Molecular phylogeny of Systellognatha (Plecoptera: Arctoperlaria) inferred from mitochondrial genome sequences

Characterization of the complete mitochondrial genome of the longhorn beetle, Batocerahorsfieldi (Coleoptera, Cerambycidae) and its phylogenetic analysis with suitable longhorn beetles

Mitochondrial genome analysis is an important tool for studying insect phylogenetics. The longhorn beetle, Batocerahorsfieldi, is a significant pest in timber, economic and protection forests. This study determined the mitochondrial genome of B.horsfieldi and compared it with the mitochondrial genomes of other Cerambycidae with the aim of exploring the phylogenetic status of the pest and the evolutionary relationships among some Cerambycidae subgroups. The complete mitochondrial genome of B.horsfieldi was sequenced by the Illumina HiSeq platform. The mitochondrial genome was aligned and compared with the existing mitochondrial genomes of Batoceralineolata and B.rubus in GenBank (MF521888, MW629558, OM161963, respectively). The secondary structure of transfer RNA (tRNA) was predicted using tRNAScan-SE server v.1.21 and MITOS WebSever. Thirteen protein-coding genes (PCGs) and two ribosomal RNA gene sequences of 21 longhorn beetles, including B.horsfieldi, plus two outgroups, Dryopsernesti (Dryopidae) and Heterocerusparallelus (Heteroceridae), were analyzed. The phylogenetic tree was constructed using maximum likelihood and Bayesian inference methods. In this study, we successfully obtained the complete mitochondrial genome of B.horsfieldi for the first time, which is 15 425 bp in length. It contains 37 genes and an A + T-rich region, arranged in the same order as the recognized ancestor of longhorn beetles. The genome of B.horsfieldi is composed of 33.12% A bases, 41.64% T bases, 12.08% C bases, and 13.16% G bases. The structure, nucleotide composition, and codon usage of the new mitochondrial genome are not significantly different from other longhorn mitochondrial genomes. Phylogenetic analyses revealed that Cerambycidae formed a highly supported single clade, and Vesperidae was either clustered with Cerambycidae or formed a separate clade. Interestingly, B.horsfieldi, B.rubus and B.lineolata were clustered with Monochamus and Anoplophora species in both analyses, with high node support. Additionally, the VesperidaeSpiniphilusspinicornis and Vesperussanzi and the 19 Cerambycidae species formed a sister clade in the Bayesian analysis. Our results have produced new complete mitogenomic data, which will provide information for future phylogenetic and taxonomic research, and provide a foundation for future relevant research.

Complete Mitochondrial Genome of Piophila casei (Diptera: Piophilidae): Genome Description and Phylogenetic Implications

Piophila casei is a flesh-feeding Diptera insect that adversely affects foodstuffs, such as dry-cured ham and cheese, and decaying human and animal carcasses. However, the unknown mitochondrial genome of P. casei can provide information on its genetic structure and phylogenetic position, which is of great significance to the research on its prevention and control. Therefore, we sequenced, annotated, and analyzed the previously unknown complete mitochondrial genome of P. casei. The complete mt genome of P. casei is a typical circular DNA, 15,785 bp in length, with a high A + T content of 76.6%. It contains 13 protein-coding genes (PCG), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 control region. Phylogenetic analysis of 25 Diptera species was conducted using Bayesian and maximum likelihood methods, and their divergence times were inferred. The comparison of the mt genomes from two morphologically similar insects P. casei and Piophila megastigmata indicates a divergence time of 7.28 MYA between these species. The study provides a reference for understanding the forensic medicine, taxonomy, and genetics of P. casei.

