BI Trees Research Articles

Mitogenome-Based Phylogeny with Divergence Time Estimates Revealed the Presence of Cryptic Species within Heptageniidae (Insecta, Ephemeroptera).

Heptageniidae are known for their flat heads and bodies and are divided into three subfamilies. Despite the extensive diversity within this group and considerable efforts made to understand their evolutionary history, the internal classifications and origin time of Heptageniidae remains controversial. In this study, we newly sequenced 17 complete mitogenomes of Heptageniidae to reconstruct their phylogenetic positions within this family. Because of the ambiguous time of origin, our study also estimated the divergence time within Heptageniidae based on five fossil calibration points. The results of BI and ML trees all highly supported the monophyly of Heptageniidae and three subfamilies. The phylogenetic relationship of Rhithrogeninae + (Ecdyonurinae + Heptageniinae) was also recovered. The divergence time showed that Heptageniidae originated from 164.38 Mya (95% HPD, 150.23-181.53 Mya) in the mid-Jurassic, and Rhithrogeninae originated from 95.54 Mya (95% HPD, 73.86-120.19 Mya) in the mid-Cretaceous. Ecdyonurinae and Heptageniinae began to diverge at 90.08 Mya (95% HPD, 68.81-113.16 Mya) in the middle Cretaceous. After morphological identification, analysis of the mitogenome's composition, genetic distance calculation, phylogenetic analysis, and divergence time calculation, we suggest that two different populations of Epeorus montanus collected from Aksu, Xinjiang Uygur Autonomous Region (40°16' N, 80°26' E) and Xinyuan, Xinjiang Uygur Autonomous Region (43°20' N, 83°43' E) in China are cryptic species of E. montanus, but further detailed information on their morphological characteristics is needed to fully identify them.

Genomic comparative analysis of Ophiocordyceps unilateralis sensu lato.

Ophiocordyceps unilateralis sensu lato is a common pathogenic fungus of ants. A new species, O. fusiformispora, was described based on morphology and phylogenetic evidence from five genes (SSU, LSU, TEF1α, RPB1, and RPB2). The whole genomes of O. fusiformispora, O. contiispora, O. subtiliphialida, O. satoi, O. flabellata, O. acroasca, and O. camponoti-leonardi were sequenced and annotated and compared with whole genome sequences of other species in O. unilateralis sensu lato. The basic genome-wide characteristics of the 12 species showed that the related species had similar GC content and genome size. AntiSMASH and local BLAST analyses revealed that the number and types of putative SM BGCs, NPPS, PKS, and hybrid PKS-NRPS domains for the 12 species differed significantly among different species in the same genus. The putative BGC of five compounds, namely, NG-391, lucilactaene, higginsianin B, pyripyropene A, and pyranonigrin E were excavated. NG-391 and lucilactaene were 7-desmethyl analogs of fusarin C. Furthermore, the 12 genomes had common domains, such as KS-AT-DH-MT-ER-KR-ACP and SAT-KS-AT-PT-ACP-ACP-Te. The ML and BI trees of SAT-KS-AT-PT-ACP-ACP-Te were highly consistent with the multigene phylogenetic tree in the 12 species. This study provided a method to obtain the living culture of O. unilateralis sensu lato species and its asexual formed on the basis of living culture, which was of great value for further study of O. unilateralis sensu lato species in the future, and also laid a foundation for further analysis of secondary metabolites of O. unilateralis sensu lato.

What happens in ice age, does not stay in ice age: Phylogeography of Bombus terrestris revealed a low genetic diversity amongst the Eurasian populations

