The mitochondrial genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the evolutionary timescale of Tachinid flies

Study of Mitogenomes Provides Implications for the Phylogenetics and Evolution of the Infraorder Muscomorpha in Diptera

The Muscomorpha is one of the most species-rich brachyceran groups in Diptera, with many species serving as important disease vectors; however, its high-level phylogenetic relationships have long been controversial and unsolved. This study comparatively analyzed the characteristics of mitogenomes of 131 species that represent 18 superfamilies in Muscomorpha, in which mitogenomes of 16 species have been newly sequenced and annotated, demonstrating that their gene composition, order, AT bias, length variation, and codon usage are consistent with documented dipteran mitogenomes. The phylogenetic topologies demonstrated that the robustness of Muscomorpha and major clades within Muscomorpha are monophyletic: Cyclorrhapha, Schizophora, and Calyptratae. A clade of Empidoidea were recovered as the sister group to Cyclorrhapha. Within Cyclorrhapha, Platypezoidea and Syrphoidea were sequentially placed as basal groups of the Cyclorrhapha. The remaining cyclorrhaph superfamilies gathered as two main clades. Ephydroidea were, in most cases, placed as the sister group to Calyptratae. Within Calyptratae, Hippoboscoidea were sister to an assemblage of lineages composed of an Oestroid grade and Muscoidea. The Muscomorpha was proposed to originate in the early Jurassic, and the main clade diversified near the Cretaceous-Paleogene extinction event, estimated using the MCMCtree and six fossil calibration points. The ancestral area of origin and geographic range of Muscomorpha was deduced to be the Palaearctic region with 56.9% probability using the RASP software based on a dated tree.

The complete mitochondrial genome of Vibrissina turrita (Meigen, 1824) (Diptera, Tachinidae)

In this study, the mitogenome of Vibrissina turrita (Meigen, 1824) (Diptera, Tachinidae) was sequenced based on the next-generation sequencing approach and analyzed here for the first time. The 17,387 bp genome has a high A + T content and consists of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one noncoding control region. The phylogenetic analysis results support that Exoristinae is monophyletic and V. turrita belongs to the subfamily. This study reveals the systematic classification status of V. turrita and will enrich the genetic data on Tachinidae.

The first mitochondrial genome of Meroplius fukuharai (Diptera: Sepsidae)

Meroplius fukuharai is an important sanitary and ecological resource insect. We sequenced and annotated the mitogenome of Meroplius fukuharai which is the first representative of the genus Meroplius with nearly complete mitochondrial data. This mitogenome is 14,803 bp long, which consists of 22 transfer RNA genes, 13 protein-coding genes (PCGs), and two ribosomal RNA genes. All genes have a conservational arrangement with other published species of Sepsidae. Our results also supported the monophyly of Sepsidae, and the genus Meroplius is more closely related to genus Sepsis, Microsepsis, and Archisepsis.

The complete mitochondrial genome of Peleteria iavana (Diptera, Tachinidae) in Guizhou, China, and its phylogenetic placement

The mitochondrial genome of the tachinid fly Peleteria iavana (Wiedemann, 1819), which belongs to the family Tachinidae, was obtained for the first time using high-throughput sequencing techniques. The complete mitochondrial genome is 15,697 bp in size and consists of 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNAs and a non-coding control region. The nucleotide composition biases A and T, the overall A + T percentage is up to 78.9% of the entire mitogenome. A phylogenetic analysis of 30 species within the family Tachinidae suggested that P. iavana is most closely related to (Janthinomyia sp.+Lydina aenea). The P. iavana mitochondrial genome will be a fundamental resource for understanding the molecular phylogenetic relationships of the species-rich subfamily Tachininae of Tachinidae.

The complete mitochondrial genome of Phthiridium szechuanum (Nycteribiidae, Diptera)

Phthiridium szechuanum is a bat surface parasite under the family Nycteribiidae that prefers to roost in the hair of bats to feed on their blood. In this study, the complete mitochondrial genome of P. szechuanum was studied for the first time using Illumina sequencing technology. The mitochondrial genome was 14,896 bp in size and was predicted to encode 37 genes including 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. Phylogenetic trees were constructed using the IQ-TREE web server and phylogenetic analysis was performed using the maximum likelihood method, and P. szechuanum was found to be phylogenetically closest to Basilia ansifera. These data will provide a molecular biological approach to the species identification of P. szechuanum and provide a new reference for further studies on the population genetics and phylogeny of the family Nycteribiidae.

Eighteen mitochondrial genomes of Syrphidae (Insecta: Diptera: Brachycera) with a phylogenetic analysis of Muscomorpha

In this study, 18 mitochondrial genomes (mitogenomes) of Syrphidae were sequenced. These mitogenomes ranged from 15,648 to 16,405 bp and contained 37 genes that were similar to those from other Syrphidae species. Most protein-coding genes (PCGs) started with a standard ATN codon and ended with TAA/G. All transfer RNAs (tRNAs) could be folded into the cloverleaf secondary structure except tRNA-Ser (AGN), which lacks a dihydrouridine arm. The secondary structures of ribosomal RNAs (rRNAs) were predicted. Six domains (III is absent in arthropods) and 44 helices were included in the 16S rRNA, and three domains and 24 helices were included in the 12S rRNA. We found three conserved fragments in all syrphid mitogenomes. Phylogenetic analyses were performed based on the nucleotide data of 13 PCGs and two rRNAs from 76 Muscomorpha and three outgroup species. In results the paraphyly of Aschiza and Schizophora were supported, the Acalyptratae was also paraphyletic but the relationships of its superfamilies were difficult to determine, the monophyly of Calyptratea was supported with the relationships of Oestroidea and Muscoidea need to be further reconsidered. Within Syrphidae the monophyly of family level was supported, the Syrphinae were clustered into one branch, while the paraphyly of Eristalinae was still well supported.

