogene, and it is likely that the major diversification events happened at the middle Paleogene, well into the next geologic time. We estimated that crickets (Tettigoniidae) likely diverged from other groups in the early Cretaceous. Acrididae and Romaleinae group, Pyrgacrididae and Ommexechidae group, the youngest two clades we observed, were estimated to have diverged 58.79 Mya, between the middle and early Paleogene. C. versicolor is a sister to the group containing C. kiangsu and C. fasciata. First, C. versicolor diverged from the sister group (C. kiangsu + C. fasciata) around 44.81 Mya, and then the C. kiangsu and C. fasciata group separated at 43.04 Mya.

The mitochondrial genome of Caenis sp. (Ephemeroptera: Caenidae) and the phylogeny of Ephemeroptera in Pterygota

The phylogenetic relationship between Ephemeroptera (mayflies) and Odonata (dragonflies and damselflies) remains hotly debated in the insect evolution community. We sequenced the complete mitochondrial genome of Caenis sp. (Ephemeroptera: Caenidae) to discuss the phylogenetic relationship of Palaeoptera. The mitochondrial genome of Caenis sp. is a circular molecule of 15,254 bp in length containing 37 genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs), which showed the typical insect mitochondrial gene arrangement. In BI and ML phylogenetic trees using 71 species of 12 orders, our results support the Ephemeroptera as the basal group of winged insects.

Complete mitochondrial genomes of Nanorana taihangnica and N. yunnanensis (Anura: Dicroglossidae) with novel gene arrangements and phylogenetic relationship of Dicroglossidae

BACKGROUND

Complete mitochondrial (mt) genomes have been used extensively to test hypotheses about microevolution and to study population structure, phylogeography, and phylogenetic relationships of Anura at various taxonomic levels. Large-scale mt genomic reorganizations have been observed among many fork-tongued frogs (family Dicroglossidae). The relationships among Dicroglossidae and validation of the genus Feirana are still problematic. Hence, we sequenced the complete mt genomes of Nanorana taihangnica (=F. taihangnica) and N. yunnanensis as well as partial mt genomes of six Quasipaa species (dicroglossid taxa), two Odorrana and two Amolops species (Ranidae), and one Rhacophorus species (Rhacophoridae) in order to identify unknown mt gene rearrangements, to investigate the validity of the genus Feirana, and to test the phylogenetic relationship of Dicroglossidae.

RESULTS

In the mt genome of N. taihangnica two trnM genes, two trnP genes and two control regions were found. In addition, the trnA, trnN, trnC, and trnQ genes were translocated from their typical positions. In the mt genome of N. yunnanensis, three control regions were found and eight genes (ND6, trnP, trnQ, trnA, trnN, trnC, trnY and trnS genes) in the L-stand were translocated from their typical position and grouped together. We also found intraspecific rearrangement of the mitochondrial genomes in N. taihangnica and Quasipaa boulengeri. In phylogenetic trees, the genus Feirana nested deeply within the clade of genus Nanorana, indicating that the genus Feirana may be a synonym to Nanorana. Ranidae as a sister clade to Dicroglossidae and the clade of (Ranidae + Dicroglossidae) as a sister clade to (Mantellidae + Rhacophoridae) were well supported in BI analysis but low bootstrap in ML analysis.

CONCLUSIONS

We found that the gene arrangements of N. taihangnica and N. yunnanensis differed from other published dicroglossid mt genomes. The gene arrangements in N. taihangnica and N. yunnanensis could be explained by the Tandem Duplication and Random Loss (TDRL) and the Dimer-Mitogenome and Non-Random Loss (DMNR) models, respectively. The invalidation of the genus Feirana is supported in this study.

The impact of GC bias on phylogenetic accuracy using targeted enrichment phylogenomic data

The field of sequence based phylogenetic analyses is currently being transformed by novel hybrid-based targeted enrichment methods, such as the use of ultraconserved elements (UCEs). Rather than analyzing relationships among organisms using a small number of genes, these methods now allow us to evaluate relationships with many hundreds to thousands of individual gene loci. However, the inclusion of thousands of loci does not necessarily overcome the long-standing challenge of incongruence among phylogenetic trees derived from different genes or gene regions. One factor that impacts the level of incongruence in phylogenomic data sets is the level of GC bias. GC rich gene regions are prone to higher recombination rates than AT rich regions, driven by a process referred to as "GC biased gene conversion". As a result, high GC content can be negatively associated with phylogenetic accuracy, but the extent to which this impacts incongruence among UCEs is currently unstudied. We investigated the impact of GC content on phylogeny reconstruction using in silico captured UCE data for the corbiculate bees (Hymenoptera: Apidae). The phylogeny of this group has been the subject of extensive study, and incongruence among gene trees is thought to be a source of phylogenetic error. We conducted coalescent- and concatenation-based analyses of 810 individual gene loci from all 13 currently available bee genomes, including 8 corbiculate taxa. Both coalescent- and concatenation-based methods converged on a single topology for the corbiculate tribes. In contrast to concatenation, the coalescent-based methods revealed significant topological conflict at nodes involving the orchid bees (Euglossini) and honeybees (Apini). Partitioning the loci by GC content reveals decreasing support for the inferred topology with increasing GC bias. Based on the results of this study, we report the first evidence that GC biased gene conversion may contribute to topological incongruence in studies based on ultraconserved elements.

