The first mitogenomic phylogenetic framework of Dorcus sensu lato (Coleoptera: Lucanidae), with an emphasis on generic taxonomy in Eastern Asia

BACKGROUND

Dorcus stag beetles in broad sense are one of the most diverse group in Lucanidae and important saproxylic insects playing a crucial role in nutrient recycling and forest biomonitoring. However, the dazzling morphological differentiations have caused numerous systematic confusion within the big genus, especially the puzzlingly generic taxonomy. So far, there is lack of molecular phylogenetic study to address the chaotic situation. In this study, we undertook mitochondrial genome sequencing of 42 representative species including 18 newly-sequenced ones from Eastern Asia and reconstructed the phylogenetic framework of stag beetles in Dorcus sensu lato for the first time.

RESULTS

The mitogenome datasets of Dorcus species have indicated the variable mitogenomic lengths ranged from 15,785 to 19,813 bp. Each mitogenome contained 13 PCGs, 2 rRNAs, 22 tRNAs, and a control region, and all PCGs were under strong purifying selection (Ka/Ks < 1). Notably, we have identified the presence of a substantial intergenic spacer (IGS) between the trnAser (UCN) and NAD1 genes, with varying lengths ranging from 129 bp (in D. hansi) to 158 bp (in D. tityus). The mitogenomic phylogenetic analysis of 42 species showed that Eastern Asia Dorcus was monophyletic, and divided into eight clades with significant genetic distance. Four of them, Clade VIII, VII, VI and I are clustered by the representative species of Serrognathus Motschulsky, Kirchnerius Schenk, Falcicornis Séguy and Dorcus s.s. respectively, which supported their fully generic positions as the previous morphological study presented. The topology also showed the remaining clades were distinctly separated from the species of Dorcus sensu lato, which implied that each of them might demonstrate independent generic status. The Linnaeus nomenclatures were suggested as Eurydorcus Didier stat. res., Eurytrachellelus Didier stat. res., Hemisodorcus Thomson stat. res. and Velutinodorcus Maes stat. res. For Clade V, IV, III and II respectively.

CONCLUSION

This study recognized the monophyly of Dorcus stag beetles and provided a framework for the molecular phylogeny of this group for the first time. The newly generated mitogenomic data serves as a valuable resource for future investigations on lucanid beetles. The generic relationship would facilitate the systematics of Dorcus stag beetles and thus be useful for exploring their evolutionary, ecological, and conservation aspects.

Characterization of Four Complete Mitogenomes of Monolepta Species and Their Related Phylogenetic Implications

Monolepta is one of the diverse genera in the subfamily Galerucinae, including 708 species and 6 sub-species worldwide. To explore the information on the mitogenome characteristics and phylogeny of the section "Monoleptites", especially the genus Monolepta, we obtained the newly completed mitochondrial genomes (mitogenomes) of four Monolepta species using high-throughput sequencing technology. The lengths of these four new mitochondrial genomes are 16,672 bp, 16,965 bp, 16,012 bp, and 15,866 bp in size, respectively. All four mitochondrial genomes include 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and one control region, which is consistent with other Coleoptera. The results of the nonsynonymous with synonymous substitution rates showed that ND6 had the highest evolution rate, while COI displayed the lowest evolution rate. The substitution saturation of three datasets (13 PCGs_codon1, 13 PCGs_codon2, 13 PCGs_codon3) showed that there was no saturation across all datasets. Phylogenetic analyses based on three datasets (ND1, 15 genes of mitogenomes, and 13 PCGs_AA) were carried out using maximum likelihood (ML) and Bayesian inference (BI) methods. The results showed that mitogenomes had a greater capacity to resolve the main clades than the ND1 gene at the suprageneric and species levels. The section "Monoleptites" was proven to be a monophyletic group, while Monolepta was a non-monophyletic group. Based on ND1 data, the newly sequenced species whose antennal segment 2 was shorter than 3 were split into several clades, while, based on the mitogenomic dataset, the four newly sequenced species had close relationships with Paleosepharia. The species whose antennal segment 2 was as long as 3 were split into two clades, which indicated that the characteristic of "antennal segment 2 as long as 3" of the true "Monolepta" evolved multiple times in several subgroups. Therefore, to explore the relationships among the true Monolepta, the most important thing is to perform a thorough revision of Monolepta and related genera in the future.

A Guide to Phylogenomic Inference

Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. Phylogenomics has significant applications in fields such as evolutionary biology, systematics, comparative genomics, and conservation genetics, providing valuable insights into the origins and relationships of species and contributing to our understanding of biological diversity and evolution. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs. A practical phylogenomic analysis example including bacterial genomes is presented at the end of the chapter.

Mitogenomic analysis and phylogenetic relationships of Agrilinae: Insights into the evolutionary patterns of a diverse buprestid subfamily

Agrilinae is the largest subfamily in Buprestidae, which includes the four tribes, namely Coraebini, Agrilini, Aphanisticini, and Tracheini. However, there is a need to verify the evolutionary relationships among the taxa in Buprestidae. Thus, to explore the phylogenetic position of Aphanisticini, the mitochondrial genomes of Endelus continentalis and Cantonius szechuanensis were sequenced using next-generation sequencing technology. Three other mitogenomes of agriline beetles, Agrilus discalis, Sambus kanssuensis, and Habroloma sp., were also sequenced for the phylogenetic analyses. The divergence time of Buprestidae was estimated based on the mitogenomes. The general features of the known mitogenomes of Agrilinae were compared, analyzed, and summarized. Out of these five species, S. kanssuensis had the shortest mitogenome length (15,411), while Habroloma sp. had the longest (16,273). The gene arrangement of the five new sequences was identical to that of the reported buprestid mitogenomes. The Ka/Ks ratios of Meliboeus (0.79) and Endelus (0.78) were significantly larger than those of the other agriline genera. The results of the phylogeny indicated that Aphanisticini was more closely related to Tracheini and that the genus Sambus separated from the base of the Agrilinae clade at about 130 Ma. Moreover, Aphanisticini and Tracheini diverged at around 26 Ma.