Four New Species of Macquartia (Diptera: Oestroidea) from China and Phylogenetic Implications of Tachinidae

Macquartia Robineau-Desvoidy (Diptera: Tachinidae, Tachininae) represents one of the most ancient evolutionary lineages of tachinids, parasitizing Chrysomelidae larvae. We found four new Macquartia species collected by malaise traps, namely M. brunneisquama sp. nov., M. chinensis sp. nov., M. flavifemorata sp. nov., and M. flavipedicel sp. nov. These new species are described and illustrated, and their comparison with congeners as well as an identification key to the 12 species of Macquartia from China known to date are included. To determine the significance of the mitogenome architecture and evolution across different tachinid lineages of this primitive taxonomic group, four complete mitochondrial genomes were sequenced, annotated, and analyzed. The gene arrangements are consistent with the ancestral insect mitogenomes. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the four species are all AT-biased. Analyses of Ka/Ks and overall p-genetic distance demonstrated that nad5 showed the highest evolutionary rate and nad1/nad4L were the most conserved genes among the four species. Phylogenetic reconstruction based on 13 PCGs strongly supported the monophyly of Macquartia, and the relationships of the four species are (M. flavifemorata + (M. flavipedicel + (M. brunneisquama + M. chinensis))). This study will help enhance our understanding of the taxonomic status and phylogenetic relationships in Tachinidae.

Ghost lineages can invalidate or even reverse findings regarding gene flow

Introgression, endosymbiosis, and gene transfer, i.e., horizontal gene flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has been formalized in statistical tests for HGF detection and used for example to detect massive adaptive gene flows in malaria vectors or to order evolutionary events involved in eukaryogenesis. However, these studies rely on the assumption that ghost lineages (all unsampled extant and extinct taxa) have little influence. We demonstrate here with simulations and data reanalysis that when considering the more realistic condition that unsampled taxa are legion compared to sampled ones, the conclusion of these studies become unfounded or even reversed. This illustrates the necessity to recognize the existence of ghosts in evolutionary studies.

Comparative Mitogenomics of Flesh Flies: Implications for Phylogeny

Flesh flies (Diptera: Sarcophagidae) represent a rapid radiation belonging to the Calyptratae. With more than 3000 known species, they are extraordinarily diverse in terms of their breeding habits and are therefore of particular importance in human and veterinary medicine, forensics, and ecology. To better comprehend the phylogenetic relationships and evolutionary characteristics of the Sarcophagidae, we sequenced the complete mitochondrial genomes of five species of flesh flies and performed mitogenomic comparisons amongst the three subfamilies. The mitochondrial genomes match the hypothetical condition of the insect ancestor in terms of gene content and gene arrangement. The evolutionary rates of the subfamilies of Sarcophagidae differ significantly, with Miltogramminae exhibiting a higher rate than the other two subfamilies. The monophyly of the Sarcophagidae and each subfamily is strongly supported by phylogenetic analysis, with the subfamily-level relationship inferred as (Sarcophaginae, (Miltogramminae, Paramacronychiinae)). This study suggests that phylogenetic analysis based on mitochondrial genomes may not be appropriate for rapidly evolving groups such as Miltogramminae and that the third-codon positions could play a considerable role in reconstructing the phylogeny of Sarcophagidae. The protein-coding genes ND2 and ND6 have the potential to be employed as DNA markers for species identification and delimitation in flesh flies.

Characterization of the complete mitochondrial genome of Gymnosoma dolycoridis (Diptera, Tachinidae) and phylogenetic analysis

The complete mitogenome of Gymnosoma dolycoridis Dupuis, 1960 was determined in this study. It is 15,185 bp in length, consisting of 13 protein-coding genes (PCG), 22 transfer RNA genes, two ribosomal RNA genes and one non-coding control region. The A + T content of the mitogenome is 78.5%. A maximum-likelihood phylogenetic tree built on 13 PCGs of 15 tachinid species indicated that Gymnosoma dolycoridis is clustered with other members of the subfamily Phasiinae as conventional taxonomy predicted.

Mitochondrial Genomes Provide New Phylogenetic and Evolutionary Insights into Psilidae (Diptera: Brachycera)

Psilidae (Diptera: Brachycera) is a moderate-sized family currently placed in the superfamily Diopsoidea and contains some destructive agricultural and forestry pests. The systematic position and intrafamilial classification of rust flies are in need of further study, and the available molecular data of Psilidae are still limited. In this study, we present the mitochondrial genomes of 6 Psilidae species (Chamaepsilatestudinaria Wang and Yang, Chyliza bambusae Wang and Yang, Chy. chikuni Wang, Loxocera lunata Wang and Yang, L. planivena Wang and Yang and L. sinica Wang and Yang). Comparative analyses show a conserved genome structure, in terms of gene composition and arrangement, and a highly Adenine plus Thymine biased nucleotide composition of the 6 psilid mitogenomes. Mitochondrial evolutionary rates vary among the 6 species, with species of Chylizinae exhibiting a slower average rate than species of Psilinae. The length, the nucleotide composition, and the copy number of repeat units of the control region are variable among the 6 species, which may offer useful information for phylogenetic and evolutionary studies of Psilidae. Phylogenetic analyses based on 4 mitogenomic datasets (AA, PCG, PCG12RNA, and PCGRNA) support the monophyly of Psilidae, and the sister relationship between Chylizinae and Psilinae, while Diopsoidea is suggested to be non-monophyletic. Our study enlightens the future application of mitogenomic data in the phylogenetic and evolutionary studies of Psilidae, based on denser taxon sampling.

The complete mitochondrial genome of Ornithomya biloba (Diptera, Hippoboscidae)

The mitochondrial genome (mitogenome) of Ornithomya biloba (Dufour 1827) was first sequenced and annotated in this study as the first representative of the genus Ornithomya. The complete mitogenome is 18,654 bp in length and contains 37 genes (13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and control region). The phylogenetic analysis based on 13 PCGs in IQ-TREE supports the monophyly of Hippoboscidae, which was a sister group of Streblidae. Families Hippoboscidae and Streblidae formed the monophyletic Hippoboscoidea clade.

Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

Uziflies (Family: Tachinidae) are dipteran endoparasites of sericigenous insects which cause major economic loss in the silk industry globally. Here, we are presenting the first full mitogenome of Blepharipa sp. (Acc: KY644698, 15,080 bp, A + T = 78.41%), a dipteran parasitoid of Muga silkworm (Antheraea assamensis) found in the Indian states of Assam and Meghalaya. This study has confirmed that Blepharipa sp. mitogenome gene content and arrangement is similar to other Tachinidae and Sarcophagidae flies of Oestroidea superfamily, typical of ancestral Diptera. Although, Calliphoridae and Oestridae flies have undergone tRNA translocation and insertion, forming unique intergenic spacers (IGS) and overlapping regions (OL) and a few of them (IGS, OL) have been conserved across Oestroidea flies. The Tachinidae mitogenomes exhibit more AT content and AT biased codons in their protein-coding genes (PCGs) than the Oestroidea counterpart. About 92.07% of all (3722) codons in PCGs of this new species have A/T in their 3rd codon position. The high proportion of AT and repeats in the control region (CR) affects sequence coverage, resulting in a short CR (Blepharipa sp.: 168 bp) and a smaller tachinid mitogenome. Our research unveils those genes with a high AT content had a reduced effective number of codons, leading to high codon usage bias. The neutrality test shows that natural selection has a stronger influence on codon usage bias than directed mutational pressure. This study also reveals that longer PCGs (e.g., nad5, cox1) have a higher codon usage bias than shorter PCGs (e.g., atp8, nad4l). The divergence rates increase nonlinearly as AT content at the 3rd codon position increases and higher rate of synonymous divergence than nonsynonymous divergence causes strong purifying selection. The phylogenetic analysis explains that Blepharipa sp. is well suited in the family of insectivorous tachinid maggots. It's possible that biased codon usage in the Tachinidae family reduces the effective number of codons, and purifying selection retains the core functions in their mitogenome, which could help with efficient metabolism in their endo-parasitic life style and survival strategy.

A Mitochondrial Genome Phylogeny of Cleridae (Coleoptera, Cleroidea)

The predaceous beetle family Cleridae includes a large and widely distributed rapid radiation, which is vital for the ecosystem. Despite its important role, a number of problems remain to be solved regarding the phylogenetic inter-relationships, the timing of divergence, and the mitochondrial biology. Mitochondrial genomes have been widely used to reconstruct phylogenies of various insect groups, but never introduced to Cleridae until now. Here, we generated 18 mitochondrial genomes to address these issues, which are all novel to the family. In addition to phylogenomic analysis, we have leveraged our new sources to study the mitochondrial biology in terms of nucleotide composition, codon usage and substitutional rate, to understand how these vital cellular components may have contributed to the divergence of the Cleridae. Our results recovered Korynetinae sister to the remaining clerids, and the calde of Clerinae+Hydnocerinae is indicated more related to Tillinae. A time-calibrated phylogeny estimated the earliest divergence time of Cleridae was soon after the origin of the family, not later than 160.18 Mya (95% HPD: 158.18–162.07 Mya) during the mid-Jurassic. This is the first mitochondrial genome-based phylogenetic study of the Cleridae that covers nearly all subfamily members, which provides an alternative evidence for reconstructing the phylogenetic relationships.

Monophyletic blowflies revealed by phylogenomics

BACKGROUND

Blowflies are ubiquitous insects, often shiny and metallic, and the larvae of many species provide important ecosystem services (e.g., recycling carrion) and are used in forensics and debridement therapy. Yet, the taxon has repeatedly been recovered to be para- or polyphyletic, and the lack of a well-corroborated phylogeny has prevented a robust classification.

RESULTS

We here resolve the relationships between the different blowfly subclades by including all recognized subfamilies in a phylogenomic analysis using 2221 single-copy nuclear protein-coding genes of Diptera. Maximum likelihood (ML), maximum parsimony (MP), and coalescent-based phylogeny reconstructions all support the same relationships for the full data set. Based on this backbone phylogeny, blowflies are redefined as the most inclusive monophylum within the superfamily Oestroidea not containing Mesembrinellidae, Mystacinobiidae, Oestridae, Polleniidae, Sarcophagidae, Tachinidae, and Ulurumyiidae. The constituent subfamilies are re-classified as Ameniinae (including the Helicoboscinae, syn. nov.), Bengaliinae, Calliphorinae (including Aphyssurinae, syn. nov., Melanomyinae, syn. nov., and Toxotarsinae, syn. nov.), Chrysomyinae, Luciliinae, Phumosiinae, Rhiniinae stat. rev., and Rhinophorinae stat. rev. Metallic coloration in the adult is shown to be widespread but does not emerge as the most likely ground plan feature.

CONCLUSIONS

Our study provides the first phylogeny of oestroid calyptrates including all blowfly subfamilies. This allows settling a long-lasting controversy in Diptera by redefining blowflies as a well-supported monophylum, and blowfly classification is adjusted accordingly. The archetypical blowfly trait of carrion-feeding maggots most likely evolved twice, and the metallic color may not belong to the blowfly ground plan.

A phylotranscriptomic framework for flesh fly evolution (Diptera, Calyptratae, Sarcophagidae)

The Sarcophagidae (flesh flies) comprise a large and widely distributed radiation within the Calyptratae (Diptera). Larval feeding habits are ecologically diverse and include sarcosaprophagy, coprophagy, herbivory, invertebrate and vertebrate predation, and kleptoparasitism. To elucidate the geographic origin and evolution of flesh fly life-history, we inferred a backbone phylogeny based on transcriptomic data from 26 sarcophagid species covering all three subfamilies plus 15 outgroups. The phylogeny was inferred using maximum parsimony and maximum likelihood methods based on a series of supermatrices, one set with overall information content improved by MARE (2290 loci), one set with 100% gene coverage for all included species (587 loci), and the last set including mitochondrial and nuclear genes (589 loci) and additional taxa. In order to obtain a more detailed hypothesis, we utilized the supertree approach to combine results from the present study with previously published hypotheses. This resulted supertree covers 84 of the one hundred currently recognized sarcophagid genera and formed the basis for the ancestral state reconstructions. The monophyletic Sarcophagidae is well-supported as sister to {Mystacinobiidae + Oestridae}, and relationships at the subfamily level are inferred as {Sarcophaginae, (Paramacronychiinae + Miltogramminae)}. The Sarcophagidae and each subfamily originated in the Americas, with Sarcophaginae diversifying mainly in the Neotropics, whereas the major radiation of both Miltogramminae and Paramacronychiinae occurred in the Palaearctic. Sarcosaprophagy is reconstructed as the ancestral larval feeding habit of the family Sarcophagidae and each subfamily. The ancestral sarcophagid larva probably utilized dead invertebrates as food, and the food spectrum expanded together with the diversification of breeding strategies. Particularly, kleptoparasitism in Miltogramminae is derived from sarcosaprophagy and may be seen as having derived from the breeding biology of 'lower' miltogrammines, the larvae of which feed on buried vertebrate carrion.