Mitochondrial genomes of the hoverflies Episyrphus balteatus and Eupeodes corollae (Diptera: Syrphidae), with a phylogenetic analysis of Muscomorpha

The hoverflies Episyrphus balteatus and Eupeodes corollae (Diptera: Muscomorpha: Syrphidae) are important natural aphid predators. We obtained mitochondrial genome sequences from these two species using methods of PCR amplification and sequencing. The complete Episyrphus mitochondrial genome is 16,175 bp long while the incomplete one of Eupeodes is 15,326 bp long. All 37 typical mitochondrial genes are present in both species and arranged in ancestral positions and directions. The two mitochondrial genomes showed a biased A/T usage versus G/C. The cox1, cox2, cox3, cob and nad1 showed relatively low level of nucleotide diversity among protein-coding genes, while the trnM was the most conserved one without any nucleotide variation in stem regions within Muscomorpha. Phylogenetic relationships among the major lineages of Muscomorpha were reconstructed using a complete set of mitochondrial genes. Bayesian and maximum likelihood analyses generated congruent topologies. Our results supported the monophyly of five species within the Syrphidae (Syrphoidea). The Platypezoidea was sister to all other species of Muscomorpha in our phylogeny. Our study demonstrated the power of the complete mitochondrial gene set for phylogenetic analysis in Muscomorpha.

Progress, pitfalls and parallel universes: a history of insect phylogenetics

The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985-2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.

Characterization of the complete mitogenomes of two Neoscona spiders (Araneae: Araneidae) and its phylogenetic implications

The complete mitogenomes of two orb-weaving spiders Neoscona doenitzi and Neoscona nautica were determined and a comparative mitogenomic analysis was performed to depict evolutionary trends of spider mitogenomes. The circular mitogenomes are 14,161bp with A+T content of 74.6% in N. doenitzi and 14,049bp with A+T content of 78.8% in N. nautica, respectively. Both mitogenomes contain a standard set of 37 genes typically presented in metazoans. Gene content and orientation are identical to all previously sequenced spider mitogenomes, while gene order is rearranged by tRNAs translocation when compared with the putative ancestral gene arrangement pattern presented by Limulus polyphemus. A comparative mitogenomic analysis reveals that the nucleotide composition bias is obviously divergent between spiders in suborder Opisthothelae and Mesothelae. The loss of D-arm in the trnS(UCN) among all of Opisthothelae spiders highly suggested that this common feature is a synapomorphy for entire suborder Opisthothelae. Moreover, the trnS(AGN) in araneoids preferred to use TCT as an anticodon rather than the typical anticodon GCT. Phylogenetic analysis based on the 13 protein-coding gene sequences consistently yields trees that nest the two Neoscona spiders within Araneidae and recover superfamily Araneoidea as a monophyletic group. The molecular information acquired from the results of this study should be very useful for future research on mitogenomic evolution and genetic diversities in spiders.

Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site-Heterogeneous Mixture Models

After decades of debate, a mostly satisfactory resolution of relationships among the 11 recognized holometabolan orders of insects has been reached based on nuclear genes, resolving one of the most substantial branches of the tree-of-life, but the relationships are still not well established with mitochondrial genome data. The main reasons have been the absence of sufficient data in several orders and lack of appropriate phylogenetic methods that avoid the systematic errors from compositional and mutational biases in insect mitochondrial genomes. In this study, we assembled the richest taxon sampling of Holometabola to date (199 species in 11 orders), and analyzed both nucleotide and amino acid data sets using several methods. We find the standard Bayesian inference and maximum-likelihood analyses were strongly affected by systematic biases, but the site-heterogeneous mixture model implemented in PhyloBayes avoided the false grouping of unrelated taxa exhibiting similar base composition and accelerated evolutionary rate. The inclusion of rRNA genes and removal of fast-evolving sites with the observed variability sorting method for identifying sites deviating from the mean rates improved the phylogenetic inferences under a site-heterogeneous model, correctly recovering most deep branches of the Holometabola phylogeny. We suggest that the use of mitochondrial genome data for resolving deep phylogenetic relationships requires an assessment of the potential impact of substitutional saturation and compositional biases through data deletion strategies and by using site-heterogeneous mixture models. Our study suggests a practical approach for how to use densely sampled mitochondrial genome data in phylogenetic analyses.

Large-scale mitogenomics enables insights into Schizophora (Diptera) radiation and population diversity

True flies are insects of the order Diptera and encompass one of the most diverse groups of animals on Earth. Within dipterans, Schizophora represents a recent radiation of insects that was used as a model to develop a pipeline for generating complete mitogenomes using various sequencing platforms and strategies. 91 mitogenomes from 32 different species were sequenced and assembled with high fidelity, using amplicon, whole genome shotgun or single molecule sequencing approaches. Based on the novel mitogenomes, we estimate the origin of Schizophora within the Cretaceous-Paleogene (K-Pg) boundary, about 68.3 Ma. Detailed analyses of the blowfly family (Calliphoridae) place its origin at 22 Ma, concomitant with the radiation of grazing mammals. The emergence of ectoparasitism within calliphorids was dated 6.95 Ma for the screwworm fly and 2.3 Ma for the Australian sheep blowfly. Varying population histories were observed for the blowfly Chrysomya megacephala and the housefly Musca domestica samples in our dataset. Whereas blowflies (n = 50) appear to have undergone selective sweeps and/or severe bottlenecks in the New World, houseflies (n = 14) display variation among populations from different zoogeographical zones and low levels of gene flow. The reported high-throughput mitogenomics approach for insects enables new insights into schizophoran diversity and population history of flies.