Comparative analysis of mitochondrial genomes among the family Peltoperlidae (Plecoptera: Systellognatha) and phylogenetic implications

Nowadays, the position of Peltoperlidae in Systellognatha has been resolved based on morphological analyses. However, there are different opinions based on molecular data. To date, only three peltoperlid mitogenomes are available, and more sampling is needed to obtain precise phylogenetic relationships. In this study, we obtained the complete mitogenomes of Cryptoperla kawasawai (15,832 bp) and Peltoperlopsis sagittata (15,756 bp). Our results show that gene content, gene order, DmTTF binding site, nucleotide composition, codon usage, ribonucleic acid (RNA) structure, and structural elements in the control region are highly conserved in peltoperlids. Heatmap analysis of codon usage shows that the AT-rich codons UUA, AUU, UUU, and AUA were commonly used codons in the Peltoperlidae. Evolutionary rate analyses of protein-coding genes reveal that different genes have been subject to different rates of molecular evolution correlated with the GC content. All tRNA genes in peltoperlid mitogenomes have a canonical cloverleaf secondary structure except for trnS1, whose dihydrouridine arm simply forms a loop. The control region of the family has several distinct structural characteristics and has the potential to serve as effective phylogenetic markers. Phylogenetic analyses support the monophyly of Perloidea, but the monophyly of Pteronarcyoidea is still not supported. The Peltoperlidae is placed as the earliest branch within the Systellognatha, and the estimated phylogenetic relationship is: Peltoperlidae + {(Styloperlidae + Pteronarcyidae) + [Perlidae + (Chloroperlidae + Perlodidae)]}. Our results provide new insight into the phylogeny of this group.

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.

DNA barcoding for biodiversity assessment: Croatian stoneflies (Insecta: Plecoptera)

Background

The hemi-metabolous aquatic order Plecoptera (stoneflies) constitutes an indispensable part of terrestrial and aquatic food webs due to their specific life cycle and habitat requirements. Stoneflies are considered one of the most sensitive groups to environmental changes in freshwater ecosystems and anthropogenic changes have caused range contraction of many species. Given the critical threat to stoneflies, the study of their distribution, morphological variability and genetic diversity should be one of the priorities in conservation biology. However, some aspects about stoneflies, especially a fully resolved phylogeny and their patterns of distribution are not well known. A study that includes comprehensive field research and combines morphological and molecular identification of stoneflies has not been conducted in Croatia so far. Thus, the major aim of this study was to regenerate a comprehensive and taxonomically well-curated DNA barcode database for Croatian stoneflies, to highlight the morphological variability obtained for several species and to elucidate results in light of recent taxonomy.

Methods

A morphological examination of adult specimens was made using basic characteristics for distinguishing species: terminalia in males and females, head and pronotum patterns, penial morphology, and egg structures. DNA barcoding was applied to many specimens to help circumscribe known species, identify cryptic or yet undescribed species, and to construct a preliminary phylogeny for Croatian stoneflies.

Results

Sequences (658 bp in length) of 74 morphospecies from all families present in Croatia were recovered from 87% of the analysed specimens (355 of 410), with one partial sequence of 605 bp in length for Capnopsis schilleri balcanica Zwick, 1984. A total of 84% morphological species could be unambiguously identified using COI sequences. Species delineation methods confirmed the existence of five deeply divergent genetic lineages, with monophyletic origin, which also differ morphologically from their congeners and represent distinct entities. BIN (Barcode Index Number) assignment and species delineation methods clustered COI sequences into different numbers of operational taxonomic units (OTUs). ASAP delimited 76 putative species and achieved a maximum match score with morphology (97%). ABGD resulted in 62 and mPTP in 61 OTUs, indicating a more conservative approach. Most BINs were congruent with traditionally recognized species. Deep intraspecific genetic divergences in some clades highlighted the need for taxonomic revision in several species-complexes and species-groups. Research has yielded the first molecular characterization of nine species, with most having restricted distributions and confirmed the existence of several species which had been declared extinct regionally.