The objective of this research was to assess the genetic diversity and phylogeography of Bombus terrestris and examine the historical events that shaped its contemporary genetic structures using the COI mitochondrial marker. Specimens of the species were collected from its distribution range alongside the Alborz Mountain range, and GenBank sequences from the Eurasian distribution range were incorporated into the dataset. The COI sequences were employed in Bayesian and Maximum Likelihood analyses to generate phylogenetic trees for the species populations and to investigate the evolutionary history of the species. Additionally, species occurrence points and climate data were utilized in Species Distribution Modeling (SDM) analyses to reconstruct the species range under past, present, and future climate conditions. The ML and BI trees yielded similar topologies, indicating extremely low genetic diversity and a homogeneous structure in the species population distribution range in Eurasia. Demographic analyses suggested that the species may have experienced a bottleneck during the last glacial maximum in Eurasia, followed by a recent expansion. The SDM analyses revealed significant fluctuations in the species range in the past and expansion under present conditions. Given the high dispersal ability of the species, the population expansion rate has surpassed the rate of developing new genetic diversity, and the estimated polymorphic sites for the species are likely relatively recent. This low level of genetic variation can also be attributed to the absence of geographical barriers and the excellent flying ability of the queen bee, leading to sustained gene flow throughout the entire continent. Despite the general correlation between larger populations and higher genetic diversity, bumblebees can expand their population size without increasing genetic diversity when residing in resourceful habitats.

Characterization of Two New Apodemus Mitogenomes (Rodentia: Muridae) and Mitochondrial Phylogeny of Muridae

Apodemus is the most common small rodent species in the Palearctic realm and an ideal species for biogeographical research and understanding environmental changes. Elucidating phylogenetic relationships will help us better understand species adaptation and genetic evolution. Due to its stable structure, maternal inheritance, and rapid evolution, the mitogenome has become a hot spot for taxonomic and evolutionary studies. In this research, we determined the mitochondrial genome of Apodemus agrarius ningpoensis and Apodemus draco draco and studied the phylogeny of Muridae using ML and BI trees based on all known complete mitogenomes. The mitochondrial genome of Apodemus agrarius ningpoensis was 16,262 bp, whereas that of Apodemus draco draco was 16,222 bp, and both encoded 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Analysis of base composition showed a clear A-T preference. All tRNAs except tRNASer and tRNALys formed a typical trilobal structure. All protein-coding genes contained T- and TAA as stop codons. Phylogeny analysis revealed two main branches in the Muridae family. Apodemus agrarius ningpoensis formed sister species with Apodemus chevrieri, whereas Apodemus draco draco with Apodemus latronum. Our findings provide theoretical basis for future studies focusing on the mitogenome evolution of Apodemus.

New Morphological and Molecular Data Reveal an Underestimation of Species Diversity of Mites of the Genus Geckobia (Acariformes: Pterygosomatidae) in India

Mites of the genus Geckobia (Acariformes: Pterygosomatidae) are permanent and highly specialised ectoparasites of geckos (Gekkota). We conducted a local study on Geckobia mites associated with the geckos of the family Gekkonidae found mainly in the territory of the Indian Institute of Science’s campus (Bangalore, India). In total, we examined 208 lizards belonging to two genera: Hemidactylus and Cnemaspis. We assessed the prevalence of the mites and identified the preferred site for their infestation. We extended the standard morphological identification of the mite species by using DNA barcode markers, partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and nuclear ribosomal gene sequences: 18S rRNA and hypervariable region D2 of nuclear 28S rRNA. We checked the suitability of COI and nuclear (D2 of 28S rRNA) markers for species delimitations and identification purposes of the genus. The distance- and phylogeny-based approaches were applied: (i) to test the presence of a barcoding gap, we used the automated barcoding gap discovery tool (ABGD) and investigated intra- and interspecific genetic distances, and (ii) to reconstruct evolutionary relationships within the species, we performed maximum likelihood (ML) and Bayesian inference with Markov-Chain Monte Carlo (BI) analyses. As a result, we described five new species—Geckobia gigantea sp. n., G. treutleri sp. n., G. unica sp. n. and G. brevicephala sp. n.—from four Hemidactylus species: H. giganteus, H. treutleri, H. parvimaculatus and H. frenatus, respectively, and G. mysoriensis sp. n. from Cnemaspis mysoriensis. Additionally, we found three already described species: Geckobia indica Hirst, 1917 on H. treutleri (new host), Geckobia bataviensis Vitzhum, 1926 on H. parvimaculatus (new host) and H. frenatus (new locality) and Geckobia phillipinensis Lawrence, 1953 on H. frenatus (new locality). The diagnoses of G. indica and G. phillipinensis were improved and supplemented by descriptions of the males and juveniles. Both topologies of the BI and ML phylogenetic trees, as well as genetic distances, supported the species boundaries in the mite population shown by the morphological data. Hemidactylus frenatus was the most infected gecko species (61% prevalence), with the highest number of mite species (three spp.). The scale-mite richness was higher than expected; therefore, further research is required to evaluate the true diversity of Geckobia mites.