The morphology of the eggs of three species of Zoraptera (Insecta)

The egg structure of Zorotypus magnicaudelli, Zorotypus hubbardi and Zorotypus impolitus was examined and described in detail. Major characteristics of zorapteran eggs previously reported were confirmed in these species, with the partial exception of Z. impolitus: 1) a pair of micropyles at the equator of the egg's ventral side, 2) a honeycomb pattern on the egg surface, 3) a two-layered chorion, 4) micropylar canals running laterally, 5) a flap covering the inner opening of the micropylar canal and 6) no region specialized for hatching. These features are probably part of the groundplan of the order. Three groups (A-C) and two subgroups (A1 and A2) of Zoraptera can be distinguished based on characters of the reproductive apparatus including eggs. However, information for more species is needed for a reliable interpretation of the complex and apparently fast evolving character system. The egg of Z. impolitus presumably shows apomorphic characteristics not occurring in other species, a chorion without layered construction and polygonal surface compartments with different sculptures on the dorsal and ventral sides of the egg. Another feature found in this species, distinct enlargement of the micropyles, is also found in Z. hubbardi. The increased micropylar size is likely correlated with the giant spermatozoa produced by males of these two species. These two features combined with the large size of the spermatheca are arguably a complex synapomorphy of Z. hubbardi and Z. impolitus. The phylogenetic placement of Zoraptera is discussed based on the egg structure. A clade of Zoraptera + Eukinolabia appears most plausible, but the issue remains an open question.

Morphological and molecular characterization of Thelohanellus hoffmanni sp. nov. (Myxozoa) infecting goldfish Carassius auratus auratus

A new species of the genus Thelohanellus Kudo, 1933 (Myxosporea, Bivalvulida) was isolated from the fins of goldfish Carassius auratus auratus (Linnaeus 1758). The fish had been imported from China by an Austrian retailer. Nodules from the margins of the fins contained pyriform myxospores with a singular polar capsule. In valvular view, the spores measured 12.2 µm in length and 6.4 µm in width. In sutural view, the thickness was 2.9 µm. The polar capsule measured 4.2 × 3.1 µm and contained a polar filament with 8 to 9 coils. Histological sections showed plasmodia of 0.2 to 4.0 mm diameter with the earlier developmental stages of the parasite in the periphery and the mature spores closer to the center. In the transmission electron microscope examination, the different developmental stages could be observed. Morphological data, host specificity, tissue tropism, and molecular analysis of the small subunit rDNA identify this parasite as a new species of Thelohanellus, which we have named Thelohanellus hoffmanni sp. nov.

Genome of the Rusty Millipede, Trigoniulus corallinus, Illuminates Diplopod, Myriapod, and Arthropod Evolution

The increasing availability of genomic information from the Arthropoda continues to revolutionize our understanding of the biology of this most diverse animal phylum. However, our sampling of arthropod diversity remains uneven, and key clade such as the Myriapoda are severely underrepresented. Here we present the genome of the cosmopolitanly distributed Rusty Millipede Trigoniulus corallinus, which represents the first diplopod genome to be published, and the second example from the Myriapoda as a whole. This genomic resource contains the majority of core eukaryotic genes (94.3%), and key transcription factor classes that were thought to be lost in the Ecdysozoa. Mitochondrial genome and gene family (transcription factor, Dscam, circadian clock-driving protein, odorant receptor cassette, bioactive compound, and cuticular protein) analyses were also carried out to shed light on their states in the Diplopoda and Myriapoda. The ready availability of T. corallinus recommends it as a new model for evolutionary developmental biology, and the data set described here will be of widespread utility in investigating myriapod and arthropod genomics and evolution.

Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences

Mitochondrial (mt) genome data have been proven to be informative for animal phylogenetic studies but may also suffer from systematic errors, due to the effects of accelerated substitution rate and compositional heterogeneity. We analyzed the mt genomes of 25 insect species from the four paraneopteran orders, aiming to better understand how accelerated substitution rate and compositional heterogeneity affect the inferences of the higher-level phylogeny of this diverse group of hemimetabolous insects. We found substantial heterogeneity in base composition and contrasting rates in nucleotide substitution among these paraneopteran insects, which complicate the inference of higher-level phylogeny. The phylogenies inferred with concatenated sequences of mt genes using maximum likelihood and Bayesian methods and homogeneous models failed to recover Psocodea and Hemiptera as monophyletic groups but grouped, instead, the taxa that had accelerated substitution rates together, including Sternorrhyncha (a suborder of Hemiptera), Thysanoptera, Phthiraptera and Liposcelididae (a family of Psocoptera). Bayesian inference with nucleotide sequences and heterogeneous models (CAT and CAT + GTR), however, recovered Psocodea, Thysanoptera and Hemiptera each as a monophyletic group. Within Psocodea, Liposcelididae is more closely related to Phthiraptera than to other species of Psocoptera. Furthermore, Thysanoptera was recovered as the sister group to Hemiptera.

The complete mitochondrial genomes of three bristletails (Insecta: Archaeognatha): the paraphyly of Machilidae and insights into archaeognathan phylogeny

The order Archaeognatha was an ancient group of Hexapoda and was considered as the most primitive of living insects. Two extant families (Meinertellidae and Machilidae) consisted of approximately 500 species. This study determined 3 complete mitochondrial genomes and 2 nearly complete mitochondrial genome sequences of the bristletail. The size of the 5 mitochondrial genome sequences of bristletail were relatively modest, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. The gene orders were identical to that of Drosophila yakuba and most bristletail species suggesting a conserved genome evolution within the Archaeognatha. In order to estimate archaeognathan evolutionary relationships, phylogenetic analyses were conducted using concatenated nucleotide sequences of 13 protein-coding genes, with four different computational algorithms (NJ, MP, ML and BI). Based on the results, the monophyly of the family Machilidae was challenged by both datasets (W12 and G12 datasets). The relationships among archaeognathan subfamilies seemed to be tangled and the subfamily Machilinae was also believed to be a paraphyletic group in our study.