Mitochondrial Genomes of the Genus Claassenia (Plecoptera: Perlidae) and Phylogenetic Assignment to Subfamily Perlinae

Mitochondrial genomes of three stoneflies, e.g., Claassenia magna Wu, 1948, Claassenia sp. 2 and Claassenia xucheni Chen, 2019 were sequenced in this study with 15,774, 15,777 and 15,746 bp in length, respectively. Each mitogenome contained 37 genes including 22 tRNAs, two ribosomal RNAs, 13 protein-coding genes (PCGs), and a noncoding control region (CR). In general, standard ATN start and TAN termination codons were evident in the PCGs. Although the dihydrouridine arm was absent in trnSer, the remaining 21 tRNAs displayed the characteristic cloverleaf secondary structure. Stem-loop structures were identified in the CRs of all three mitogenomes, but tandem repeats were only apparent in Claassenia xucheni. The mitogenomes of three Claassenia species were analyzed and compared with mitogenomes in 21 other stoneflies from the Perlidae and three Euholognatha species (Rhopalopsole bulbifera, Capnia zijinshana and Amphinemura longispina) as outgroups. Phylogenetic analyses using maximum likelihood and Bayesian inference. Phylogenetic analysis supported that Claassenia was recovered as the sister group of other Perlinae and Claassenia+Perlinae emerged from the paraphyletic Acroneuriinae. The final results supported that Claassenia was classified into subfamily Perlinae and proposed Claassenia represent a transitional group of the subfamilies Acroneuriinae and Perlinae. This study provided new molecular evidence for exploring the debatable taxonomic position of the genus Claassenia in Perlidae.

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.

Mitochondrial genome of Arcynopteryx dichroa (McLachlan, 1872) (Plecoptera: Perlodidae) and phylogenetic analysis

To better understand the diversity and phylogeny of Perlodidae, we sequenced and annotated the complete mitochondrial genome (mitogenome) of Arcynopteryx dichroa. This mitogenome was 16,215 bp long and encoded 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA unit genes (rRNAs), and a control region like other plecopteran. The nucleotide composition of A. dichroa mitochondrial genome obviously biases toward A and T. The A + T content of the whole mitochondrial genome, the PCGs, tRNAs, rRNAs, and the control region were: 69.3%, 67.6%, 69.8%, 71.3%, and 78.7%. Phylogenetic relationship based on the concatenated sequences of 13 PCGs and two ribosomal RNAs showed that the family Perlodidae and Chloroperlidae are sister relationship, family Perlidae being the sister group to the clade (Perlodidae + Chloroperlidae). The monophyly of the family Perlodidae is well supported but the subfamily Perlodinae and Isoperlinae are not monophyletic groups.

Two Complete Mitochondrial Genomes From Leuctridae (Plecoptera: Nemouroidea): Implications for the Phylogenetic Relationships Among Stoneflies

The family-level relationships within Plecoptera have been a focused area of research for a long time. Its higher classification remains unstable, and the phylogenetic relationships within Plecoptera should be re-examined. Here, we sequenced and analyzed two complete mitochondrial genomes (mitogenomes) of Paraleuctra cercia and Perlomyia isobeae of the family Leuctridae. We reconstructed the phylogeny of Plecoptera based on 13 protein-coding genes (PCGs) from published stoneflies. Our results showed that the Bayesian inference and maximum-likelihood tree had similar topological structures except for the positions of two families, Peltoperlidae and Scopuridae. The Plecoptera is divided into two clades, the suborder Antarctoperlaria and the suborder Arctoperlaria. The two suborders subsequently formed two groups, Eusthenioidea and Gripopterygoidea, and Euholognatha and Systellognatha, which is consistent with the results of morphological studies. In addition, the Leuctridae is the earliest branch within the superfamily Nemouroidea. But the monophyly of Perloidea and Pteronarcyoidea are still not well supported.

Perlidae (Plecoptera) from the Paranapiacaba Mountains, Atlantic Forest, Brazil: Diversity and implications of the integrative approach and teneral specimens on taxonomy