The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea.

In this study, the complete mitogenome of Hemigrapsus sinensis was the first identified and analyzed. The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea. The sample of Hemigrapsus sinensis was collected and DNA was extracted. After sequencing, NOVOPlasty was used for sequence assembly. Annotate sequences with MITOS WebServer, tRNAscan-SE2.0, and NCBI database. MEGA was used for sequence analysis and Phylosuite was used for phylogenetic tree construction. DnaSP was used to calculate Ka/Ks. This mitochondrial genome shows that it was 15,900bp and encoded 13 PCGs, 22 tRNA genes, two rRNA genes, and one control region. The genome composition tends to A + T (74.34%) and presents a negative GC-skew (- 0.22) and AT-skew (- 0.03). The PCGs initiation codon was the typical ATN and termination codon was the typical TAN, incomplete T or missing. The ML and BI trees showed that H. sinensis was most closely related to Hemigrapsus and clustered together with the Varunidae. And our phylogenetic trees provide proof that Ocypodoidea and Grapsoidea may be of common origin. Meanwhile, in the phylogenetic tree, parallel mixing of Chiromantes and Orisarma raised doubts over the traditional classification system. Besides, Incomplete Lineage sorting (ILS) was observed in Varunidae. In the subsequent analysis of evolution rate, we found that all of the PCGs (NAD4 was not calculated) had undergone negative selections, indicating the conservation of mitochondrial genes of H. sinensis during the evolution. Therefore, researching the complete mitogenome of H. sinensis would be contributing to molecular taxonomy, phylogenetic relationship, and breeding optimization within the Grapsoidea superfamily.

Multilocus evidence provides insight into the demographic history and asymmetrical gene flow between Ostrinia furnacalis and Ostrinia nubilalis (Lepidoptera: Crambidae) in the Yili area, Xinjiang, China.

Tianshan Mountains provide a model for studying biological evolution and speciation. Here we assess the evolutionary history of Ostrinia furnacalis (ACB) and Ostrinia nubilalis (ECB), which are sympatric in the Yili River Valley in Xinjiang, China.Our study is based on the historical gene flow analyses of two species by using three mitochondrial DNA (mtDNA, COI, COII, Cytb) and four nuclear DNA (nuDNA, EF-1α, Wingless, RPS5, CAD) markers obtained from representatives of HC (Huocheng), YN (Yining), XY (Xinyuan), and MNS (Manasi).Our results reveal that there is an asymmetrical gene flow pattern between the four populations. The population migratory pathways between these different populations show inflow into HC and YN, outflow from XY, and that MNS maintained a flow balance. Bayesian divergence time dating based on the COI gene suggests that the genetic divergence between the two species in this area may have occurred in Holocene at 0.008 Mya. Neutrality tests (Tajima's D, Fu's F s), and mismatch distribution test results suggest that population expansion events may not have occurred in the recent past. The demographic history and gene flow pattern between ACB and ECB may follow the "mountain isolation" hypothesis. The ML and BI trees of the mtDNA haplotype dataset show that ECB haplotypes are grouped together in a distinct clade and are clearly separate from ACB haplotypes. However, the geographical pattern of haplotype distribution is less clear for both ACB and ECB, supporting that there has been frequent gene flow among the geographic populations in the Tianshan Mountains.These findings indicate that the Tianshan Mountains are less likely a barrier to gene flow of the two species.

The Complete Mitochondrial Genomes of Three Sphenomorphinae Species (Squamata: Scincidae) and the Selective Pressure Analysis on Mitochondrial Genomes of Limbless Isopachys gyldenstolpei.