The mitochondrial genome of the land snail Camaenacicatricosa (Müller, 1774) (Stylommatophora, Camaenidae): the first complete sequence in the family Camaenidae

The complete mitochondrial (mt) genome of the snail Camaenacicatricosa (Müller, 1774) has been sequenced and annotated in this study. The entire circular genome is 13,843 bp in size and represents the first camaenid mt genome, with content of 31.9%A, 37.9%T, 13.5%C and 16.7%G. Gene content, codon usage and base organization show similarity to a great extent to the sequenced mt genome from Stylommatophora, whereas, gene order is different from them, especially the positions of tRNA(Cys) , tRNA(Phe) , COII, tRNA(Asp) , tRNA(Gly) , tRNA(His) and tRNA(Trp) . All protein coding genes use standard initiation codons ATN except for COII with GTG as start signal. Conventional stop codons TAA and TAG have been assigned to all protein coding genes. All tRNA genes possess the typical clover leaf structure, but the TψC arm of tRNA(Asp) and dihydrouridine arm of tRNA(Ser(AGN)) only form a simple loop. Shorter intergenic spacers have been found in this mt genome. Phylogenetic study based on protein coding genes shows close relationship of Camaenidae and Bradybaenidae. The presented phylogeny is consistent with the monophyly of Stylommatophora.

Comparative mitogenomics of plant bugs (Hemiptera: Miridae): identifying the AGG codon reassignments between serine and lysine

Insect mitochondrial genomes are very important to understand the molecular evolution as well as for phylogenetic and phylogeographic studies of the insects. The Miridae are the largest family of Heteroptera encompassing more than 11,000 described species and of great economic importance. For better understanding the diversity and the evolution of plant bugs, we sequence five new mitochondrial genomes and present the first comparative analysis of nine mitochondrial genomes of mirids available to date. Our result showed that gene content, gene arrangement, base composition and sequences of mitochondrial transcription termination factor were conserved in plant bugs. Intra-genus species shared more conserved genomic characteristics, such as nucleotide and amino acid composition of protein-coding genes, secondary structure and anticodon mutations of tRNAs, and non-coding sequences. Control region possessed several distinct characteristics, including: variable size, abundant tandem repetitions, and intra-genus conservation; and was useful in evolutionary and population genetic studies. The AGG codon reassignments were investigated between serine and lysine in the genera Adelphocoris and other cimicomorphans. Our analysis revealed correlated evolution between reassignments of the AGG codon and specific point mutations at the antidocons of tRNALys and tRNASer(AGN). Phylogenetic analysis indicated that mitochondrial genome sequences were useful in resolving family level relationship of Cimicomorpha. Comparative evolutionary analysis of plant bug mitochondrial genomes allowed the identification of previously neglected coding genes or non-coding regions as potential molecular markers. The finding of the AGG codon reassignments between serine and lysine indicated the parallel evolution of the genetic code in Hemiptera mitochondrial genomes.

The complete nucleotide sequence of the mitochondrial genome of Bactrocera minax (Diptera: Tephritidae)

The complete 16,043 bp mitochondrial genome (mitogenome) of Bactrocera minax (Diptera: Tephritidae) has been sequenced. The genome encodes 37 genes usually found in insect mitogenomes. The mitogenome information for B. minax was compared to the homologous sequences of Bactrocera oleae, Bactrocera tryoni, Bactrocera philippinensis, Bactrocera carambolae, Bactrocera papayae, Bactrocera dorsalis, Bactrocera correcta, Bactrocera cucurbitae and Ceratitis capitata. The analysis indicated the structure and organization are typical of, and similar to, the nine closely related species mentioned above, although it contains the lowest genome-wide A+T content (67.3%). Four short intergenic spacers with a high degree of conservation among the nine tephritid species mentioned above and B. minax were observed, which also have clear counterparts in the control regions (CRs). Correlation analysis among these ten tephritid species revealed close positive correlation between the A+T content of zero-fold degenerate sites (P0FD), the ratio of nucleotide substitution frequency at P0FD sites to all degenerate sites (zero-fold degenerate sites, two-fold degenerate sites and four-fold degenerate sites) and amino acid sequence distance (ASD) were found. Further, significant positive correlation was observed between the A+T content of four-fold degenerate sites (P4FD) and the ratio of nucleotide substitution frequency at P4FD sites to all degenerate sites; however, we found significant negative correlation between ASD and the A+T content of P4FD, and the ratio of nucleotide substitution frequency at P4FD sites to all degenerate sites. A higher nucleotide substitution frequency at non-synonymous sites compared to synonymous sites was observed in nad4, the first time that has been observed in an insect mitogenome. A poly(T) stretch at the 5' end of the CR followed by a [TA(A)]n-like stretch was also found. In addition, a highly conserved G+A-rich sequence block was observed in front of the poly(T) stretch among the ten tephritid species and two tandem repeats were present in the CR.