The study of complementary sources of biological variation (e.g. morphological, molecular) has allowed a better understanding of biodiversity through the construction of an integrative taxonomy. Using this approach, specimens from the Paranapiacaba Mountains, southeastern Brazil, were studied to update the knowledge on the stonefly family Perlidae from the region, characterize the species, and make associations between nymphs and adults using a fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. The study also discusses the implications of integrative taxonomy and teneral specimens for the study of South American Perlidae. The molecular data were analyzed using Bayesian inference, Neighbor-joining, and delimiting species methods. Our results revealed that, in general, there was a morphological and molecular congruence between species. In the Paranapiacaba Mountains, three genera and 15 species were recorded: Anacroneuria boraceiensis Froehlich 2004, A. debilis (Pictet 1841) (new record), A. fiorentini De Ribeiro and Froehlich 2007 (new record), A. flintorum Froehlich 2002, A. iporanga Bispo and Froehlich 2004, A. itajaimirim Bispo and Froehlich 2004, A. polita (Burmeister 1913), A. subcostalis Klapálek 1921, A. tupi Bispo and Froehlich 2004 (with a description of the nymph), Kempnyia auberti Froehlich 1996, K. colossica (Navás 1934), K. flava Klapálek 1916, K. neotropica (Jacobson and Bianchi 1905) (including its new junior synonym K. petersorum Froehlich 1996), Kempnyia sp., and Macrogynoplax veneranda Froehlich 1984. COI sequences were obtained for 11 species, five of which had nymphs associated with adults. Among the five associated nymphs, the nymph of A. tupi is described here. The results of this study indicate that the color of adult teneral specimens differs from that of mature specimens. Given this, the synonym of K. neotropica and K. petersorum was proposed since these species have high morphological and molecular similarities and differ only in color patterns. In addition, the previous record of A. petersi Froehlich 2002 from the Paranapiacaba Mountains was invalidated since it was considered a teneral specimen of A. flintorum. These results suggest that the development of an integrative taxonomy is essential to continue advancing the study of Perlidae diversity in South America.

Molecular phylogeny inferred from the mitochondrial genomes of Plecoptera with Oyamia nigribasis (Plecoptera: Perlidae)

In this study, the mitochondrial genome of the stonefly, Oyamia nigribasis Banks, 1920 (Plecoptera: Perlidae), was sequenced and compared with the mtDNA genomes of 38 other stoneflies and two Ephemerae. The O. nigribasis mitogenome is a circular 15,923 bp molecule that encodes a large, noncoding control region (CR) and 37 typical mtDNA genes; these include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), respectively. Most of the PCGs initiated with ATN and terminated with TAN. The dihydrouridine (DHU) arm of tRNASer (AGN) was missing, whereas the other 21 tRNAs all exhibited the typical cloverleaf secondary structure. Stem-loop (SL) structures and tandem repeats were identified in the CR. Phylogenetic analyses using Bayesian inference and maximum likelihood were undertaken to determine relationships between stoneflies. Results indicated that the Antarctoperlaria, which contains Gripopterygidae, was absolutely separated from Arctoperlaria; this finding agrees with morphology. Finally, the overall relationships could be summarized as follows ((((Notonemouridae + Nemouridae) + Leuctridae) + (Scopuridae + (Capniidae + Taeniopterygidae))) + (((Perlodidae + Chloroperlidae) + Perlidae) + (Pteronarcyidae + (Peltoperlidae + Styloperlidae))) + ((Diamphipnoidae + Eustheniidae) + Gripopterygidae)).

Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

The highly rearranged mitochondrial genomes of three economically important scale insects and the mitochondrial phylogeny of Coccoidea (Hemiptera: Sternorrhyncha)

The mitochondrial genomes (mitogenomes) of scale insects are less known in comparison to other insects, which hinders the phylogenetic and evolutionary studies of Coccoidea and higher taxa. Herein, the complete mitogenomes of Unaspis yanonensis, Planococcus citri and Ceroplastes rubens were sequenced for Coccoidea. The 15,220-bp long mitogenome of U. yanonensis contained the typical set of 37 genes including 13 PCGs, 22 tRNA genes and two rRNA genes; the 15,549-bp long mitogenome of P. citri lacked the tRNA gene trnV; the 15,387-bp long mitogenome of C. rubens exhibited several shortened PCGs and lacked five tRNA genes. The mitochondrial gene arrangement of the three mitogenomes was different from other scale insects and Drosophila yakuba. Most PCGs used standard ATN (ATA, ATT, ATC and ATG) start codons and complete TAN (TAA or TAG) termination codons. The ND4L had the highest evolutionary rate but COX1 and CYTB were the lowest. Most tRNA genes had cloverleaf secondary structures, whereas the reduction of dihydrouridine (DHU) arms and TψC arms were detected. Tandem repeats, stem-loop (SL) structures and poly-[TA]n stretch were found in the control regions (CRs) of the three mitogenomes. The phylogenetic analyses using Bayesian inference (BI) and maximum likelihood methods (ML) showed identical results, both supporting the inner relationship of Coccoidea as Coccidae + (Pseudococcidae + Diaspididae).