The first mitochondrial genome of Sepsis monostigma (Diptera: Sepsidae)

The sepsid fly Sepsis monostigma belongs to the genus Sepsis of Sepsidae. We sequenced and annotated the mitogenome of S. monostigma which as the first representative of genus Sepsis with nearly complete mitochondrial data. This mitogenome is 14,887bp long, which contains of 22 transfer RNA genes, 13 protein coding genes (PCGs) and 2 ribosomal RNA genes and a part of the AT control region. ML phylogenetic outcome strongly supported the monophyly of Sepsidae, and the family Sepsidae is more close to the family Heleomyzidae. It also indicated that the genus Sepsis is the sister group to Nemopoda, and the genus Archisepsis is the sister group to Microsepsis.

Middle Jurassic origin in India: a new look at evolution of Vermileonidae and time-scaled relationships of lower brachyceran flies

Vermileonidae (wormlions) comprises 61 described species in 12 genera and is one of the oddest and most rarely collected dipteran families. Larvae of Vermileonidae are famous for their pitfall prey behaviour, whereas the adults are rarely seen. Here we report, for the first time, the complete mitochondrial genome from members of Vermileonidae. Phylogenetic reconstruction based on a representative sampling of the order reveals new insights into relationships between the Vermileonidae and other members of lower brachyceran flies. A sister-group relationship between Vermileonidae and Xylophagidae is supported, and the higher-level clade relationships are Tabanomorpha + (Muscomorpha + (Xylophagomorpha + Stratiomyomorpha)). Combining mitochondrial genome data with a morphological phylogeny, geographical distribution and geological history, we propose that the Vermileonidae originated in India during the Middle Jurassic, spreading to Africa via land bridges during the Late Jurassic, to the Palaearctic after the collision of India with Laurasia in the Late Oligocene, and to the Nearctic in the Early Miocene, via either North Atlantic or Beringian land bridges. Wet forested regions have proved to be barriers to their dispersal, explaining their absence from Central Africa, South America and eastern North America.

Extraordinary diversification of the “bristle flies” (Diptera: Tachinidae) and its underlying causes

The family Tachinidae (“bristle flies”) is the most diverse and ecologically important group of insect parasitoids outside the parasitic wasps. It is among the most species rich families of flies (Diptera) and has experienced a recent adaptive radiation across the globe. We make use of a molecular phylogeny of the family to examine its rapid radiation and explore the traits of tachinid lineages that may have contributed to variation in their diversification. We apply a range of diversification analyses to assess the consistency and robustness of effects. We find that the Tachinidae are among the most rapidly diversifying families of animals. Six to eight clades of bristle flies, distributed across the phylogeny, exhibit strong evidence of accelerated diversification. Our results suggest that the use of holometabolous insect larvae, and specifically caterpillars (Lepidoptera), as hosts, is associated with increased diversification rates. However, these effects were inconsistent across analyses. We detected little influence of oviposition strategy (egg type) or host feeding habit, and we recovered evidence that unmeasured “hidden” traits may explain greater variance in diversification. We evaluated the strengths and weaknesses of different Maximum Likelihood and Bayesian approaches for analysing diversification and the potential for extrinsic factors, such as geography, to influence patterns of richness and diversification. In general, we conclude that although certain traits may provide opportunities for diversification, whether this is capitalized on may depend on additional traits and/or historical contingency.

Complete mitochondrial genome of Compsilura concinnata (Meigen) (Diptera, Tachinidae)

The complete mitochondrial genome of Compsilura concinnata (Meigen), was analyzed by next-generation sequencing approach. Its mitogenome is 15,841 bp totally, which consists of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one non-coding control region. The nucleotide composition biases toward A and T, the overall A + T% was up to 80.9% of the entire mitogenome. Phylogenetic analysis supported the sister relationship between Goniini and Blondeliini. The result also suggested that the monophyly of the Exoristinae.

Five mitochondrial genomes of black fungus gnats (Sciaridae) and their phylogenetic implications

Sciaridae is a family of great species diversity, distributed worldwide, that includes important agricultural pests of cultivated mushrooms and plants produced in greenhouses. Here we sequenced five nearly complete mitochondrial genomes representing three subfamilies of Sciaridae. The lengths of these mitogenomes range from 13,849 bp to 16,923 bp with 13 protein-coding genes (PCGs), 20-22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (CR). Compared with other dipteran species, rearrangements in Sciaridae are more common. Inversion or transition is observed frequently of trnL2, and in the tRNA clusters trnI-trnQ-trnM, trnW-trnC-trnY, and trnA-trnR-trnN-trnS1-trnE-trnF. Phylogenetic relationships within the family were reconstructed based on these newly sequenced species, combined with the published mitogenomes of related families, and recovered the topology within Sciaroidea as Cecidomyiidae + (Sciaridae + Keroplatidae). Relationships recovered within Sciaridae were Sciarinae + ('Pseudolycoriella group' + Megalosphyinae).

Characterization of the complete mitogenome of Anopheles aquasalis, and phylogenetic divergences among Anopheles from diverse geographic zones

Whole mitogenome sequences (mtDNA) have been exploited for insect ecology studies, using them as molecular markers to reconstruct phylogenies, or to infer phylogeographic relationships and gene flow. Recent Anopheles phylogenomic studies have provided information regarding the time of deep lineage divergences within the genus. Here we report the complete 15,393 bp mtDNA sequences of Anopheles aquasalis, a Neotropical human malaria vector. When comparing its structure and base composition with other relevant and available anopheline mitogenomes, high similarity and conserved genomic features were observed. Furthermore, 22 mtDNA sequences comprising anopheline and Dipteran sibling species were analyzed to reconstruct phylogenies and estimate dates of divergence between taxa. Phylogenetic analysis using complete mtDNA sequences suggests that A. aquasalis diverged from the Anopheles albitarsis complex ~28 million years ago (MYA), and ~38 MYA from Anopheles darlingi. Bayesian analysis suggests that the most recent ancestor of Nyssorhynchus and Anopheles + Cellia was extant ~83 MYA, corroborating current estimates of ~79–100 MYA. Additional sampling and publication of African, Asian, and North American anopheline mitogenomes would improve the resolution of the Anopheles phylogeny and clarify early continental dispersal routes.