Mitogenomic sequences effectively recover relationships within brush-footed butterflies (Lepidoptera: Nymphalidae)

BACKGROUND

Mitogenomic phylogenies have revealed well-supported relationships for many eukaryote groups. In the order Lepidoptera, 113 species mitogenomes had been sequenced (May 14, 2014). However, these data are restricted to ten of the forty-three recognised superfamilies, while it has been challenging to recover large numbers of mitogenomes due to the time and cost required for primer design and sequencing. Nuclear rather than mitochondrial genes have been preferred to reconstruct deep-level lepidopteran phylogenies, without seriously evaluating the potential of entire mitogenomes. Next-generation sequencing methods remove these limitations by providing efficiently massive amounts of sequence data. In the present study, we simultaneously obtained a large number of nymphalid butterfly mitogenomes to evaluate the utility of mitogenomic phylogenies by comparing reconstructions to the now quite well established phylogeny of Nymphalidae.

RESULTS

We newly obtained 30 nymphalid mitogenomes via pyrosequencing on the Roche 454 GS Junior system, and combined these sequences with publicly accessible data to provide a 70-taxa dataset covering 37 genes for a 15,495 bp alignment. Polymorphic sites were not homogeneously distributed across the gene. Two gene regions, nad6 and 3' end of nad5, were most variable, whereas the cox1 and 5' ends of rrnL were most conserved. Phylogenetic relationships inferred by two likelihood methods were congruent and strongly supported (>0.95 posterior probability; ML bootstrap >85%), across the majority of nodes for multiple partitioning strategies and substitution models. Bayes factor results showed that the most highly partitioned dataset is the preferred strategy among different partitioning schemes. The most striking phylogenetic findings were that the subfamily Danainae not Libytheinae was sister of the remaining brush-footed butterflies and that, within Limenitidini, the genus Athyma was clearly polyphyletic. None of the single-gene phylogenies recovered the highly supported topologies generated on the basis of the whole mitogenomic data.

CONCLUSIONS

Thirty mitogenomes were assembled with 89% completeness from the contigs of pyrosequencing-derived reads. Entire mitogenomes or higher-quality sequences could be obtained by increasing pyrosequencing read coverage or by additional Sanger sequencing. Our mitogenomic phylogenies provide robust nodal support at a range of levels, demonstrating that mitogenomes are both accurate and efficient molecular markers for inferring butterfly phylogeny.

Molecular phylogeny of Myriapoda provides insights into evolutionary patterns of the mode in post-embryonic development

Myriapoda, a subphylum of Arthropoda, comprises four classes, Chilopoda, Diplopoda, Pauropoda, and Symphyla. While recent molecular evidence has shown that Myriapoda is monophyletic, the internal phylogeny, which is pivotal for understanding the evolutionary history of myriapods, remains unresolved. Here we report the results of phylogenetic analyses and estimations of divergence time and ancestral state of myriapods. Phylogenetic analyses were performed based on three nuclear protein-coding genes determined from 19 myriapods representing the four classes (17 orders) and 11 outgroup species. The results revealed that Symphyla whose phylogenetic position has long been debated is the sister lineage to all other myriapods, and that the interordinal relationships within classes were consistent with traditional classifications. Ancestral state estimation based on the tree topology suggests that myriapods evolved from an ancestral state that was characterized by a hemianamorphic mode of post-embryonic development and had a relatively low number of body segments and legs.

Comparative analysis of mitochondrial genomes in Diplura (hexapoda, arthropoda): taxon sampling is crucial for phylogenetic inferences

Two-pronged bristletails (Diplura) are traditionally classified into three major superfamilies: Campodeoidea, Projapygoidea, and Japygoidea. The interrelationships of these three superfamilies and the monophyly of Diplura have been much debated. Few previous studies included Projapygoidea in their phylogenetic considerations, and its position within Diplura still is a puzzle from both morphological and molecular points of view. Until now, no mitochondrial genome has been sequenced for any projapygoid species. To fill in this gap, we determined and annotated the complete mitochondrial genome of Octostigma sinensis (Octostigmatidae, Projapygoidea), and of three more dipluran species, one each from the Campodeidae, Parajapygidae, and Japygidae. All four newly sequenced dipluran mtDNAs encode the same set of genes in the same gene order as shared by most crustaceans and hexapods. Secondary structure truncations have occurred in trnR, trnC, trnS1, and trnS2, and the reduction of transfer RNA D-arms was found to be taxonomically correlated, with Campodeoidea having experienced the most reduction. Partitioned phylogenetic analyses, based on both amino acids and nucleotides of the protein-coding genes plus the ribosomal RNA genes, retrieve significant support for a monophyletic Diplura within Pancrustacea, with Projapygoidea more closely related to Campodeoidea than to Japygoidea. Another key finding is that monophyly of Diplura cannot be recovered unless Projapygoidea is included in the phylogenetic analyses; this explains the dipluran polyphyly found by past mitogenomic studies. Including Projapygoidea increased the sampling density within Diplura and probably helped by breaking up a long-branch-attraction artifact. This finding provides an example of how proper sampling is significant for phylogenetic inference.

Molecular phylogenetic analyses support the monophyly of Hexapoda and suggest the paraphyly of Entognatha

BACKGROUND

Molecular phylogenetic analyses have revealed that Hexapoda and Crustacea form a common clade (the Pancrustacea), which is now widely accepted among zoologists; however, the origin of Hexapoda remains unresolved. The main problems are the unclear relationships among the basal hexapod lineages, Protura (proturans), Collembola (springtails), Diplura (diplurans), and Ectognatha (bristletails, silverfishes, and all winged insects). Mitogenomic analyses have challenged hexapod monophyly and suggested the reciprocal paraphyly of Hexapoda and Crustacea, whereas studies based on nuclear molecular data support the monophyletic origin of hexapods. Additionally, there are significant discrepancies with respect to these issues between the results of morphological and molecular studies. To investigate these problems, we performed phylogenetic analyses of Pancrustacea based on the protein sequences of three orthologous nuclear genes encoding the catalytic subunit of DNA polymerase delta and the largest and second largest subunits of RNA polymerase II from 64 species of arthropods, including representatives of all hexapod orders.