Complete mitochondrial genome of the Themus foveicollis (Coleoptera: Cantharidae)

The genus Themus Motschulsky, 1858 is one of the largest genera of beetle family Cantharidae, however, no complete mitochondrial genome is available in the public database so far. Here, we sequenced and analyzed the first complete mitochondrial genome of Themus, with T. foveicollis as the representative species. The mitochondrial genome was 16,469 bp in size with 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes, as well as a non-coding region, which are arranged in the same way as the hypothetical ancestral insect. It exhibited a typical high A + T bias and a higher proportion of bases A and C than T and G (A: 41.1%, T: 37.5%, G: 8.6%, C: 12.9%). The phylogenetic trees of Elateroidea were reconstructed based on 13 PCGs sequences using the Bayesian inference (BI) and maximum-likelihood (ML) analyses to investigate its phylogenetic position. The results showed that Themus was consistently grouped with the remaining genera of Cantharidae and placed in a monophyletic clade of Cantharinae in high supporting values, which are congruent with the morphological classification. The newly sequenced mitochondrial genome in this study constitutes important reference data for reconstructing phylogeny of the family Cantharidae or the superfamily Elateroidea.

Exploring the Mitogenomes of Mantodea: New Insights from Structural Diversity and Higher-Level Phylogenomic Analyses

The recently reorganized classification of Mantodea has made significant progress in resolving past homoplasy problems, although some relationships among higher taxa remain uncertain. In the present study, we utilized newly sequenced mitogenomes and nuclear gene sequences of 23 mantid species, along with published data of 53 mantises, to perform familial-sampling structural comparisons of mantodean mitogenomes and phylogenomic studies. Our rstructural analysis revealed generally conserved mitogenome organizations, with a few cases of tRNA gene rearrangements, including the detection of trnL₂ duplication for the first time. In our phylogenetic analysis, we found a high degree of compositional heterogeneity and lineage-specific evolutionary rates among mantodean mitogenomes, which frequently corresponded to several unexpected groupings in the topologies under site-homogeneous models. In contrast, the topologies obtained using the site-heterogeneous mixture model fit the currently accepted phylogeny of Mantodea better. Topology tests and four-cluster likelihood mapping analyses further determined the preferred topologies. Our phylogenetic results confirm the monophyly of superfamilial groups Schizomantodea, Amerimantodea, Heteromantodea, Promantidea, and Mantidea and recover the early-branching relationships as (Mantoidoidea + (Amerimantodea + (Metallyticoidea + Cernomantodea))). Additionally, the results suggest that the long-unresolved phylogenetic position of Majangidae should be placed within Mantidea, close to Mantoidea, rather than within Epaphroditoidea. Our findings contribute to understanding the compositional and structural diversity in mantodean mitogenomes, underscore the importance of evolutionary model selection in phylogenomic studies, and provide new insights into the high-level phylogeny of Mantodea.

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.

Analysis of the Mitogenomes of Two Helotid Species Provides New Insights into the Phylogenetic Relationship of the Basal Cucujoidea (Insecta: Coleoptera)

Helotid beetles are commonly found in places where sap flows from tree trunks and in crevices in bark. The Helotidae family is a rare and primitive group of Cucujoidea. To date, no complete mitochondrial (mt) genome has been sequenced for this family. To better understand the characteristics of the mt genome and the evolution of Cucujoidea, we sequenced and annotated the complete mt genomes of Helota thoracica (Ritsema, 1895) and Helota yehi Lee, 2017 using next-generation sequencing. These are the first record of Helotidae mt genomes. The RNA secondary structures of both species were also predicted in this study. The mt genomes of H. thoracica and H. yehi are circular, with total lengths of 16,112 bp and 16,401 bp, respectively. After comparing the mt genomes of H. thoracica and H. yehi, we observed the gene arrangement, codon usage patterns, base content, and RNA secondary structures of both species to be similar, which has also been noted in other Coleoptera insects. The nucleotide sequence of the coding regions and the control region has small differences. The phylogenetic analysis indicated that Helotidae and Protocucujidae are sister groups and revealed the relationship between seven families; however, the validity of the two series (Erotylid series and Nitidulid series) as larger groups in the superfamily was not supported. The mt phylogenomic relationships have strong statistical support. Therefore, the division of Cucujoidea into series should be re-examined. Our results will provide a better understanding of the mt genome and phylogeny of Helotidae and Cucujoidea and will provide valuable molecular markers for further genetic studies.

First mitochondrial genome of subfamily Julodinae (Coleoptera, Buprestidae) with its phylogenetic implications

Complete mitochondrial genomes of three species of the family Buprestidae were sequenced, annotated, and analyzed in this study. To explore the mitogenome features of the subfamily Julodinae and verify its phylogenetic position, the complete mitogenome of Julodisvariolaris was sequenced and annotated. The complete mitogenomes of Ptosimachinensis and Chalcophorajaponica were also provided for the phylogenetic analyses within Buprestidae. Compared to the known mitogenomes of Buprestidae species varied from 15,499 bp to 16,771 bp in length, three newly sequenced mitogenomes were medium length (15,759-16,227 bp). These mitogenomes were encoded 37 typical mitochondrial genes. Among the three studied mitogenomes, Leu2 (L2), Ser2 (S2), and Pro (P) were the three most frequently encoded amino acids. Within the Buprestidae, the heterogeneity in sequence divergences of Agrilinae was highest, whereas the sequence homogeneity of Chrysochroinae was highest. Moreover, phylogenetic analyses were performed based on nucleotide matrix (13 PCGs + 2 rRNAs) among the available sequenced species of Buprestidae using Bayesian Inference and Maximum Likelihood methods. The results showed that the Julodinae was closely related to the subfamily Polycestinae. Meanwhile, the genera Melanophila, Dicerca, and Coomaniella were included in Buprestinae, which was inconsistent with the current classification system of Buprestidae. These results could contribute to further studies on genetic diversity and phylogeny of Buprestidae.

Complete mitochondrial genome of Distenia punctulatoides (Coleoptera: Chrysomeloidea: Disteniinae) and its phylogenetic implications

The family Disteniidae is a moderately large and widely distributed lineage. Distenia punctulatoides belongs to the family Disteniidae from the cerambycoid assemblage. Here, we report the complete mitogenome of D. punctulatoides, which is 15,675 bp in length. It contains 37 genes and a noncoding control region, which are arranged in the same order as that of the putative ancestor of beetles. The total base composition of the new mitogenome is 40.2% for A, 17.1% for C, 10.0% for G, and 32.7% for T. The new mitogenomic organization, nucleotide composition, and codon usage do not differ significantly from other beetles. Using available complete mitogenomes, the high-level phylogeny of the family Disteniidae was explored. The phylogenetic analyses showed that Disteniidae were monophyletic, and the genus Distenia grouped with the genus Clytomelegena as sister groups. Combining the morphological and molecular data, Typodryas Thomson, 1864 is suggested to be a junior synonym of Distenia Lepeletier and Audinet-Serville, 1828.

Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS)

Nilaparvata lugens is the main rice pest in India. Until now, the Indian N. lugens mitochondrial genome has not been sequenced, which is a very important basis for population genetics and phylogenetic evolution studies. An attempt was made to sequence two examples of the whole mitochondrial genome of N. lugens biotype 4 from the Indian population for the first time. The mitogenomes of N. lugens are 16,072 and 16,081 bp long with 77.50% and 77.45% A + T contents, respectively, for both of the samples. The mitochondrial genome of N. lugens contains 37 genes, including 13 protein-coding genes (PCGs) (cox1-3, atp6, atp8, nad1-6, nad4l, and cob), 22 transfer RNA genes, and two ribosomal RNA (rrnS and rrnL) subunits genes, which are typical of metazoan mitogenomes. However, both samples of N. lugens mitogenome in the present study retained one extra copy of the trnC gene. Additionally, we also found 93 bp lengths for the atp8 gene in both of the samples, which were 60–70 bp less than that of the other sequenced mitogenomes of hemipteran insects. The phylogenetic analysis of the 19 delphacids mitogenome dataset yielded two identical topologies when rooted with Ugyops sp. in one clade, and the remaining species formed another clade with P. maidis and M. muiri being sisters to the remaining species. Further, the genus Nilaparvata formed a separate subclade with the other genera (Sogatella, Laodelphax, Changeondelphax, and Unkanodes) of Delphacidae. Additionally, the relationship among the biotypes of N. lugens was recovered as the present study samples (biotype-4) were separated from the three biotypes reported earlier. The present study provides the reference mitogenome for N. lugens biotype 4 that may be utilized for biotype differentiation and molecular-aspect-based future studies of N. lugens.

First report of complete mitochondrial genome in the subfamily Alleculinae and mitochondrial genome-based phylogenetics in Tenebrionidae (Coleoptera: Tenebrionoidea)

Despite worldwide distribution and rich diversity, the knowledge of mitochondrial genome (mtgenome) characteristics within the family Tenebrionidae (Coleoptera) is still very limited, and phylogenetics remain unresolved for the family. In this study, the mtgenomes for 12 species are newly sequenced and annotated. Three of the species represent the first report of complete mtgenomes from the subfamily Alleculinae. Comparative analysis of 36 tenebrionid mtgenomes finds that gene composition and order are the same as a theoretical ancestral insect mtgenome, and AT bias, length variation, and codon usage are consistent with other reported beetle mtgenomes. Some intergenic overlap and gap sequences may contain phylogenetically informative information, whereas neither the conserved nor repeat sequences in the control region do. The subfamilies Lagriinae, Pimeliinae, Stenochiinae, and Alleculinae are found to be monophyletic, and the subfamilies Diaperinae and Tenebrioninae polyphyletic in our study. Furthermore, Lagriinae is sister to the rest of the subfamilies. At the tribal level, the tribes Lagriini in the subfamily Lagrrinae; Strongyliini in Stenochiinae; Cteniopodini in Alleculinae; and Triboliini, Opatrini, and Amarygmini in Tenebrioninae are monophyletic; while Diaperini in Diaperinae, and Tenebrionini in Tenebrioninae are polyphyletic.

First Report of Complete Mitochondrial Genome in the Tribes Coomaniellini and Dicercini (Coleoptera: Buprestidae) and Phylogenetic Implications

The complete mitochondrial genomes (mitogenomes) of the tribes Coomaniellini and Dicercini were sequenced and described in this study, including Coomaniella copipes (16,196 bp), Coomaniella dentata (16,179 bp), and Dicerca corrugata (16,276 bp). These complete mitogenomes are very similar in length and encoded 37 typical mitochondrial genes, including 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and 13 protein-coding genes (PCGs). Most of PCGs had typical ATN start codons and terminated with TAR. Among these mitogenomes, Leu2 (L2), Ile (I), Ser2 (S2), and Phe (F) were the four most frequently encoded amino acids. Moreover, phylogenetic analyses were performed based on three kinds of nucleotide matrixes (13 PCGs, 2 rRNAs, and 13 PCGs + 2 rRNAs) among the available sequenced species of the family Buprestidae using Bayesian inference and Maximum-likelihood methods. The results showed that a Chrysochroninae species interspersed in Buprestinae, and Coomaniellini is more closely related to Dicercini than Melanophilini. Moreover, the clade of Buprestidae was well separated from outgroups and the monophyly of Agrilinae is confirmed again. Our whole mitogenome phylogenetic results support that the genus Dicerca can be transferred from Chrysochroinae to Buprestinae; whether Dicercini can be completely transferred remains to be further verified after enriching samples. Our results have produced new complete mitogenomic data, which will provide information for future phylogenetic and taxonomic research.

The complete mitochondrial genomes of five Agrilinae (Coleoptera, Buprestidae) species and phylogenetic implications

Five complete mitochondrial genomes of five species from the subfamily Agrilinae were sequenced and annotated, including Coraebusdiminutus Gebhardt, 1928 (15,499 bp), Coraebuscloueti Théry, 1893 (15,514 bp), Meliboeussinae Obenberger, 1935 (16,108 bp), Agrilussichuanus Jendek, 2011 (16,521 bp), and Sambusfemoralis Kerremans, 1892 (15,367 bp). These mitogenomes ranged from 15,367 to 16,521 bp in length and encoded 37 typical mitochondrial genes: 13 protein-coding genes (13 PCGs), 2 ribosomal RNA genes (2 rRNAs), 22 transfer RNA genes (22 tRNAs), and a control region (CR). Most of PCGs had typical ATN start codons and terminated with TAR or an incomplete stop codon T–. Among these five mitogenomes, Leu2, Ile, Phe, Ser2, Gly, Met, and Val were the seven most frequently encoded amino acids. Interestingly, in A.sichuanus, a 774 bp insertion was present at trnW and trnC junction, which is unusual in Buprestidae. Additionally, phylogenetic analyses were performed based on three kinds of nucleotide matrixes (13 PCGs, 2 rRNAs, and 13 PCGs + 2 rRNAs) using Bayesian inference and maximum-likelihood methods. The results showed that the clade of Buprestidae was well separated from outgroups and all Agrilinae species formed to a single highly supported clade. The tribe Coraebini was polyphyletic, as the genus Meliboeus (Coraebini) clustered with the genus Trachys (Tracheini). The rRNA genes had important impact for the tree topology of Agrilinae. Compared to the tribes Tracheini and Agrilini, the tribe Coraebini is a younger group.