The complete mitochondrial genome of Flavoperla biocellata Chu, 1929 (Plecoptera: Perlidae) and the phylogenetic analyses of Plecoptera

Of the roughly 400 species of Perlidae in the world, most species are widely distributed in the northern hemisphere, but a few can be found in South Africa and South America. There are only five species in the genus Flavoperla of the family Perlidae in China. To gain a better understanding of the architecture and evolution of mitochondrial genome in Flavoperla, the entire mitochondrial genome (mitogenome) of a Chinese Flavoperla biocellata Chu, 1929 from family Perlidae (Insecta: Plecoptera) was sequenced. The 15,805-bp long mitochondrial genome of F. biocellata contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a putative control region (CR). The gene arrangement of F. biocellata was identical with that of other stoneflies and with the fly Drosophila yakuba. Most PCGs of F. biocellata used the standard ATN start codons and complete TAN termination codons. Twenty-one of the 22 tRNA genes exhibited cloverleaf secondary structures, but the dihydrouridine (DHU) arm of trnSer (AGN) was completely reduced. Phylogenetic analyses with both Bayesian inference (BI) and maximum likelihood methods (ML) generated similar topology, both supporting the monophyly of all stonefly families and the infraorder Systellognatha. The phylogenetic analysis based on mitochondrial genomic data from 30 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera. The northern hemisphere suborder Arctoperlaria divided into two groups, Euholognatha and Systellognatha. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae+Diamphipnoidae and Austroperlidae+ Gripopterygidae; consistent with relationships proposed based on morphology. The final relationships within Plecoptera were recovered as (((Perlidae+(Perlodidae+Chloroperlidae))+(Pteronarcyidae+(Peltoperlidae+Styloperlidae))) +(Taeniopterygidae+(Capniidae+(Nemouridae+Notonemouridae))))+ (Gripopterygoidae+Eusthenioidae).

First mitochondrial genome of a stonefly from the subfamily Microperlinae: Microperla geei (Plecoptera: Peltoperlidae)

The stonefly Microperla geei is the fourth sequenced peltoperlid and the first entire mitochondrial genome of M. geei representing the subfamily Microperlinae. The nearly complete mitogenome of M geei is 15,216 bp in size, has 37 genes and one partial control region, which is the classical structure for insect mitogenome. All PCGs started with ATN, except ND1 and ND5 genes used TTG and GTG. Eleven PCGs used the termination codon TAA or TAG and the COII and ND5 genes stopped with a single T. Our phylogenetic topology tree supported Peltoperlidae was monophyletic and M. geei was a sister-group to the clade (Soliperla sp. + (Cryptoperla stilifera + Peltoperlopsis cebuano)). This study could provide new information for the further phylogenetic studies.

Comparative mitogenomic analysis of species in the subfamily Amphinemurinae (Plecoptera: Nemouridae) reveal conserved mitochondrial genome organization