RESULTS

Phylogenetic analyses were conducted based on the inferred amino acid (aa) sequences (~3400 aa in total) of the three genes using the maximum likelihood (ML) method and Bayesian inference. Analyses were also performed with additional datasets generated by excluding long-branch taxa or by using different outgroups. These analyses all yielded essentially the same results. All hexapods were clustered into a common clade, with Branchiopoda as its sister lineage, whereas Crustacea was paraphyletic. Within Hexapoda, the lineages Ectognatha, Palaeoptera, Neoptera, Polyneoptera, and Holometabola were each confirmed to be monophyletic with robust support, but monophyly was not supported for Entognatha (Protura + Collembola + Diplura), Ellipura (Protura + Collembola), or Nonoculata (Protura + Diplura). Instead, our results showed that Protura is the sister lineage to all other hexapods and that Diplura or Diplura + Collembola is closely related to Ectognatha.

CONCLUSION

This is the first study to include all hexapod orders in a phylogenetic analysis using multiple nuclear protein-coding genes to investigate the phylogeny of Hexapoda, with an emphasis on Entognatha. The results strongly support the monophyletic origin of hexapods but reject the monophyly of Entognatha, Ellipura, and Nonoculata. Our results provided the first molecular evidence in support of Protura as the sister group to other hexapods. These findings are expected to provide additional insights into the origin of hexapods and the processes involved in the adaptation of insects to life on land.

The phylogeny of the Orthoptera (Insecta) as deduced from mitogenomic gene sequences

Background

The phylogeny of the Orthoptera was analyzed based on 6 datasets from 47 orthopteran mitochondrial genomes (mitogenomes). The phylogenetic signals in the mitogenomes were rigorously examined under analytical regimens of maximum likelihood (ML) and Bayesian inference (BI), along with how gene types and different partitioning schemes influenced the phylogenetic reconstruction within the Orthoptera. The monophyly of the Orthoptera and its two suborders (Caelifera and Ensifera) was consistently recovered in the analyses based on most of the datasets we selected, regardless of the optimality criteria.

Results

When the seven NADH dehydrogenase subunits were concatenated into a single alignment (NADH) and were analyzed; a near-identical topology to the traditional morphological analysis was recovered, especially for BI_NADH. In both the concatenated cytochrome oxidase (COX) subunits and COX + cytochrome b (Cyt b) datasets, the small extent of sequence divergence seemed to be helpful for resolving relationships among major Orthoptera lineages (between suborders or among superfamilies). The conserved and variable domains of ribosomal (r)RNAs performed poorly when respectively analyzed but provided signals at some taxonomic levels.

Conclusions

Our findings suggest that the best phylogenetic inferences can be made when moderately divergent nucleotide data from mitogenomes are analyzed, and that the NADH dataset was suited for studying orthopteran phylogenetic relationships at different taxonomic levels, which may have been due to the larger amount of DNA sequence data and the larger number of phylogenetically informative sites.

Insect mitochondrial genomics: implications for evolution and phylogeny

The mitochondrial (mt) genome is, to date, the most extensively studied genomic system in insects, outnumbering nuclear genomes tenfold and representing all orders versus very few. Phylogenomic analysis methods have been tested extensively, identifying compositional bias and rate variation, both within and between lineages, as the principal issues confronting accurate analyses. Major studies at both inter- and intraordinal levels have contributed to our understanding of phylogenetic relationships within many groups. Genome rearrangements are an additional data type for defining relationships, with rearrangement synapomorphies identified across multiple orders and at many different taxonomic levels. Hymenoptera and Psocodea have greatly elevated rates of rearrangement offering both opportunities and pitfalls for identifying rearrangement synapomorphies in each group. Finally, insects are model systems for studying aberrant mt genomes, including truncated tRNAs and multichromosomal genomes. Greater integration of nuclear and mt genomic studies is necessary to further our understanding of insect genomic evolution.

Arthropod phylogenetics in light of three novel millipede (myriapoda: diplopoda) mitochondrial genomes with comments on the appropriateness of mitochondrial genome sequence data for inferring deep level relationships

BACKGROUND

Arthropods are the most diverse group of eukaryotic organisms, but their phylogenetic relationships are poorly understood. Herein, we describe three mitochondrial genomes representing orders of millipedes for which complete genomes had not been characterized. Newly sequenced genomes are combined with existing data to characterize the protein coding regions of myriapods and to attempt to reconstruct the evolutionary relationships within the Myriapoda and Arthropoda.

RESULTS

The newly sequenced genomes are similar to previously characterized millipede sequences in terms of synteny and length. Unique translocations occurred within the newly sequenced taxa, including one half of the Appalachioria falcifera genome, which is inverted with respect to other millipede genomes. Across myriapods, amino acid conservation levels are highly dependent on the gene region. Additionally, individual loci varied in the level of amino acid conservation. Overall, most gene regions showed low levels of conservation at many sites. Attempts to reconstruct the evolutionary relationships suffered from questionable relationships and low support values. Analyses of phylogenetic informativeness show the lack of signal deep in the trees (i.e., genes evolve too quickly). As a result, the myriapod tree resembles previously published results but lacks convincing support, and, within the arthropod tree, well established groups were recovered as polyphyletic.