Integrated phylogenomics and fossil data illuminate the evolution of beetles

Beetles constitute the most biodiverse animal order with over 380 000 described species and possibly several million more yet unnamed. Recent phylogenomic studies have arrived at considerably incongruent topologies and widely varying estimates of divergence dates for major beetle clades. Here, we use a dataset of 68 single-copy nuclear protein-coding (NPC) genes sampling 129 out of the 193 recognized extant families as well as the first comprehensive set of fully justified fossil calibrations to recover a refined timescale of beetle evolution. Using phylogenetic methods that counter the effects of compositional and rate heterogeneity, we recover a topology congruent with morphological studies, which we use, combined with other recent phylogenomic studies, to propose several formal changes in the classification of Coleoptera: Scirtiformia and Scirtoidea sensu nov., Clambiformia ser. nov. and Clamboidea sensu nov., Rhinorhipiformia ser. nov., Byrrhoidea sensu nov., Dryopoidea stat. res., Nosodendriformia ser. nov. and Staphyliniformia sensu nov., and Erotyloidea stat. nov., Nitiduloidea stat. nov. and Cucujoidea sensu nov., alongside changes below the superfamily level. Our divergence time analyses recovered a late Carboniferous origin of Coleoptera, a late Palaeozoic origin of all modern beetle suborders and a Triassic-Jurassic origin of most extant families, while fundamental divergences within beetle phylogeny did not coincide with the hypothesis of a Cretaceous Terrestrial Revolution.

The investigation of intraspecific characteristics and comparative analyses of the complete mitochondrial genome of Stegobium paniceum (Linnaeus, 1758) (Coleoptera: Ptinidae) assembled from public NGS raw reads of the black truffle, Tuber melanosporum

Due to the rapid development of NGS technologies, a huge amount of NGS raw reads have been accumulated in public repositories, such as the Short Read Archive of NCBI. We successfully rescued the complete mitochondrial genome of Stegobium paniceum, a drug store beetle, from public NGS raw reads of truffle generated from the whole genome project. The circular mitogenome of S. paniceum is 15,474 bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 803 bp. Intraspecific transfer RNAs structure and sequence variations were investigated and simple sequence repeats identified from three S. paniceum mitochondrial genomes were compared showing their diversities as fundamental data to utilize them in various aspects including developing efficient molecular markers in the family, Ptinidae. Phylogenetic analysis of 23 Bostrichoidea mitochondrial genomes presented better species identification based on phylogenetic analyses and the optimal options for constructing phylogenetic trees based on Bostrichoidea mitochondrial genomes. Our results present not only utilization of public NGS raw read sequences but also intraspecific features of S. paniceum mitochondrial genomes and comparative analysis of Bostrichoidea mitochondrial genomes in various aspects.

Characterization of the morphology and complete mitochondrial genomes of Eupteryx minusula and Eupteryx gracilirama (Hemiptera: Cicadellidae: Typhlocybinae) from Karst area, Southwest China

Background

The hemipteran insect family Cicadellidae (leafhoppers) includes >2,600 valid genera and >22,000 valid species worldwide, including >2,000 species in China. Typhlocybinae, second largest subfamilies of Cicadellidae, is widely distributed in the six major zoogeographic regions of the world, including >4,000 species worldwide and >1,000 species in China. Previously, morphological analysis are often effective to the way of taxonomy, but it did not combine with molecular biology. Therefore, morphology and mitochondrial genomes (mitogenomes) of two leafhopper species, Eupteryx (Eupteryx) minusculaLindberg, 1929 and Eupteryx (Stacla) graciliramaHou, Zhang & Huang, 2016 were studied and analyzed. This study analyzed the morphological and molecular characteristics of the two leafhoppers, and showed whether the results of the two identifications were consistent.

Methods

Based on the method of comparison, mitogenomes and morphology were analyzed to prove the relationship between the two leafhoppers.

Results

Although two focal species are classified in two different subgenera of the same genus, they still share many morphological features, such as the moderately produced crown fore margin; the milky yellow apical part of scutellum; the pronotum, basal triangles of scutellum, and forewing are dark with several colorless patches on the surface; the light yellow face, without any spots or stripes, and so on. The circular mitogenomes are 16,944 bp long in E. minuscula (GenBank: MN910279) and 17,173 bp long in E. gracilirama (GenBank: MT594485). All of the protein-coding genes are starting with ATN, except for some in mitogenome, which has a single T or TAN as a stop codon. All tRNAs have the typical cloverleaf-shaped structure except for trnS1 (AGN) (E. minuscula) which has a reduced DHU arm. Moreover, these two mitogenomes have trnR with an unpaired base in the acceptor stem. The phylogenetic relationships between E. minuscula and E. gracilirama in respect to related lineages were reconstructed using Maximum likelihood and Maximum parsimony analyses.

Discussion

The result showed that the tribe Typhlocybini is a sister to the tribes Erythroneurini and Empoascini, and five genera, Bolanusoides, Typhlocyba, Eupteryx, Zyginella and Limassolla are forming a single clade. E. minuscula and E. gracilirama are clustered together, supporting the monophyly of the genus Eupteryx. The above conclusions are consistent with the traditional classification of the subfamily.

The complete mitochondrial genome of the firefly Curtos fulvocapitalis (Coleoptera: Lampyridae)

We report the complete mitochondrial genome of the firefly Curtos fulvocapitalis Jeng et Yang 1998. The circular genome is 16,398 bp and has a base composition of A (42.21%), C (11.22%), G (7.73%), and T (38.85%). Our sequence is similar to those of other metazoans, which contain 13 protein-coding genes. All 13 protein-coding genes were initiated by the ATN (ATT, ATA, and ATG) codon. Nine protein-coding genes stopped with TAA or TAG codons, and the other four genes had an incomplete termination codon, a single T. We sequenced the mitochondrial genome of fireflies to analyze phylogenetic relationships and determine the evolution of their flashing signals.

Complete mitochondrial genome of Morphostenophanes sinicus (Zhou, 2020) (Insecta: Coleoptera: Tenebrionidae)

The genus Morphostenophanes is a small arboreal group of darkling beetles that are endemic to the Oriental region. The complete mitochondrial genome of the M. sinicus population from the Manwan Town was first characterized. The mitogenome consisted of a circular DNA molecule of 15,662 bp with a 66.352% AT content. It comprises 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes. The PCGs have a typical ATN (Met) start codon, except for nad1 (TTG as a start codon), and are terminated by typical TAN stop codons.