Simple SummarySkinks are the most species-rich group of lizards and are widely distributed around the world. The family Scincidae (Reptilia: Lacertiformes) includes limbed and limbless representatives occupying diverse habitats and showing a range of morphologies. Both limbed and limbless skinks have unique locomotion patterns in their habitats. Locomotion is the process of energy consumption, of which different modes may have different energy demands. As the center of energy metabolism in organisms, mitochondria provide most of the energy for physiological and biochemical activities via oxidative phosphorylation. Here, we employed mitochondrial genomes to investigate potential selective pressures among limbless skinks. Isopachys gyldenstolpei, as a typical limbless skink, has a different locomotion pattern compared to a limbed skink. Thus, I. gyldenstolpei can be used to study whether limb loss has a positive selection on mitochondrial genes. Two typical limbed skinks, Sphenomorphus indicus and Tropidophorus hainanus, were included in this study to compare the selective pressure analysis on mitochondrial genomes. In addition, the phylogenetic relationships within Scincidae are also discussed.In order to adapt to diverse habitats, organisms often evolve corresponding adaptive mechanisms to cope with their survival needs. The species-rich family of Scincidae contains both limbed and limbless species, which differ fundamentally in their locomotor demands, such as relying on the movement of limbs or only body swing to move. Locomotion requires energy, and different types of locomotion have their own energy requirements. Mitochondria are the energy factories of living things, which provide a lot of energy for various physiological activities of organisms. Therefore, mitochondrial genomes could be tools to explore whether the limb loss of skinks are selected by adaptive evolution. Isopachys gyldenstolpei is a typical limbless skink. Here, we report the complete mitochondrial genomes of I. gyldenstolpei, Sphenomorphus indicus, and Tropidophorus hainanus. The latter two species were included as limbed comparator species to the limbless I. gyldenstolpei. The results showed that the full lengths of the mitochondrial genomes of I. gyldenstolpei, S. indicus, and T. hainanus were 17,210, 16,944, and 17,001 bp, respectively. Three mitochondrial genomes have typical circular double-stranded structures similar to other reptiles, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and the control region. Three mitochondrial genomes obtained in this study were combined with fifteen mitochondrially complete genomes of Scincidae in the NCBI database; the phylogenetic relationship between limbless I. gyldenstolpei and limbed skinks (S. indicus and T. hainanus) is discussed. Through BI and ML trees, Sphenomorphinae and Mabuyinae were monophyletic, while the paraphyly of Scincinae was also recovered. The limbless skink I. gyldenstolpei is closer to the species of Tropidophorus, which has formed a sister group with (T. hainanus + T. hangman). In the mitochondrial genome adaptations between limbless I. gyldenstolpei and limbed skinks, one positively selected site was found in the branch-site model analysis, which was located in ND2 (at position 28, BEB value = 0.907). Through analyzing the protein structure and function of the selected site, we found it was distributed in mitochondrial protein complex I. Positive selection of some mitochondrial genes in limbless skinks may be related to the requirement of energy to fit in their locomotion. Further research is still needed to confirm this conclusion though.

The Genetic Diversity in Thereuonema tuberculata (Wood, 1862) (Scutigeromorpha: Scutigeridae) and the Phylogenetic Relationship of Scutigeromorpha Using the Mitochondrial Genome.