The mitochondrial genome of Formicosepsis sp. (Diptera: Cypselosomatidae)

The mitochondrial genome of Formicosepsis sp. was sequenced and annotated as the first representative of family Cypselosomatidae and superfamily Nerioidea. The part mitochondrial genome of Formicosepsis sp. is 15,144 bp totally, consisting of 13 protein-coding genes, two rRNAs, and 22 transfer RNAs, which has a similar gene structure with other published species of Diptera. The nucleotide composition biases toward A and T is 76.4% of the entirety. IQ-tree analysis revealed that the outgroups Anopheles oryzalimnetes and Simulium variegatum diverged from the rest. The Nerioidea represented by Formicosepsis sp. was sister group to Opomyzoidea. The Sciomyzoidea consisting of Sciomyzidae and Sepsidae is a monophyletic clade at the base of Acalyptratae.

First mitochondrial genomes of five hoverfly species of the genus Eristalinus (Diptera: Syrphidae)

The hoverfly genus Eristalinus (Diptera, Syrphidae) contains many widespread pollinators. The majority of the species of Eristalinus occur in the Afrotropics and their molecular systematics still needs to be investigated. This study presents the first complete and annotated mitochondrial genomes for five species of Eristalinus. They were obtained by high-throughput sequencing of total genomic DNA. The total length of the mitogenomes varied between 15 757 and 16 245 base pairs. Gene composition, positions, and orientation were shared across species, and were identical to those observed for other Diptera. Phylogenetic analyses (maximum likelihood and Bayesian inference) based on the 13 protein coding and both rRNA genes suggested that the subgenus Eristalinus was paraphyletic with respect to the subgenus Eristalodes. An analysis of the phylogenetic informativeness of all protein coding and rRNA genes suggested that NADH dehydrogenase subunit 5 (nad5), cytochrome c oxidase subunit 1, nad4, nad2, cytochrome b, and 16S rRNA genes are the most promising mitochondrial molecular markers to result in supported phylogenetic hypotheses of the genus. In addition to the five complete mitogenomes currently available for hoverflies, the five mitogenomes published here will be useful for broader molecular phylogenetic analyses among hoverflies.

The mitochondrial genome of Drino Sp. (Diptera, Tachinidae)

The tachinid fly Drino sp. belongs to the subfamily Exoristinae of Tachinidae. We sequenced and annotated the mitogenome of Drino sp. which makes this species first representative of the tribe Eryciini (Tachinidae: Exoristinae) with nearly complete mitochondrial data. This mitogenome is 15437 bp in total, which consists of 22 transfer RNAs, 13 protein-coding genes, 2 ribosomal RNAs and non-coding control region. All genes have the conservational arrangement with other published species of Tachinidae. The nucleotide composition biases toward A and T, the overall A + T% was up to 80.4% of the entire mitogenome. Bayesian inference analysis strongly supported the monophyly of Tachinidae and Exoristinae. Our results also suggested that Exoristinae is the sister group to Phasiinae, and Dexiinae is the sister group to the clade of Phasiinae + Exoristinae.

Analysis of the complete mitochondrial genomes of two forensically important blowfly species: Lucilia caesar and Lucilia illustris

Blowfly species of the family Calliphoridae can be used in forensic investigations to estimate the minimum post-mortem interval (PMImin). Lucilia caesar and Lucilia illustris (Diptera: Calliphoridae) are closely related and phenotypically similar, making reliable identification difficult. To identify potential genetic markers to distinguish these species, five complete mitochondrial genomes were sequenced: three for L. caesar (KM657111-KM657113) and two for L. illustris (KM657109, KM657110). The ND6 gene contained the most species-specific SNPs (1.71%), followed by the ND5 gene (1.68%) and the COI gene (1.56%), identifying ND6 and ND5 as valuable loci for differentiating L. caesar and L. illustris specimens.

Extinction vs. Rapid Radiation: The Juxtaposed Evolutionary Histories of Coelotine Spiders Support the Eocene-Oligocene Orogenesis of the Tibetan Plateau

Evolutionary biology has long been concerned with how changing environments affect and drive the spatiotemporal development of organisms. Coelotine spiders (Agelenidae: Coelotinae) are common species in the temperate and subtropical areas of the Northern Hemisphere. Their long evolutionary history and the extremely imbalanced distribution of species richness suggest that Eurasian environments, especially since the Cenozoic, are the drivers of their diversification. We use phylogenetics, molecular dating, ancestral area reconstructions, diversity, and ecological niche analyses to investigate the spatiotemporal evolution of 286 coelotine species from throughout the region. Based on eight genes (6.5 kb) and 2323 de novo DNA sequences, analyses suggest an Eocene South China origin for them. Most extant, widespread species belong to the southern (SCG) or northern (NCG) clades. The origin of coelotine spiders appears to associate with either the Paleocene-Eocene Thermal Maximum or the hot period in early Eocene. Tibetan uplifting events influenced the current diversity patterns of coelotines. The origin of SCG lies outside of the Tibetan Plateau. Uplifting in the southeastern area of the plateau blocked dispersal since the Late Eocene. Continuous orogenesis appears to have created localized vicariant events, which drove rapid radiation in SCG. North-central Tibet is the likely location of origin for NCG and many lineages likely experienced extinction owing to uplifting since early Oligocene. Their evolutionary histories correspond with recent geological evidence that high-elevation orographical features existed in the Tibetan region as early as 40-35 Ma. Our discoveries may be the first empirical evidence that links the evolution of organisms to the Eocene-Oligocene uplifting of the Tibetan Plateau. [Tibet; biogeography; ecology; molecular clock; diversification.].

First fossil of an oestroid fly (Diptera: Calyptratae: Oestroidea) and the dating of oestroid divergences

Calyptrate flies include about 22,000 extant species currently classified into Hippoboscoidea (tsetse, louse, and bat flies), the muscoid grade (house flies and relatives) and the Oestroidea (blow flies, bot flies, flesh flies, and relatives). Calyptrates are abundant in nearly all terrestrial ecosystems, often playing key roles as decomposers, parasites, parasitoids, vectors of pathogens, and pollinators. For oestroids, the most diverse group within calyptrates, definitive fossils have been lacking. The first unambiguous fossil of Oestroidea is described based on a specimen discovered in amber from the Dominican Republic. The specimen was identified through digital dissection by CT scans, which provided morphological data for a cladistic analysis of its phylogenetic position among extant oestroids. The few known calyptrate fossils were used as calibration points for a molecular phylogeny (16S, 28S, CAD) to estimate the timing of major diversification events among the Oestroidea. Results indicate that: (a) the fossil belongs to the family Mesembrinellidae, and it is identified and described as Mesembrinella caenozoica sp. nov.; (b) the mesembrinellids form a sister clade to the Australian endemic Ulurumyia macalpinei (Ulurumyiidae) (McAlpine's fly), which in turn is sister to all remaining oestroids; (c) the most recent common ancestor of extant Calyptratae lived just before the K-Pg boundary (ca. 70 mya); and (d) the radiation of oestroids began in the Eocene (ca. 50 mya), with the origin of the family Mesembrinellidae dated at ca. 40 mya. These results provide new insight into the timing and rate of oestroid diversification and highlight the rapid radiation of some of the most diverse and ecologically important families of flies. ZooBank accession number-urn:lsid:zoobank.org:pub:0DC5170B-1D16-407A-889E-56EED3FE3627.