Structural features of the mitogenome of the leafhopper genus Cladolidia (Hemiptera: Cicadellidae: Coelidiinae) and phylogenetic implications in Cicadellidae

The first two complete mitogenomes of the leafhopper genus Cladolidia (C. biungulata and C. robusta) were sequenced and annotated to further explore the phylogeny of Cladolidia. Both the newly sequenced mitogenomes have a typical circular structure, with lengths of 15,247 and 15,376 bp and A + T contents of 78.2% and 78%, respectively. We identified a highly conserved genome organization in the two Cladolidia spp. through comparative analysis that included the following assessments: genome content, gene order, nucleotide composition, codon usage, amino acid composition, and tRNA secondary structure. Moreover, we detected the base heterogeneity of Cicadellidae mitogenomic data and constructed phylogenetic trees using the nucleotide alignments of 12 subfamilies of 58 leafhopper species. We noted a weak heterogeneity in the base composition among the Cicadellidae mitogenomes. Phylogenetic analyses showed that the monophyly of each subfamily was generally well supported in the family Cicadellidae; the main topology was as follows: (Deltocephalinae + (Treehoppers + ((Megophthalminae + (Macropsinae + (Hylicinae + (Coelidiinae +Iassinae)) + (Idiocerinae + (Cicadellinae + (Typhlocybinae + (Mileewinae + (Evacanthinae +Ledrinae)))))))))). Within Coelidiinae, phylogenetic analyses revealed that C. biungulata and C. robusta belong to Coelidiinae and the monophyly of Cladolidia is well supported. In addition, on the basis of complete mitogenome phylogenetic analysis and the comparison of morphological characteristics, we further confirm the genus Olidiana as a paraphyletic group, suggesting that the genus may need taxonomic revisions.

Mitogenome of Coprophanaeus ensifer and phylogenetic analysis of the Scarabaeidae family (Coleoptera)

Several studies about the phylogenetic relationships of the Scarabaeinae subfamily (Coleoptera: Scarabaeidae) have been performed, but some phylogenetic uncertainties persist including the relationship and monophyly of different tribes and some genera. The aim of this study was to characterize the mitogenome of Coprophanaeus ensifer in order to establish its position within the Scarabaeidae family and to contribute to the resolution of some phylogenetic uncertainties. The mitogenome was sequenced on the Illumina HiSeq 4000, assembled using the Mitobim software and annotated in MITOS WebServer. The phylogenetic trees were reconstructed by Bayesian inference. The C. ensifer mitogenome is a molecule of 14,964 bp that contains the number and organization of the genes similar to those of most Coleoptera species. Phylogenetic reconstruction suggests monophyly of the tribe Phanaeini and supports the hypothesis that Coprini is a sister group of Phanaeini. The results also revealed the position of the tribe Oniticellini which is grouped with Onthophagini and Onitini. The geographic distribution of these species that form the most ancestral clade suggests with Scarabaeinae originated in Africa.

New insights into the phylogeny and evolution of lady beetles (Coleoptera: Coccinellidae) by extensive sampling of genes and species

Ladybirds (family Coccinellidae) are one of the most diverse groups of beetles and globally comprise over 6000 species. Despite their scientific and economic significance, the taxonomy of Coccinellidae remains unstable, and we still know little about their evolutionary history. By using a small number of genes, previous phylogenetic analyses have not reliably resolved the relationships among major ladybird lineages. In this study, we sequenced 94 nuclear protein-coding genes for 214 species of Coccinellidae and 14 outgroups, covering 90 genera and 35 tribes. We found that nucleotide compositional heterogeneity is present among ladybird tribes so that phylogenetic inference at the amino acid level is more reliable than at the DNA level. Based on the maximum likelihood analyses of the amino acid dataset, we recognize three subfamilies in Coccinellidae: Microweiseinae, Monocoryninae stat. nov., and Coccinellinae. The subfamily relationships are strongly supported as (Microweiseinae, (Monocoryninae stat. nov., Coccinellinae)). The tribes of ladybirds are mostly monophyletic, except Ortaliini, Sticholotidini, Scymnini, and Coccidulini. The phylogenetic relationships among tribes of Coccinellinae are still not well resolved, with many nodes weakly supported. Our divergence time analysis suggests that the crown group of extant lady beetles arose in the Early Cretaceous ~ 143 million years ago (Mya) and experienced a rapid diversification during the Late Cretaceous (120-70 Mya). We hypothesize that the boom of angiosperms in the Late Cretaceous promoted the diversification of herbivorous Sternorrhyncha insects, especially aphids, which in turn drove the rapid radiation of predatory lady beetles. In summary, our work provides a comprehensive time-calibrated phylogeny of Coccinellidae that provides a sound framework for revising their classification and understanding the origin of their biodiversity.

Phylogenomics of Parasitic and Nonparasitic Lice (Insecta: Psocodea): Combining Sequence Data and Exploring Compositional Bias Solutions in Next Generation Data Sets

The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and nonparasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and nonparasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2370 orthologous genes. All phylogenomic analyses, including both concatenated and coalescent methods suggest a single origin of parasitism within the order Psocodea, resolving conflicting results from previous studies. This phylogeny allows us to propose a stable ordinal level classification scheme that retains significant taxonomic names present in historical scientific literature and reflects the evolution of the group as a whole. A dating analysis, with internal nodes calibrated by fossil evidence, suggests an origin of parasitism that predates the K-Pg boundary. Nucleotide compositional biases are detected in third and first codon positions and result in the anomalous placement of the Amphientometae as sister to Psocomorpha when all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling methods demonstrate that base compositional biases can also have an effect on quartet-based methods.[Illumina; Phthiraptera; Psocoptera; quartet sampling; recoding methods.].

Comprehensive Analyses of the Complete Mitochondrial Genome of Figulus binodulus (Coleoptera: Lucanidae)

Figulus binodulus Waterhouse is a small stag beetle distributed in East Asia. We determined the first mitochondrial genome of F. binodulus of which is 16,261-bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large noncoding region of 1,717 bp. Gene order of F. binodulus is identical to the ancestral insect mitochondrial gene order as in most other stag beetle species. All of 22 tRNAs could be shaped into typical clover-leaf structure except trnSer1. Comparative analyses of 21 Lucanidae mitochondrial genomes was conducted in aspect of their length and AT-GC ratio. Nucleotide diversities analyses provide that cox1 and cox2 in Lucanidae are less diverse than those of Scarabaeoidea. Fifty simple sequence repeats (SSRs) were identified on F. binodulus mitochondrial genome. Comparative analysis of SSRs among five mitochondrial genomes displayed similar trend along with SSR types. Figulus binodulus was sister to all other available family Lucanidae species in the phylogenetic tree.