The subfamily Amphinemurinae has five genera in China, with each genus of similar morphology. To gain a better understanding of architecture and evolution of mitogenome in Amphinemurinae, mitogenomes of eight species representing four genera (Amphinemura, Indonemoura, Protonemura and Sphaeronemoura) in the subfamily Amphinemurinae were sequenced, and a comparative mitogenomic analysis of five genera (including a published stonefly genus, Mesonemoura) was carried out. By comparative analysis, we found highly conserved genome organization of ten Amphinemurinae species including genome contents, gene order, nucleotide composition, codon usage, amino acid composition, as well as genome asymmetry. GC content was the most significant factor in determining codon bias among organisms. The Ka/Ks values for all PCGs were far lower than 1, indicating that these genes were evolving under purifying selection. We also found some important conserved stem and loop in the cloverleaf structure of tRNAs, and found conserved helices and loops in each domain of the secondary structure of rRNAs. The presence of structural elements in the control region is also discussed. The phylogenetic analyses indicated that within Amphinemurinae, Sphaeronemoura was assigned the sister group of Mesonemoura. Our analyses inferred a relationship within Euholognatha: ((Nemouridae + Notonemouridae) + (Taeniopterygidae + Capniidae) + Scopuridae) + Leuctridae.

Mitochondrial genomes of the stoneflies Mesonemourametafiligera and Mesonemouratritaenia (Plecoptera, Nemouridae), with a phylogenetic analysis of Nemouroidea

In this study, two new mitochondrial genomes (mitogenomes) of Mesonemourametafiligera and Mesonemouratritaenia from the family Nemouridae (Insecta: Plecoptera) were sequenced. The Mesonemourametafiligera mitogenome was a 15,739 bp circular DNA molecule, which was smaller than that of M.tritaenia (15,778 bp) due to differences in the size of the A+T-rich region. Results show that gene content, gene arrangement, base composition, and codon usage were highly conserved in two species. Ka/Ks ratios analyses of protein-coding genes revealed that the highest and lowest rates were found in ND6 and COI and that all these genes were evolving under purifying selection. All tRNA genes in nemourid mitogenomes had a typical cloverleaf secondary structure, except for tRNA^Ser(AGN) which appeared to lack the dihydrouridine arm. The multiple alignments of nemourid lrRNA and srRNA genes showed that sequences of three species were highly conserved. All the A+T-rich region included tandem repeats regions and stem-loop structures. The phylogenetic analyses using Bayesian inference (BI) and maximum likelihood methods (ML) generated identical results. Amphinemurinae and Nemourinae were sister-groups and the family Nemouridae was placed as sister to Capniidae and Taeniopterygidae.

The phylogeny and evolutionary timescale of stoneflies (Insecta: Plecoptera) inferred from mitochondrial genomes

Phylogenetic analysis based on mitochondrial genomic data from 25 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera (stoneflies). The monophyly of both currently recognized suborders was strongly supported, concordant with previous molecular analyses of Plecoptera. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae + Diamphipnoidae and Austroperlidae + Gripopterygidae; consistent with relationships proposed based on morphology. The largely northern hemisphere suborder Arctoperlaria also divided into two groups, Euholognatha and Systellognatha, each composed of the five families traditionally assigned to each infraorder (the placement Scopuridae by mt genome data remains untested at this time). Within Euholognatha, strong support for the clade Nemouridae + Notonemouridae confirmed the northern origin of the currently southern hemisphere restricted Notonemouridae. Other family level relationships within the Arctoperlaria differ from those recovered by previous morphology and molecular based analyses. A fossil-calibrated divergence estimation suggests the formation of two suborders dates back to the Jurassic (181 Ma), with subsequent diversification of most stonefly families during the Cretaceous. This result confirms the hypothesis that initial divergence between the suborders was driven by the breakup of the supercontinent Pangaea into Laurasia and Gondwanaland (commencing 200 Ma and complete by 150 Ma).

Complete mitochondrial genomes of three Oxya grasshoppers (Orthoptera) and their implications for phylogenetic reconstruction

Oxya is a genus of grasshoppers (Orthoptera: Acridoidea) attacking rice and other gramineous plants in Africa and Asia. In the present study, we characterized complete mitochondrial genomes (mitogenomes) of three species, Oxya japonica japonica (15,427 bp), Oxya hainanensis (15,443 bp) and Oxya agavisa robusta (15,552 bp) collected from China. The three mitogenomes contained a typical gene set of metazoan mitogenomes and shared the same gene order with other Acridid grasshoppers, including the rearrangement of tRNA^Asp and tRNA^Lys. Analyses of pairwise genetic distances showed that ATP8 was the least conserved gene, while COI the most conserved. To determine the position of Oxya grasshoppers in the phylogeny of Acrididae, we reconstructed phylogenetic trees among 64 species from across 11 subfamilies using nucleotide sequences of mitogenomes. While the tree confirms traditional classifications of Acrididae at major higher-levels, it suggests a few modifications for classifications at lower-levels.