Simple SummaryThe sequencing of mitochondrial genomes promotes the study of cryptic species and the phylogenetic relationship of species. Thus far, only one complete mitochondrial genome of Scutigeromorpha is available in the NCBI. In this study, four specimens of Thereuonema tuberculata (Scutigeromorpha: Scutigeridae), collected from four different localities of China, were identified, and the four mitochondrial genomes of those were sequenced and annotated. Based on the gene organization and genetic diversity of the mitochondrial genomes, we hypothesized that cryptic species could exist in T. tuberculata. We further constructed BI and ML phylogenetic trees to reveal the relationship of Scutigeromorpha.Based on morphological characteristics to make species identification, the cryptic species of the Scutigeromorpha can be greatly underestimated. The mitochondrial genome provides a desirable tool for the biological identifications and the discovery of the cryptic species. The capacity to acquire mitochondrial genome sequences has substantially improved in recent years using next-generation sequencing (NGS) technology. On the basis of the next-generation sequencing, we obtained four complete mitochondrial genomes of Thereuonema tuberculata (Wood, 1862) from Nanyang, Henan Province (NY), Nanchang, Jiangxi Province (NC), Jinan, Shandong Province (JN), and Dali, Yunnan Province (DL) in China with GenBank numbers OK513221, OL449685, ON058988 and ON058989, respectively. The lengths of the four mitochondrial genomes ranged from 14,903 to 14,909 bp. The composition and order of genes of the four mitochondrial genomes were identical to the published mitochondrial genome of Scutigera coleoptrata (Linnaeus, 1758) (Scutigeromorpha: Scutigerdae). It was the first time that the tandem repeats in the control region were detected in Scutigeromorpha. We also calculated the corrected pairwise genetic distance of four complete mitochondrial genomes of T. tuberculata, ranging from 7.7 to 15.2%. The results showed that the T. tuberculata NC belonged to the typical sample of T. tuberculata, and T. tuberculata DL was hypothesized as a cryptic species of T. tuberculata. Meanwhile, T. tuberculata NY and T. tuberculata JN were hypothesized as potential cryptic species of T. tuberculata in this study. In both BI and ML trees, the monophyly of Scutigeromorpha, Scolopendromorpha, Geophilomorpha, and Lithobiomorpha was forcefully advocated. Moreover, Scutigeromorpha was recovered as the sister clade of (Scolopendromorpha + (Lithobiomorpha + Geophilomorpha)). Four specimens of T. tuberculata were clustered into one clade, which was the sister to the clade of S. coleoptrata.

Molecular Phylogeny and Adaptive Mitochondrial DNA Evolution of Salmonids (Pisces: Salmonidae).

Salmonids are composed of anadromous and freshwater fishes, which is an important model for studying adaptive evolution. Herein, 49 salmonid complete mitochondrial genomes and those of two outgroups were used to infer a robust phylogeny for the family Salmonidae. The BI and RAxML phylogenetic trees based on 13 concatenated mitochondrial protein-coding genes showed well-supported nodes, and topologies were highly congruent. The concatenated 13 mitochondrial protein-coding genes, ND2, ND3, and ND5 genes were shown to have significantly larger dN/dS ratios in anadromous species than in freshwater species of Salmonidae, but the CYTB gene had significantly smaller dN/dS in anadromous species. The FEL analysis identified positively selected sites and negatively selected sites in each mitochondrial protein-coding gene separately. The RELAX program revealed that the ATP8 and CYTB genes supported intensified selection of the anadromous lineages. Our results demonstrated the phylogeny of Salmonidae and explored the mitochondrial DNA evolution pattern between anadromous and freshwater salmonids.

The first complete mitochondrial genome of Hexagenia rigida Mc Dunnough, 1924 (Ephemeroptera: Ephemeridae) and its phylogeny

The phylogenetic relationship of Ephemeridae (Insect: Ephemeroptera) remains hotly debated using mitochondrial (mt) genomes. All previously reported mt genomes of Ephemeridae belong to the genus Ephemera. This study provides the first complete mt genome sequence from the genus Hexagenia with an analysis of the mitogenome of Hexagenia rigida Mc Dunnough, 1924 (Ephemeroptera: Ephemeridae) and providing new information to discuss the phylogenetic relationships within Ephemeroptera. The complete mt genome of H. rigida was a circular molecule of 16,159 bp in length, containing 37 genes (2 rRNA genes, 13 protein-coding genes, 22 tRNA genes), which showed the typical mt gene arrangement of insects. The AT content of the whole genome was 70.0% and the length of the control region was 1091 bp. All protein-coding genes used ATN as the start codon, and most PCGs used TAA/TAG as the stop codons excluding COI, COII, ND5 and Cyt b that used T as the stop codon. BI and ML phylogenetic trees constructed from 27 species of 13 families showed that Ephemeridae is a sister clade to the clade Polymitarcyidae.