The genetic variations in the mitochondrial genomes of three Luciolinae fireflies

This paper studied the complete mitochondrial genomes of three fireflies, Pygoluciola qingyu, Emeia pseudosauteri and Abscondita terminalis. We discussed the variations in the mitochondrial genomes of samples of each firefly from different populations. The mitochondrial genomes of Abs. terminalis and P. qingyu are very stable among their different populations. The mitochondrial genome of E. pseudosauteri shows some variations among the different populations, especially in the COI sequence.

The complete mitochondrial genome sequence and phylogenetic analysis of Cantharis plagiata (Coleoptera, Canthridae)

The complete mitochondrial genome of a soldier beetle, Cantharis plagiata (Coleoptera, Canthridae), was sequenced. The mitogenome is a double-stranded circular molecule, and the obtained sequence had 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA subunits, and an AT-rich region, as in other insects. Total length of this mitogenome is 16,315 bp and the composition of each base is A (41.4%), T (37.5%), C (12.7%), G (8.4%), respectively. The phylogenetic tree analysis using 25 species of Elateroidea showed that C. plagiata is closest to C. pellucida, which confirms its systematic status in Cantharidae.

Data curation and modeling of compositional heterogeneity in insect phylogenomics: A case study of the phylogeny of Dytiscoidea (Coleoptera: Adephaga)

Diving beetles and their allies are an almost ubiquitous group of freshwater predators. Knowledge of the phylogeny of the adephagan superfamily Dytiscoidea has significantly improved since the advent of molecular phylogenetics. However, despite recent comprehensive phylogenomic studies, some phylogenetic relationships among the constituent families remain elusive. In particular, the position of the family Hygrobiidae remains uncertain. We address these issues by re-analyzing recently published phylogenomic datasets for Dytiscoidea, using approaches to reduce compositional heterogeneity and adopting a site-heterogeneous mixture model. We obtained a consistent, well-resolved, and strongly supported tree. Consistent with previous studies, our analyses support Aspidytidae as the monophyletic sister group of Amphizoidae, and more importantly, Hygrobiidae as the sister of the diverse Dytiscidae, in agreement with morphology-based phylogenies. Our analyses provide a backbone phylogeny of Dytiscoidea, which lays the foundation for better understanding the evolution of morphological characters, life habits, and feeding behaviors of dytiscoid beetles.

Mitochondrial genomes of three Bostrichiformia species and phylogenetic analysis of Polyphaga (Insecta, Coleoptera)

Here we determined mitogenomes of three Bostrichiformia species. These data were combined with 51 previously sequenced Polyphaga mitogenomes to explore the higher-level relationships within Polyphaga by using four different mitogenomic datasets and three tree inference approaches. Among Polyphaga mitogenomes we observed heterogeneity in nucleotide composition and evolutionary rates, which may have affected phylogenetic inferences across the different mitogenomic datasets. Elateriformia, Cucujiformia, and Scarabaeiformia were each inferred to be monophyletic by all analyses, as was Bostrichiformia by most analyses based on two datasets with low heterogeneity. The large series Staphyliniformia was never recovered as monophyletic in our analyses. The Bayesian tree using a degenerated nucleotide dataset (P123_Degen) and a site-heterogeneous mixture model in PhyloBayes was supported as the best Polyphaga phylogeny: (Scirtiformia, (Elateriformia, ((Bostrichiformia, Cucujiformia), (Scarabaeiformia + Staphyliniformia)))). For Cucujiformia, the largest series, we inferred a superfamily-level phylogeny: ((Cleroidea, Coccinelloidea), (Tenebrionoidea, (Cucujoidea + Curculionoidea + Chrysomeloidea))).

The conserved mitochondrial genome of the jewel beetle (Coleoptera: Buprestidae) and its phylogenetic implications for the suborder Polyphaga

In this study, we sequenced the mitochondrial (mt) genome of Agrilus mali (Coleoptera: Buprestidae) using next-generation sequencing, and accordingly annotated 13 protein-coding, 22 tRNA, and 2 rRNA genes and a 1458-bp non-coding region. Comparative analysis indicated that the mt genome of A. mali is relatively conserved, with a typical gene content and order identical to those of other coleopterans. However, the newly sequenced mt genome is characterized by a relatively higher A + T content compared with that of other species within the family Buprestidae. Phylogenetic analysis based on Bayesian inference revealed that the evolutionary relationship among the six infraorders of the suborder Polyphaga is (Scirtiformia + (Elateriformia + ((Scarabaeiformia + Staphyliniformia) + (Bostrichiformia + (Cucujiformia))))). However, the topology indicated that the family Buprestidae is a sister group to other Polyphaga infraorders, excluding Scirtiformia as a monophyly, and thus the monophyly of Elateriformia was not supported. This study not only presents the mt genome of a species in the family Buprestidae and a comparative analysis of jewel beetles but also examines the contribution of mt genomes in elucidating phylogenetic relationships within the suborder Polyphaga of Coleoptera.

A Novel Test for Absolute Fit of Evolutionary Models Provides a Means to Correctly Identify the Substitution Model and the Model Tree

A novel test is described that visualizes the absolute model-data fit of the substitution and tree components of an evolutionary model. The test utilizes statistics based on counts of character state matches and mismatches in alignments of observed and simulated sequences. This comparison is used to assess model-data fit. In simulations conducted to evaluate the performance of the test, the test estimator was able to identify both the correct tree topology and substitution model under conditions where the Goldman-Cox test-which tests the fit of a substitution model to sequence data and is also based on comparing simulated replicates with observed data-showed high error rates. The novel test was found to identify the correct tree topology within a wide range of DNA substitution model misspecifications, indicating the high discriminatory power of the test. Use of this test provides a practical approach for assessing absolute model-data fit when testing phylogenetic hypotheses.