CONCLUSIONS

The novel genome sequences described herein provide useful genomic information concerning millipede groups that had not been investigated. Taken together with existing sequences, the variety of compositions and evolution of myriapod mitochondrial genomes are shown to be more complex than previously thought. Unfortunately, the use of mitochondrial protein-coding regions in deep arthropod phylogenetics appears problematic, a result consistent with previously published studies. Lack of phylogenetic signal renders the resulting tree topologies as suspect. As such, these data are likely inappropriate for investigating such ancient relationships.

Phylogeny of the Paracalanidae Giesbrecht, 1888 (Crustacea: Copepoda: Calanoida)

The Paracalanidae are ecologically-important marine planktonic copepods that occur in the epipelagic zone in temperate and tropical waters. They are often the dominant taxon - in terms of biomass and abundance - in continental shelf regions. As primary consumers, they form a vital link in the pelagic food web between primary producers and higher trophic levels. Despite the ecological importance of the taxon, evolutionary and systematic relationships within the family remain largely unknown. A multigene phylogeny including 24 species, including representatives for all seven genera, was determined based on two nuclear genes, small-subunit (18S) ribosomal RNA and Histone 3 (H3) and one mitochondrial gene, cytochrome c oxidase subunit I (COI). The molecular phylogeny was well supported by Maximum likelihood and Bayesian inference analysis; all genera were found to be monophyletic, except for Paracalanus, which was separated into two distinct clades: the Paracalanus aculeatus group and Paracalanus parvus group. The molecular phylogeny also confirmed previous findings that Mecynocera and Calocalanus are genera of the family Paracalanidae. For comparison, a morphological phylogeny was created for 35 paracalanid species based on 54 morphological characters derived from published descriptions. The morphological phylogeny did not resolve all genera as monophyletic and bootstrap support was not strong. Molecular and morphological phylogenies were not congruent in the positioning of Bestiolina and the Paracalanus species groups, possibly due to the lack of sufficient phylogenetically-informative morphological characters.

The first mitochondrial genome for the wasp superfamily Platygastroidea: the egg parasitoid Trissolcus basalis

The nearly complete mitochondrial (mt) genome of an egg parasitoid, Trissolcus basalis (Wollaston), was sequenced using both 454 and Illumina next-generation sequencing technologies. A portion of the noncoding region remained unsequenced, possibly owing to the presence of repeats. The sequenced portion of the genome is 15,768 bp and has a high A+T content (84.2%), as is typical for hymenopteran mt genomes. A total of 36 of the 37 genes normally present in animal mt genomes were located. The one exception was trnR; a truncated version of this gene is present between trnS(1) and nd5, but it is unclear whether this gene fragment could code for the entire trnR gene. The mt gene arrangement of T. basalis is different from other Proctotrupomorpha mt genomes, with a number of trn genes in different positions. However, no shared derived gene rearrangements were identified in the present study. Bayesian analyses of mt genomes from 29 hymenopteran taxa and seven other orders of holometabolous insects support some uncontroversial evolutionary relationships, but indicate that much higher levels of taxonomic sampling are necessary for the resolution of family and superfamily relationships.

The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae)

Many of true bugs are important insect pests to cultivated crops and some are important vectors of human diseases, but few cladistic analyses have addressed relationships among the seven infraorders of Heteroptera. The Enicocephalomorpha and Nepomorpha are consider the basal groups of Heteroptera, but the basal-most lineage remains unresolved. Here we report the mitochondrial genome of the unique-headed bug Stenopirates sp., the first mitochondrial genome sequenced from Enicocephalomorpha. The Stenopirates sp. mitochondrial genome is a typical circular DNA molecule of 15, 384 bp in length, and contains 37 genes and a large non-coding fragment. The gene order differs substantially from other known insect mitochondrial genomes, with rearrangements of both tRNA genes and protein-coding genes. The overall AT content (82.5%) of Stenopirates sp. is the highest among all the known heteropteran mitochondrial genomes. The strand bias is consistent with other true bugs with negative GC-skew and positive AT-skew for the J-strand. The heteropteran mitochondrial atp8 exhibits the highest evolutionary rate, whereas cox1 appears to have the lowest rate. Furthermore, a negative correlation was observed between the variation of nucleotide substitutions and the GC content of each protein-coding gene. A microsatellite was identified in the putative control region. Finally, phylogenetic reconstruction suggests that Enicocephalomorpha is the sister group to all the remaining Heteroptera.

What is the phylogenetic signal limit from mitogenomes? The reconciliation between mitochondrial and nuclear data in the Insecta class phylogeny

BACKGROUND

Efforts to solve higher-level evolutionary relationships within the class Insecta by using mitochondrial genomic data are hindered due to fast sequence evolution of several groups, most notably Hymenoptera, Strepsiptera, Phthiraptera, Hemiptera and Thysanoptera. Accelerated rates of substitution on their sequences have been shown to have negative consequences in phylogenetic inference. In this study, we tested several methodological approaches to recover phylogenetic signal from whole mitochondrial genomes. As a model, we used two classical problems in insect phylogenetics: The relationships within Paraneoptera and within Holometabola. Moreover, we assessed the mitochondrial phylogenetic signal limits in the deeper Eumetabola dataset, and we studied the contribution of individual genes.