Two new species of Dugesia (Platyhelminthes, Tricladida, Dugesiidae) from the subtropical monsoon region in Southern China, with a discussion on reproductive modalities

BackgroundFreshwater planarians of the genus Dugesia (Platyhelminthes, Tricladida, Dugesiidae) are distributed in a major part of the Old World and Australia, although until recently only very few species were known from China.ResultsTwo new species of Dugesia from Southern China are described on the basis of an integrative taxonomic approach. BI and ML phylogenetic trees based on the independent genes and on the concatenated dataset had similar topologies, only differing in some nodes that were weakly supported. Phylogenetic trees based on the concatenated dataset revealed that D. adunca Chen & Sluys, sp. nov. and D. tumida Chen & Sluys, sp. nov. are not closely related and belong to different clades. The two new species occupy separate long branches with high support values and, thus, are well-differentiated from their congeners. Separate species status of D. adunca and D. tumida is supported also by the genetic distances between the species included in our analysis, albeit that COI distances varied greatly among species. Dugesia adunca from Guangxi Province is characterized by the following features: living mature animals rather small; asymmetrical openings of the oviducts into the bursal canal; penis papilla with shape of an aquiline bill, albeit with a blunt tip; asymmetrical penis papilla, with a large antero-dorsal lip and a much smaller ventro-posterior lip; very large seminal vesicle, provided with trabeculae; small diaphragm; mixoploid karyotype with diploid complements of 2n = 2x = 16 and triploid complements of 2n = 3x = 24, with all chromosomes being metacentric. Dugesia tumida from Guangdong Province is characterized by a penis papilla provided with a large, symmetrical penial valve from the middle of which arises the small, distal section of the papilla; a duct intercalated between the seminal vesicle and the small diaphragm; ventrally displaced ejaculatory duct curving upwards before opening to the exterior; penis papilla highly asymmetrical, having a slim and long ventral portion and a short and stubby dorsal part; vasa deferentia separately opening into antero-dorsal portion of seminal vesicle; oviducts openings symmetrically into ventral portion of the bursal canal, near its opening into the atrium; mixoploid karyotype, with diploid chromosome portraits of 2n = 2x = 16, and triploid complements of 2n = 3x = 24, with all chromosomes being metacentric. In the context of the various kinds of mixoploidy and the sexualization of specimens, reproductive modalities within the genus Dugesia are shortly discussed.ConclusionMolecular, morphological, and karyological markers show that the two populations examined represent members of the genus Dugesia and constitute two new, distinct species.

Characterization of the complete mitogenome of Gymnocypris dobula (Günther, 1868) (Cypriniformes: Cyprinidae)

Gymnocypris dobula, classified into the highly specialized Schizothoracine fish, is endemic to Tibet, China. The complete mitochondrial DNA sequence of G. dobula was 16,728 base pairs in length and comprised 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes as well as one control region as in a typical vertebrate mitochondrial DNA gene. The ML and BI trees showed that G. dobula was most closely related to Gymnocypris scleracanthus within the highly specialized group. This mitogenome provides new molecular data for further taxonomic and phylogenetic studies of Schizothoracine fish.

The Mitochondrial Genomes of 18 New Pleurosticti (Coleoptera: Scarabaeidae) Exhibit a Novel trnQ-NCR-trnI-trnM Gene Rearrangement and Clarify Phylogenetic Relationships of Subfamilies within Scarabaeidae.