A survey of five Pireneitega species (Agelenidae, Coelotinae) from China

Five species of Pireneitega spiders from China are surveyed, of which three are new to science: P.huashanensis Zhao & Li, sp. n. (♂♀), P.lushuiensis Zhao & Li, sp. n. (♂♀), P.xiyankouensis Zhao & Li, sp. n. (♂♀). Two known species are redescribed: P.liansui (Bao & Yin, 2004) and P.triglochinata (Zhu & Wang, 1991). The males of P.liansui and P.triglochinata (Zhu & Wang, 1991) are described for the first time. DNA barcodes for five species are documented for future use and as proof of molecular differences between species.

Mitochondrial genome analysis of Ectophasia roundiventris (Diptera, Tachinidae)

The mitochondrial genome of Ectophasia roundiventris (Loew, 1858), the first representative of subfamily Phasiinae, was sequenced and annotated. So far, there are four Tachinidae mitochondrial genomes, here, all of them are used in Neighbour-Join and Maximum Likelihood analyses. The nucleotide composition of Ectophasia roundiventris mitochondrial genome was 40.4% of A, 39.0% of T, 11.8% of C, 8.8% of G, 79.4% of A + T content. The codon ATG was the most popular start codon. The conservative stop codon was TAA, COX2, and ND5 terminated with an incomplete stop codon T, while the gene ND4 was ended with stop codon TA.

A new species of Longicoelotes (Araneae, Agelenidae) from China, with the first description of the male of L. kulianganus (Chamberlin, 1924)

A new Longicoeletes species is described from Jiangxi Province, China: L.geeisp. n. (♂♀). In addition, the male of L.kulianganus (Chamberlin, 1924) is described for the first time. DNA barcodes of the two species are documented for future use and as proof of molecular differences between these species.

Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha)

The superfamily Lauxanioidea is a significant dipteran clade including over 2500 known species in three families: Lauxaniidae, Celyphidae and Chamaemyiidae. We sequenced the first five (three complete and two partial) lauxanioid mitochondrial (mt) genomes, and used them to reconstruct the phylogeny of this group. The lauxanioid mt genomes are typical of the Diptera, containing all 37 genes usually present in bilaterian animals. A total of three conserved intergenic sequences have been reported across the Cyclorrhapha. The inferred secondary structure of 22 tRNAs suggested five substitution patterns among the Cyclorrhapha. The control region in the Lauxanioidea has apparently evolved very fast, but four conserved structural elements were detected in all three complete mt genome sequences. Phylogenetic relationships based on the mt genome data were inferred by Maximum Likelihood and Bayesian methods. The traditional relationships between families within the Lauxanioidea, (Chamaemyiidae + (Lauxaniidae + Celyphidae)), were corroborated; however, the higher-level relationships between cyclorrhaphan superfamilies are mostly poorly supported.

A survey of Pireneitega from Tajikistan (Agelenidae, Coelotinae)

Five new species of Pireneitega species from Tajikistan are described: Pireneitegazonsteinisp. n. (♂♀), Pireneitegamuratovisp. n. (♀), Pireneitegatyuraisp. n. (♀), Pireneitegaramitensissp. n. (♀) and Pireneitegakovblyukisp. n. (♂). Pireneitegamajor (Kroneberg, 1875) is redescribed for the first time based on the lectotype designated here. DNA barcodes for the five new species are documented for future use and as proof of molecular differences between these species.

Sinocoelotes gen. n., a new genus of the subfamily Coelotinae (Araneae, Agelenidae) from Southeast Asia

A new genus of the spider subfamily Coelotinae, Sinocoelotes gen. n., with nine new species, is described from Yunnan and Sichuan Provinces in southern China. The new species are: Sinocoelotes cangshanensis sp. n. (♀), Sinocoelotes hehuaensis sp. n. (♂♀), Sinocoelotes luoshuiensis sp. n. (♀), Sinocoelotes mangbangensis sp. n. (♀) from Yunnan; Sinocoelotes kangdingensis sp. n. (♀), Sinocoelotes ludingensis sp. n. (♂♀), Sinocoelotes mahuanggouensis sp. n. (♀), Sinocoelotes muliensis sp. n. (♀), and Sinocoelotes yanyuanensis sp. n. (♂) from Sichuan. In addition, six Coelotes species are transferred to the new genus: Sinocoelotes acicularis (Wang, Griswold & Ubick, 2009), comb. n. (♂♀), Sinocoelotes forficatus (Liu & Li, 2010), comb. n. (♂♀), Sinocoelotes guangxian (Zhang, Yang, Zhu & Song, 2003), comb. n. (♂♀), Sinocoelotes pseudoterrestris (Schenkel, 1963), comb. n. (♂♀), Sinocoelotes pseudoyunnanensis (Wang, Griswold & Ubick, 2009), comb. n. (♂♀) and Sinocoelotes thailandensis (Dankittipakul & Wang, 2003), comb. n. (♂♀). DNA barcodes of all the species were documented for future use.

Nine new species of the spider genus Pireneitega Kishida, 1955 (Agelenidae, Coelotinae) from Xinjiang, China

Nine new Pireneitega species collected from Xinjiang, China are described as new to science: Pireneitega burqinensis sp. n. (♂♀), Pireneitega fuyunensis sp. n. (♂♀), Pireneitega gongliuensis sp. n. (♂♀), Pireneitega huochengensis sp. n. (♂♀), Pireneitega lini sp. n. (♀), Pireneitega liui sp. n. (♂♀), Pireneitega wensuensis sp. n. (♂), Pireneitega wui sp. n. (♂) and Pireneitega yaoi sp. n. (♀). DNA barcodes were obtained for all these species for future use.