The first mitochondrial genome from Scopuridae (Insecta: Plecoptera) reveals structural features and phylogenetic implications

This study determined the first complete mitochondrial genome (mitogenome) of a stonefly, Scopura longa (Plecoptera: Scopuridae), and reconstructed a phylogeny based on two datasets of mitogenomes in eighteen available stoneflies to examine the relationships among Plecoptera. The complete mitogenome of S. longa is a circular molecule of 15,798bp in size. It contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a control region (CR). Most PCGs used standard ATN start codons and TAN stop codons. All tRNAs could be folded as typical cloverleaf secondary structures except tRNA^Ser(AGN), with the dihydrouridine (DHU) arm missing. Tandem repeat regions, two potential stem-loop (SL) structures, Poly T structures and G+C-rich regions are detected in the control region. Finally, the phylogenetic relationships among the families within the Arctoperlaria were reconstructed. The topological structures of the two trees were almost identical. The present phylogenetic analysis shows that S. longa belongs to the infraorder Euholognatha. The monophyly of each family is generally well supported based on nucleotide sequences. The Pteronarcyidae is sister to ((Peltoperlidae+Styloperlidae)+(Perlidae+(Perlodidae+Chloroperlidae))).

'Rolling' stoneflies (Insecta: Plecoptera) from mid-Cretaceous Burmese amber

This contribution describes seven new species of fossil stoneflies from Cretaceous Burmese amber, all of which are dedicated to present and past members of the Rolling Stones. Two species-Petroperla mickjaggeri gen. nov. sp. nov. and Lapisperla keithrichardsi gen. nov. sp. nov.-are placed in a new family Petroperlidae within the stemline of Systellognatha. The first Cretaceous larval specimen of Acroneuriinae, Electroneuria ronwoodi gen. nov. sp. nov., is also described along with another four new species that are placed within the Acroneuriinae genus Largusoperla Chen et al., 2018: Largusoperla charliewattsi sp. nov., Largusoperla brianjonesi sp. nov., Largusoperla micktaylori sp. nov., and Largusoperla billwymani sp. nov. Additional specimens of Acroneuriinae are described without formal assignment to new species due to insufficient preservation. Implications for stonefly phylogeny and palaeobiogeography are discussed.

Complete Mitochondrial Genome of Suwallia teleckojensis (Plecoptera: Chloroperlidae) and Implications for the Higher Phylogeny of Stoneflies

Stoneflies comprise an ancient group of insects, but the phylogenetic position of Plecoptera and phylogenetic relations within Plecoptera have long been controversial, and more molecular data is required to reconstruct precise phylogeny. Herein, we present the complete mitogenome of a stonefly, Suwallia teleckojensis, which is 16146 bp in length and consists of 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and a control region (CR). Most PCGs initiate with the standard start codon ATN. However, ND5 and ND1 started with GTG and TTG. Typical termination codons TAA and TAG were found in eleven PCGs, and the remaining two PCGs (COII and ND5) have incomplete termination codons. All transfer RNA genes (tRNAs) have the classic cloverleaf secondary structures, with the exception of tRNASer(AGN), which lacks the dihydrouridine (DHU) arm. Secondary structures of the two ribosomal RNAs were shown referring to previous models. A large tandem repeat region, two potential stem-loop (SL) structures, Poly N structure (2 poly-A, 1 poly-T and 1 poly-C), and four conserved sequence blocks (CSBs) were detected in the control region. Finally, both maximum likelihood (ML) and Bayesian inference (BI) analyses suggested that the Capniidae was monophyletic, and the other five stonefly families form a monophyletic group. In this study, S. teleckojensis was closely related to Sweltsa longistyla, and Chloroperlidae and Perlidae were herein supported to be a sister group.