Simple SummaryThe family Scarabaeidae is one of the largest families in the insect order Coleoptera and is comprised of two quasi-systematics groups, Pleurosticti and Laparosticti. Pleurosticti is an economically important scarab group comprising about 20,000 species, the majority of which are phytophagous. Despite the innumerable studies based on ecological, molecular, and morphological characteristics, their taxonomy is still unclear and subject to many scientific hypotheses. The mitochondrial (mt) genome can provide tangible information to resolve the phylogenetic relationships within the family Scarabaeidae. However, the available mt genomes of Scarabaeidae in GenBank are underrepresented. Thus, we sequenced and analyzed 18 new phytophagous Scarabaeidae mitochondrial genomes from two subfamilies, Cetoniinae and Dynastinae, to conduct phylogenetic analyses within Scarabaeidae. This study contributes to increasing our knowledge about phytophagous Scarabaeidae.The availability of next-generation sequencing (NGS) in recent years has facilitated a revolution in the availability of mitochondrial (mt) genome sequences. The mt genome is a powerful tool for comparative studies and resolving the phylogenetic relationships among insect lineages. The mt genomes of phytophagous scarabs of the subfamilies Cetoniinae and Dynastinae were under-represented in GenBank. Previous research found that the subfamily Rutelinae was recovered as a paraphyletic group because the few representatives of the subfamily Dynastinae clustered into Rutelinae, but the subfamily position of Dynastinae was still unclear. In the present study, we sequenced 18 mt genomes from Dynastinae and Cetoniinae using next-generation sequencing (NGS) to re-assess the phylogenetic relationships within Scarabaeidae. All sequenced mt genomes contained 37 sets of genes (13 protein-coding genes, 22 tRNAs, and two ribosomal RNAs), with one long control region, but the gene order was not the same between Cetoniinae and Dynastinae species. All mt genomes of Dynastinae species showed the same gene rearrangement of trnQ-NCR-trnI-trnM, whereas all mt genomes of Cetoniinae species showed the ancestral insect gene order of trnI-trnQ-trnM. Phylogenetic analyses (IQ-tree and MrBayes) were conducted using 13 protein-coding genes based on nucleotide and amino acid datasets. In the ML and BI trees, we recovered the monophyly of Rutelinae, Cetoniinae, Dynastinae, and Sericinae, and the non-monophyly of Melolonthinae. Cetoniinae was shown to be a sister clade to (Dynastinae + Rutelinae).

The mitochondrial genome of Eurycantha calcarata Lucas, 1869 (Phasmatodea: Lonchodinae) and its phylogeny

The Lonchodinae (Phasmatodea: Phasmatidae) is rich in insect species with more than 330 species of 40 genera. The phylogenetic relationships within Lonchodinae have been under debate. We successfully sequenced the complete mitogenome of Eurycantha calcarata Lucas, 1869 (Phasmatodea: Lonchodinae) with a length of 16,280 bp, which had the same genes and gene arrangements as those of various published papers on stick insects. The whole mitogenome and control region of E. calcarata had a high AT content of 78.2 and 85.9%, respectively. All PCGs used ATN as the start codon, and most PCGs used TAA/TAG as the stop codons excluding COX2 (T), COX3 (TA), and ND5 (TA). To discuss the phylogeny of Lonchodinae, we reconstructed the phylogenetic relationships of 27 species of Phasmatodea including E. calcarata and two species of Embioptera used as outgroups. In BI and ML trees, the monophyly of Lonchodinae and Necrosciinae was well supported, whereas the monophyly of Clitumninae was not recovered. These results indicated that Lonchodinae was a sister clade to Phylliinae and E. calcarata was a sister clade to Phraortes genus.

A New Microsporidian Pathogen of the Mediterranean Flour Moth, Ephestiae kuehniella (Zeller) (Lepidoptera: Pyralidae)

In this study, a new Vairimorpha isolate was defined from Ephestia kuehniella Zeller (Lepidoptera: Pyralidae) in Turkey (Malatya). Infection was determined in the host's hindgut, both larval and adult stages. Two types spore originated from the polymorphic sporulation was detected during the observations. While the binucleate ovocylindrical fresh spores were measured 4.38 ± 0.31 μm (5.09–3.77 μm, n = 100) in length and 2.80 ± 0.18 μm (3.21–2.43 μm, n=100) in width, the ovoid meiospores were measured as 3.50 ± 0.46 μm (4.98–2.51 μm, n = 100) in length and 2.02 ± 0.28 μm (2.94–1.50 μm, n=100) in width. The multilocus genetic analyses based on SSU rRNA and RPB1 genes were carried for determining the phylogenetic status of the current microsporidium. In ML and BI trees, the current microsporidium was separated into a different branch from V. necatrix strains within the Vairimorpha clade

Characterization of the complete mitochondrial genome of Diploastrea heliopora and phylogeny of the scleractinia species which have group I introns in their COI genes.