A further study of the spider genus Notiocoelotes (Araneae, Agelenidae) from Hainan Island, China

Two new Notiocoelotes species, Notiocoelotes maoganensis sp. n. (♂♀) and Notiocoelotes qiongzhongensis sp. n. (♂♀) are described from Hainan Island, China. In addition, the female of Notiocoelotes membranaceus Liu & Li, 2010 is described for the first time. DNA barcodes of three species treated in this paper were obtained for future use.

Papiliocoelotes gen. n., a new genus of Coelotinae (Araneae, Agelenidae) spiders from the Wuling Mountains, China

One new genus of the spider subfamily Coelotinae, Papiliocoelotesgen. n., with five new species is described for both sexes: Papiliocoelotesguanyinensissp. n., Papiliocoelotesguitangensissp. n., Papiliocoelotesjiepingensissp. n., Papiliocoelotesmeiyuensissp. n., Papiliocoelotesyezhouensissp. n. All new species were collected from caves in the Wuling Mountains of Hubei and Hunan Provinces, China. DNA barcodes were obtained for future use.

The complete mitochondrial genome of Gasterophilus intestinalis, the first representative of the family Gasterophilidae

Gasterophilus spp. (Diptera: Gasterophilidae) has a worldwide distribution; however, no complete mitochondrial (mt) genome data is available for Diptera which has greatly impeded population genetics, phylogenetics, and systematics studies in Gasterophilidae. Mt genome is known to provide genetic markers for investigations in these areas, but complete mt genomic datasets have been lacking for many Gasterophilidae species. Herein, we present the complete mt genome of the third-stage larvae (L3) of Gasterophilus intestinalis from the stomach wall of naturally infected horses in Heilongjiang province (HLJ) and Xinjiang Uygur Autonomous Region (XJ), China. The complete mt genome of G. intestinalis was 15,687 bp (HLJ) and 15,660 bp (XJ) in length and consists of 37 genes, including 13 genes for proteins, 22 genes for tRNA, and 2 genes for rRNA. The gene arrangement is the same as those of Oestroidae species. Phylogenetic analyses using concatenated amino acid sequences of 12 protein-coding genes by Bayesian inference (BI) and maximum likelihood (ML), suggested that the families Gasterophilidae and Oestroidae were more closely related than to Tachinidae. The mt genome of G. intestinalis represents the first mt genome of any member of the family Gasterophilidae. These data provide novel mtDNA markers for studying the molecular epidemiology and population genetics of the G. intestinalis and its congeners.

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

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

Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae)

The complete mitogenome of the horse stomach bot fly Gasterophilus pecorum (Fabricius) and a near-complete mitogenome of Wohlfahrt's wound myiasis fly Wohlfahrtia magnifica (Schiner) were sequenced. The mitogenomes contain the typical 37 mitogenes found in metazoans, organized in the same order and orientation as in other cyclorrhaphan Diptera. Phylogenetic analyses of mitogenomes from 38 calyptrate taxa with and without two non-calyptrate outgroups were performed using Bayesian Inference and Maximum Likelihood. Three sub-analyses were performed on the concatenated data: (1) not partitioned; (2) partitioned by gene; (3) 3rd codon positions of protein-coding genes omitted. We estimated the contribution of each of the mitochondrial genes for phylogenetic analysis, as well as the effect of some popular methodologies on calyptrate phylogeny reconstruction. In the favoured trees, the Oestroidea are nested within the muscoid grade. Relationships at the family level within Oestroidea are (remaining Calliphoridae (Sarcophagidae (Oestridae, Pollenia + Tachinidae))). Our mito-phylogenetic reconstruction of the Calyptratae presents the most extensive taxon coverage so far, and the risk of long-branch attraction is reduced by an appropriate selection of outgroups. We find that in the Calyptratae the ND2, ND5, ND1, COIII, and COI genes are more phylogenetically informative compared with other mitochondrial protein-coding genes. Our study provides evidence that data partitioning and the inclusion of conserved tRNA genes have little influence on calyptrate phylogeny reconstruction, and that the 3rd codon positions of protein-coding genes are not saturated and therefore should be included.

The Complete Mitochondrial Genome of Delia antiqua and Its Implications in Dipteran Phylogenetics

Delia antiqua is a major underground agricultural pest widely distributed in Asia, Europe and North America. In this study, we sequenced and annotated the complete mitochondrial genome of this species, which is the first report of complete mitochondrial genome in the family Anthomyiidae. This genome is a double-stranded circular molecule with a length of 16,141 bp and an A+T content of 78.5%. It contains 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) and a non-coding A+T rich region or control region. The mitochondrial genome of Delia antiqua presents a clear bias in nucleotide composition with a positive AT-skew and a negative GC-skew. All of the 13 protein-coding genes use ATN as an initiation codon except for the COI gene that starts with ATCA. Most protein-coding genes have complete termination codons but COII and ND5 that have the incomplete termination codon T. This bias is reflected in both codon usage and amino acid composition. The protein-coding genes in the D. antiqua mitochondrial genome prefer to use the codon UUA (Leu). All of the tRNAs have the typical clover-leaf structure, except for tRNA^Ser(AGN) that does not contain the dihydrouridine (DHU) arm like in many other insects. There are 7 mismatches with U-U in the tRNAs. The location and structure of the two rRNAs are conservative and stable when compared with other insects. The control region between 12S rRNA and tRNA^Ile has the highest A+T content of 93.7% in the D. antiqua mitochondrial genome. The control region includes three kinds of special regions, two highly conserved poly-T stretches, a (TA)_n stretch and several G(A)_nT structures considered important elements related to replication and transcription. The nucleotide sequences of 13 protein-coding genes are used to construct the phylogenetics of 26 representative Dipteran species. Both maximum likelihood and Bayesian inference analyses suggest a closer relationship of D. antiqua in Anthomyiidae with Calliphoridae, Calliphoridae is a paraphyly, and both Oestroidea and Muscoidea are polyphyletic.

Mitochondrial genomes of two phlebotomine sand flies, Phlebotomus chinensis and Phlebotomus papatasi (Diptera: Nematocera), the first representatives from the family Psychodidae

BACKGROUND

Leishmaniasis is a worldwide but neglected disease of humans and animal transmitted by sand flies, vectors that also transmit other important diseases. Mitochondrial genomes contain abundant information for population genetic and phylogenetic studies, important in disease management. However, the available mitochondrial sequences of these crucial vectors are limited, emphasizing the need for developing more mitochondrial genetic markers.