Characterization of the Complete Mitochondrial Genome of Epicauta impressicornis (Coleoptera: Meloidae) and Its Phylogenetic Implications for the Infraorder Cucujiformia

The complete mitochondrial genome (mitogenome) of Epicauta impressicornis Pic (Coleoptera: Meloidae) was determined. The circular genome is 15,713-bp long, and encodes 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The 13 PCGs start with the typical ATN codon and terminate with the typical stop codon TAA (ND2, ND4L, ND6, ATP6, ATP8, and CYTB), TAG (ND1 and ND3), and T- (COX1, COX2, COX3, ND4, and ND5). The two rRNA genes (rrn12S and rrn16S) are encoded on the minority strand. All tRNAs genes except trnS1 (AGN) are predicted to fold into the typical cloverleaf structure. The longest overlap (10 bp) is observed between ATP8 and ATP6. CR mainly harbors a conserved poly-T stretch (15 bp), a short repeat unit (17 bp), some universal microsatellite-like repeats, and a canonical poly-A tail. Phylogenetic analysis using Bayesian inferences and maximum likelihood based on nucleotide and corresponding amino acid sequences of the 13 PCGs showed that E. impressicornis is closely related to E. chinensis, this relationship is and supported within Cucujiformia belonging to Meloidae (Tenebrionoidea). Our results further confirmed the monophyly of Tenebrionoidea, Lymexyloidea, Curculionoidea, Chrysomeloidea, Cucujoidea, Coccinelloidea, and Cleroidea within Cucujiformia, and revealed the sister relationships of (Cleroidea + Coccinelloidea), (Lymexyloidea + Tenebrionoidea), and ((Chrysomeloidea + Cucujoidea) + Curculionoidea). We believe that the complete mitogenome of E. impressicornis will contribute to further studies on molecular bases for the classification and phylogeny of Meloidae or even Cucujiformia.

The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis

Background

The stag beetle Lucanus cervus (Coleoptera: Lucanidae) is widely distributed in Europe. Habitat loss and fragmentation has led to significant reductions in numbers of this species. In this study, we sequenced the complete mitochondrial genome of L. cervus and reconstructed phylogenetic relationships among Lucanidae using complete mitochondrial genome sequences.

Methods

Raw data sequences were generated by the next generation sequencing using Illumina platform from genomic DNA of L. cervus. The mitochondrial genome was assembled by IDBA and annotated by MITOS. The aligned sequences of mitochondrial genes were partitioned using PartitionFinder 2. Phylogenetic relationships among 19 stag beetle species were constructed using Maximum Likelihood (ML) method implemented in IQ-TREE web server and Bayesian method implemented in PhyloBayes MPI 1.5a. Three scarab beetles were used as outgroups.

Results

The complete mitochondrial genome of L. cervus is 20,109 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNAs and a control region. The A + T content is 69.93% for the majority strand. All protein-coding genes start with the typical ATN initiation codons except for cox1, which uses AAT. Phylogenetic analyses based on ML and Bayesian methods shown consistent topologies among Lucanidae.

The Prevalence and Impact of Model Violations in Phylogenetic Analysis

In phylogenetic inference, we commonly use models of substitution which assume that sequence evolution is stationary, reversible, and homogeneous (SRH). Although the use of such models is often criticized, the extent of SRH violations and their effects on phylogenetic inference of tree topologies and edge lengths are not well understood. Here, we introduce and apply the maximal matched-pairs tests of homogeneity to assess the scale and impact of SRH model violations on 3,572 partitions from 35 published phylogenetic data sets. We show that roughly one-quarter of all the partitions we analyzed (23.5%) reject the SRH assumptions, and that for 25% of data sets, tree topologies inferred from all partitions differ significantly from topologies inferred using the subset of partitions that do not reject the SRH assumptions. This proportion increases when comparing trees inferred using the subset of partitions that rejects the SRH assumptions, to those inferred from partitions that do not reject the SRH assumptions. These results suggest that the extent and effects of model violation in phylogenetics may be substantial. They highlight the importance of testing for model violations and possibly excluding partitions that violate models prior to tree reconstruction. Our results also suggest that further effort in developing models that do not require SRH assumptions could lead to large improvements in the accuracy of phylogenomic inference. The scripts necessary to perform the analysis are available in https://github.com/roblanf/SRHtests, and the new tests we describe are available as a new option in IQ-TREE (http://www.iqtree.org).

Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications

A complete mitogenome of Trachys auricollis is reported, and a mitogenome-based phylogenetic tree of Elateriformia with all protein-coding genes (PCGs), rRNAs, and tRNAs is presented for the first time. The complete mitochondrial genome of T. auricollis is 16,429 bp in size and contains 13 PCGs, two rRNA genes, 22 tRNA genes, and an A + T-rich region. The A + T content of the entire genome is approximately 71.1%, and the AT skew and GC skew are 0.10 and -0.20, respectively. According to the the nonsynonymous substitution rate to synonymous substitution rates (Ka/Ks) of all PCGs, the highest and lowest evolutionary rates were observed for atp8 and cox1, respectively, which is a common finding among animals. The start codons of all PCGs are the typical ATN. Ten PCGs have complete stop codons, but three have incomplete stop codons with T or TA. As calculated based on the relative synonymous codon usage (RSCU) values, UUA(L) is the codon with the highest frequency. Except for trnS1, all 22 tRNA genes exhibit typical cloverleaf structures. The A + T-rich region of T. auricollis is located between rrnS and the trnI-trnG-trnM gene cluster, with six 72-bp tandem repeats. Both maximum likelihood (ML) and Bayesian (BI) trees suggest that Buprestoidea is close to Byrrhoidea and that Buprestoidea and Byrrhoidea are sister groups of Elateroidea, but the position of Psephenidae is undetermined. The inclusion of tRNAs might help to resolve the phylogeny of Coleoptera.

The complete mitogenome of Lycostomus sp. (Elateroidea: Lycidae)

The complete mitochondrial genome of a net-winged beetle was sequenced, Lycostomus sp. (Coleoptera: Lycidae). The total length of this mitogenome is 16096 bp and the composition of each base is A (41.1%), T (31.9%), C (17.1%), G (9.9%), respectively. The gene arrangement of this beetle mt genome is the same as other insects. The phylogenetic tree shows that Lycostomus sp. is closest to Platerodrilus sp. with robust statistical support, which confirms the monophyly of Lycidae.

The complete mitochondrial genome sequence and phylogenetic analysis of Lycocerus asperipennis (Coleoptera, Cantharidae)

The complete mitochondrial genome of a common Chinese soldier beetle was sequenced, Lycocerus asperipennis (Coleoptera, Cantharidae, Cantharinae). The mitogenome is a double-stranded circular molecule, and the obtained sequence with 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA subunits, and an AT-rich region, as in other insects. Total length of this mitogenome is 16162 bp and the composition of each base is A (41.5%), T (37.7%), C (12.4%), G (8.4%), respectively. The phylogenetic tree analysis using 16 species of Elateriformia shows that L. asperipennis is closest to Chauliognathus opacus, which belongs to the subfamily Chauliognathinae of Cantharidae.