RESULTS

Long-branch attraction (LBA) artefacts were detected in all the datasets. Methods using Bayesian inference outperformed maximum likelihood approaches, and LBA was avoided in Paraneoptera and Holometabola when using protein sequences and the site-heterogeneous mixture model CAT. The better performance of this method was evidenced by resulting topologies matching generally accepted hypotheses based on nuclear and/or morphological data, and was confirmed by cross-validation and simulation analyses. Using the CAT model, the order Strepsiptera was recovered as sister to Coleoptera for the first time using mitochondrial sequences, in agreement with recent results based on large nuclear and morphological datasets. Also the Hymenoptera-Mecopterida association was obtained, leaving Coleoptera and Strepsiptera as the basal groups of the holometabolan insects, which coincides with one of the two main competing hypotheses. For the Paraneroptera, the currently accepted non-monophyly of Homoptera was documented as a phylogenetic novelty for mitochondrial data. However, results were not satisfactory when exploring the entire Eumetabola, revealing the limits of the phylogenetic signal that can be extracted from Insecta mitogenomes. Based on the combined use of the five best topology-performing genes we obtained comparable results to whole mitogenomes, highlighting the important role of data quality.

CONCLUSION

We show for the first time that mitogenomic data agrees with nuclear and morphological data for several of the most controversial insect evolutionary relationships, adding a new independent source of evidence to study relationships among insect orders. We propose that deeper divergences cannot be inferred with the current available methods due to sequence saturation and compositional bias inconsistencies. Our exploratory analysis indicates that the CAT model is the best dealing with LBA and it could be useful for other groups and datasets with similar phylogenetic difficulties.

The mitochondrial genome of Sinentomon erythranum (Arthropoda: Hexapoda: Protura): an example of highly divergent evolution

BACKGROUND

The phylogenetic position of the Protura, traditionally considered the most basal hexapod group, is disputed because it has many unique morphological characters compared with other hexapods. Although mitochondrial genome information has been used extensively in phylogenetic studies, such information is not available for the Protura. This has impeded phylogenetic studies on this taxon, as well as the evolution of the arthropod mitochondrial genome.

RESULTS

In this study, the mitochondrial genome of Sinentomon erythranum was sequenced, as the first proturan species to be reported. The genome contains a number of special features that differ from those of other hexapods and arthropods. As a very small arthropod mitochondrial genome, its 14,491 nucleotides encode 37 typical mitochondrial genes. Compared with other metazoan mtDNA, it has the most biased nucleotide composition with T = 52.4%, an extreme and reversed AT-skew of -0.351 and a GC-skew of 0.350. Two tandemly repeated regions occur in the A+T-rich region, and both could form stable stem-loop structures. Eighteen of the 22 tRNAs are greatly reduced in size with truncated secondary structures. The gene order is novel among available arthropod mitochondrial genomes. Rearrangements have involved in not only small tRNA genes, but also PCGs (protein-coding genes) and ribosome RNA genes. A large block of genes has experienced inversion and another nearby block has been reshuffled, which can be explained by the tandem duplication and random loss model. The most remarkable finding is that trnL2(UUR) is not located between cox1 and cox2 as observed in most hexapod and crustacean groups, but is between rrnL and nad1 as in the ancestral arthropod ground pattern. The "cox1-cox2" pattern was further confirmed in three more representative proturan species. The phylogenetic analyses based on the amino acid sequences of 13 mitochondrial PCGs suggest S. erythranum failed to group with other hexapod groups.

CONCLUSIONS

The mitochondrial genome of S. erythranum shows many different features from other hexapod and arthropod mitochondrial genomes. It underwent highly divergent evolution. The "cox1-cox2" pattern probably represents the ancestral state for all proturan mitogenomes, and suggests a long evolutionary history for the Protura.

A new view of insect-crustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics

The enormous diversity of Arthropoda has complicated attempts by systematists to deduce the history of this group in terms of phylogenetic relationships and phenotypic change. Traditional hypotheses regarding the relationships of the major arthropod groups (Chelicerata, Myriapoda, Crustacea, and Hexapoda) focus on suites of morphological characters, whereas phylogenomics relies on large amounts of molecular sequence data to infer evolutionary relationships. The present discussion is based on expressed sequence tags (ESTs) that provide large numbers of short molecular sequences and so provide an abundant source of sequence data for phylogenetic inference. This study presents well-supported phylogenies of diverse arthropod and metazoan outgroup taxa obtained from publicly-available databases. An in-house bioinformatics pipeline has been used to compile and align conserved orthologs from each taxon for maximum likelihood inferences. This approach resolves many currently accepted hypotheses regarding internal relationships between the major groups of Arthropoda, including monophyletic Hexapoda, Tetraconata (Crustacea + Hexapoda), Myriapoda, and Chelicerata sensu lato (Pycnogonida + Euchelicerata). "Crustacea" is a paraphyletic group with some taxa more closely related to the monophyletic Hexapoda. These results support studies that have utilized more restricted EST data for phylogenetic inference, yet they differ in important regards from recently published phylogenies employing nuclear protein-coding sequences. The present results do not, however, depart from other phylogenies that resolve Branchiopoda as the crustacean sister group of Hexapoda. Like other molecular phylogenies, EST-derived phylogenies alone are unable to resolve morphological convergences or evolved reversals and thus omit what may be crucial events in the history of life. For example, molecular data are unable to resolve whether a Hexapod-Branchiopod sister relationship infers a branchiopod-like ancestry of the Hexapoda, or whether this assemblage originates from a malacostracan-like ancestor, with the morphologically simpler Branchiopoda being highly derived. Whereas this study supports many internal arthropod relationships obtained by other sources of molecular data, other approaches are required to resolve such evolutionary scenarios. The approach presented here turns out to be essential: integrating results of molecular phylogenetics and neural cladistics to infer that Branchiopoda evolved simplification from a more elaborate ancestor. Whereas the phenomenon of evolved simplification may be widespread, it is largely invisible to molecular techniques unless these are performed in conjunction with morphology-based strategies.