Mitochondrial genome DNA is a powerful marker for resolving phylogenetic relationships among scleractinian corals. Here, we decode the complete mitochondrial genome of Diploastrea heliopora (Lamarck, 1816) for the first time. The general features are 18 363 bp in length, and conventionally, with 13 protein coding genes, two ribosomal RNAs, and two transfer RNAs. Gene arrangement and distribution are similar to other scleractinian corals. Moreover, the COI gene of D. heliopora is broken up into two parts by a complex group I intron. This intron is 1076 bases in length and contains helical structures (P1-P10, except P2) and four conserved regions (P, Q, R, and S). The mitochondrial genome of D. heliopora has asymmetric base composition (13.03% C, 20.29% G, 25.91% A, and 40.77% for T). Based on concatenated protein coding genes, ML and BI trees show similar phylogenetic relationship: D. heliopora clustered closely with Sclerophyllia maxima and Echinophyllia aspera into the robust branch. The data and conclusion in this study are reference for further phylogenetic studies of corals.

The first complete mitochondrial genome of Euroleon coreanus (Okamoto, 1926) (Neuroptera: Myrmeleontidae) and its phylogeny

The first complete mitochondrial genome of Euroleon coreanus (Okamoto, 1926) was 15,797 bp in length, and contained 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and the control region. Compared to the classic insect mitochondrial genome, E. coreanus showed a gene rearrangement of ND2-C-W-Y-COX1. The overall AT content of the mitochondrial genome was 75.5%. The monophyly of Ascalaphidae, Myrmeleontidae, Nemopteridae, Nymphidae, and Psychopsidae was supported in both BI and ML trees. And E. coreanus was a sister clade to the clade of genus Myrmeleon.

Identification of species in the genus Nitraria L. (Nitrariaceae) based on nucleotide variability of nuclear ribosomal DNA.

Intragenomic polymorphism of ITS1 and ITS2 of nuclear ribosomal DNA sequences was analysed in 33 samples belonging to the Nitraria species N. schoberi, N. sibirica, and N. komarovii. The nucleotide variability of the ITS region was detected in the Nitraria species as single-nucleotide substitutions (mainly transitions) and single-nucleotide deletion. Information about the nucleotide variability of fragments is given for the first time by us. The ITS1-5.8S-ITS2 region contained 17 phylogenetically informative single-nucleotide polymorphisms. Eleven single-nucleotide substitutions (transitions, C/T) were detected in ITS1. The ITS2 spacer contained 273–274 bp and was more conservative. A total of 5 phylogenetically informative single-nucleotide polymorphisms (4 transitions: C/T, G/A, one transversion: G/C), one single-nucleotide deletion (T/–) were detected in ITS2. The average GC content was 61.5 %. The GC content was lower in N. sibirica (59.2 %) than in N. schoberi and N. komarovii (62.7 %). It has been shown that the shorter ITS2 is a suitable molecular marker separating these species, due to the low interspecific variability and simultaneous available intraspecific variability. Phylogenetic ML and BI trees constructed separately for the ITS1 and ITS2 spacers, as well as separately for the full-size ITS region and the ITS2 spacer, were congruent. The results obtained on the intraspecific differentiation of N. sibirica revealed two main ribotypes among the samples of this species: the main Siberian sibirica-ribotype and the main Kazakh sibiricaribotype. Geographical features of the distribution of N. sibirica ribotypes, as well as the presence of significant differences between the main Siberian and Kazakh sibirica-ribotypes (3 single-nucleotide substitutions) indicated significant inter-population differences and taxonomic heterogeneity of N. sibirica. Most likely, the processes of homogenization of nuclear ribosomal DNA of N. sibirica samples, the origin of which is associated with hybridization and speciation, are currently continuing.

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

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