Characterisation of the complete mitochondrial genome of Lucanus chengyuani (Coleoptera: Lucanidae)

We sequenced and assembled the complete mitochondrial genome of Lucanus chengyuani, from the Alishan, Chiayi County, Taiwan. The length of the complete mitogenome of L. chengyuani is 16,926 bp and the mitogenome contains 13 protein-coding, 22 tRNA, and 2 rDNA genes. Nucleotide compositions of the whole mitogenome of L. chengyuani are 38.37% for A, 27.96% for T, 23.03% for C, and 10.637% for G. The AT and GC skewness of mitogenome sequence are 0.157 and -0.368, showing the A-skew and C-skew. The reconstructed phylogenetic relationships of 9 Lucanidae species based on 13 mitochondrial protein-coding genes are highly supported. The clade including Neolucanus maximus and Odontolabis cuvera is sister to the rest of the stag beetle clades, which contains L. chengyuani and L. mazama. Mitogenomic data from this study will provide useful information for further studies for the population genetics, speciation, biogeography, and conservation of L. chengyuani in the future.

Tick mitochondrial genomes: structural characteristics and phylogenetic implications

Ticks are obligate blood-sucking arachnid ectoparasites from the order Acarina, and many are notorious as vectors of a wide variety of zoonotic pathogens. However, the systematics of ticks in several genera is still controversial. The mitochondrial genome (mt-genome) has been widely used in arthropod phylogeny, molecular evolution and population genetics. With the development of sequencing technologies, an increasing number of tick mt-genomes have been sequenced and annotated. To date, 63 complete tick mt-genomes are available in the NCBI database, and these genomes have become an increasingly important genetic resource and source of molecular markers in phylogenetic studies of ticks in recent years. The present review summarizes all available complete mt-genomes of ticks in the NCBI database and analyses their characteristics, including structure, base composition and gene arrangement. Furthermore, a phylogenetic tree was constructed using mitochondrial protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes from ticks. The results will provide important clues for deciphering new tick mt-genomes and establish a foundation for subsequent taxonomic research.

The Complete Mitochondrial Genome and Expression Profile of Mitochondrial Protein-Coding Genes in the Bisexual and Parthenogenetic Haemaphysalis longicornis

The tick Haemaphysalis longicornis is widely distributed in eastern Asia, New Zealand and Australia, and is well-known as a vector of multiple zoonotic pathogens. This species exhibits two reproductive strategies, bisexual and obligate parthenogenetic reproduction. Hence, in the current study, the complete mitochondrial genomes of the bisexual and parthenogenetic populations were assembled and analyzed, and the expression of the mitochondrial protein-coding genes was evaluated and compared between the two reproductive populations. The results indicated that the length of the mitochondrial genomes of the two reproductive populations is 14,694 and 14,693 bp in the bisexual and parthenogenetic populations, respectively. The AT content in the mitochondrial genome of the bisexual and obligate parthenogenetic population reached 77.22 and 77.34%, respectively. The phylogenetic tree was constructed combining 13 protein-coding genes, which showed that the genetic distance between the bisexual and parthenogenetic populations was less than that between the subspecies. The expression of the mitochondrial protein-coding genes was quantitatively analyzed at different feeding status for the bisexual and parthenogenetic populations, and the results showed significant differences in the expression patterns of these genes, suggesting that they might trigger specific energy utilization mechanisms due to their different reproductive strategies and environmental pressures.

Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda

The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.

Gene Selection and Evolutionary Modeling Affect Phylogenomic Inference of Neuropterida Based on Transcriptome Data

Neuropterida is a super order of Holometabola that consists of the orders Megaloptera (dobsonflies, fishflies, and alderflies), Neuroptera (lacewings) and Raphidioptera (snakeflies). Several proposed higher-level relationships within Neuropterida, such as the relationships between the orders or between the families, have been extensively debated. To further understand the evolutionary history of Neuropterida, we conducted phylogenomic analyses of all 13 published transcriptomes of the neuropterid species, as well as of a new transcriptome of the fishfly species Ctenochauliodes similis of Liu and Yang, 2006 (Megaloptera: Corydalidae: Chauliodinae) that we sequenced. Our phylogenomic data matrix contained 1392 ortholog genes from 22 holometabolan species representing six families from Neuroptera, two families from Raphidioptera, and two families from Megaloptera as the ingroup taxa, and nine orders of Holometabola as outgroups. Phylogenetic reconstruction was performed using both concatenation and coalescent-based approaches under a site-homogeneous model as well as under a site-heterogeneous model. Surprisingly, analyses using the site-homogeneous model strongly supported a paraphyletic Neuroptera, with Coniopterygidae assigned as the sister group of all other Neuropterida. In contrast, analyses using the site-heterogeneous model recovered Neuroptera as monophyletic. The monophyly of Neuroptera was also recovered in concatenation and coalescent-based analyses using genes with stronger phylogenetic signals [i.e., higher average bootstrap support (ABS) values and higher relative tree certainty including all conflicting bipartitions (RTCA) values] under the site-homogeneous model. The present study illustrated how both data selection and model selection influence phylogenomic analyses of large-scale data matrices comprehensively.

Comparative analysis of the Liriomyza chinensis mitochondrial genome with other Agromyzids reveals conserved genome features

Liriomyza chinensis is a serious pest of onions in many countries, especially in East Asia. We sequenced the complete mitochondrial genome of this species and compared it with five other Agromyzidae species. The L. chinensis mitogenome is a double-stranded 16,175 bp circular molecule with an A + T content of 78.3%. It contains 37 genes and a control region as do the sequenced Liriomyza species. The mitogenomes of L. chinensis and other Agromyzidae species showed a clear bias in nucleotide composition with a positive AT-skew. Most PCGs used standard ATN as start codons, and TAN as termination codons. The tRNAs exhibited the typical clover-leaf structure, except for tRNASer^(AGN) and the two rRNA genes are conserved with those of other Agromyzids. The L. chinensis mitogenome control region included several conserved regions, including a poly-T, two (TA)n and one poly-A stretch, which are considered important replication and transcription. The 13 PCGs were used to study the phylogeny of L. chinensis and five related Agromyzids. Analysis by maximum likelihood, Bayesian inference and genetic distance suggest congruent phylogenetic relationships in Liriomyza spp. and provide a useful supplement to taxonomic classification by morphology.

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.