METHODS

The complete mitochondrial genome of Phlebotomus chinensis was amplified in eight fragments and sequenced using primer walking. The mitochondrial genome of Phlebotomus papatasi was reconstructed from whole-genome sequencing data available on Genbank. The phylogenetic relationship of 24 selected representatives of Diptera was deduced from codon positions 1 and 2 for 13 protein coding genes, using Bayesian inference (BI) and maximum likelihood (ML) methods.

RESULTS

We provide the first Phlebotomus (P. chinensis and P. papatasi) mitochondrial genomes. Both genomes contain 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and an A + T-rich region. The gene order of Phlebotomus mitochondrial genomes is identical with the ancestral gene order of insect. Phylogenetic analyses demonstrated that Psychodidae and Tanyderidae are sister taxa. Potential markers for population genetic study of Phlebotomus species were also revealed.

CONCLUSION

The generated mitochondrial genomes of P. chinensis and P. papatasi represent a useful resource for comparative genomic studies and provide valuable future markers for the population genetic study of these important Leishmania vectors. Our results also preliminary demonstrate the phylogenetic placement of Psychodidae based on their mitochondrial genomes.

The Phylogeny and Evolutionary Timescale of Muscoidea (Diptera: Brachycera: Calyptratae) Inferred from Mitochondrial Genomes

Muscoidea is a significant dipteran clade that includes house flies (Family Muscidae), latrine flies (F. Fannidae), dung flies (F. Scathophagidae) and root maggot flies (F. Anthomyiidae). It is comprised of approximately 7000 described species. The monophyly of the Muscoidea and the precise relationships of muscoids to the closest superfamily the Oestroidea (blow flies, flesh flies etc) are both unresolved. Until now mitochondrial (mt) genomes were available for only two of the four muscoid families precluding a thorough test of phylogenetic relationships using this data source. Here we present the first two mt genomes for the families Fanniidae (Euryomma sp.) (family Fanniidae) and Anthomyiidae (Delia platura (Meigen, 1826)). We also conducted phylogenetic analyses containing of these newly sequenced mt genomes plus 15 other species representative of dipteran diversity to address the internal relationship of Muscoidea and its systematic position. Both maximum-likelihood and Bayesian analyses suggested that Muscoidea was not a monophyletic group with the relationship: (Fanniidae + Muscidae) + ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)), supported by the majority of analysed datasets. This also infers that Oestroidea was paraphyletic in the majority of analyses. Divergence time estimation suggested that the earliest split within the Calyptratae, separating (Tachinidae + Oestridae) from the remaining families, occurred in the Early Eocene. The main divergence within the paraphyletic muscoidea grade was between Fanniidae + Muscidae and the lineage ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)) which occurred in the Late Eocene.

The mitochondrial genome of the garden pea leafminer Chromatomyia horticola (Goureau, 1851) (Diptera: Agromyzidae)

Here we report the mitochondrial genome sequence of the garden pea leafminer Chromatomyia horticola (Goureau, 1851) (Diptera: Agromyzidae) (GenBank accession no. KR047789). This is the first species with sequenced mitochondrial genome from the genus Chromatomyia. The current length with partial A  +  T-rich region of this mitochondrial genome is 15,320 bp with an A  +  T content of 77.54%. All the 13 protein-coding, two rRNA, and 22 tRNA genes were sequenced, except for the A  +  T-rich region. As in most other sequenced mitochondrial genomes of Diptera, there is no rearrangement compared with the pupative ancestral arrangement of insects. All protein-coding genes start with the ATN start codon except for the gene cox1, which uses abnormal TTG. The A  +  T-rich region is located between rrnS and trnI with a sequenced length of 503 bp. Phylogenetic analysis using the Bayesian method based on the first and second codon positions of the 13 protein-coding genes recovered the monophyly of Agromyzidae with one species of Chromatomyia and four species of Liriomyza in our study. The superfamily Oestroidea (with Agromyzidae in analysis) is sister to the Opomyzoidea.

Explosive radiation or uninformative genes? Origin and early diversification of tachinid flies (Diptera: Tachinidae)

Molecular phylogenetic studies at all taxonomic levels often infer rapid radiation events based on short, poorly resolved internodes. While such rapid episodes of diversification are an important and widespread evolutionary phenomenon, much of this poor phylogenetic resolution may be attributed to the continuing widespread use of "traditional" markers (mitochondrial, ribosomal, and some nuclear protein-coding genes) that are often poorly suited to resolve difficult, higher-level phylogenetic problems. Here we reconstruct phylogenetic relationships among a representative set of taxa of the parasitoid fly family Tachinidae and related outgroups of the superfamily Oestroidea. The Tachinidae are one of the most species rich, yet evolutionarily recent families of Diptera, providing an ideal case study for examining the differential performance of loci in resolving phylogenetic relationships and the benefits of adding more loci to phylogenetic analyses. We assess the phylogenetic utility of nine genes including both traditional genes (e.g., CO1 mtDNA, 28S rDNA) and nuclear protein-coding genes newly developed for phylogenetic analysis. Our phylogenetic findings, based on a limited set of taxa, include: a close relationship between Tachinidae and the calliphorid subfamily Polleninae, monophyly of Tachinidae and the subfamilies Exoristinae and Dexiinae, subfamily groupings of Dexiinae+Phasiinae and Tachininae+Exoristinae, and robust phylogenetic placement of the somewhat enigmatic genera Strongygaster, Euthera, and Ceracia. In contrast to poor resolution and phylogenetic incongruence of "traditional genes," we find that a more selective set of highly informative genes is able to more precisely identify regions of the phylogeny that experienced rapid radiation of lineages, while more accurately depicting their phylogenetic context. Although much expanded taxon sampling is necessary to effectively assess the monophyly of and relationships among major tachinid lineages and their relatives, we show that a small number of well-chosen nuclear protein-coding genes can successfully resolve even difficult phylogenetic problems.

The first mitochondrial genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997 (Diptera: Sciomyzoidea: Sepsidae), with mitochondrial genome phylogeny of cyclorrhapha

Sepsid flies (Diptera: Sepsidae) are important model insects for sexual selection research. In order to develop mitochondrial (mt) genome data for this significant group, we sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997. The circular 15,878 bp mt genome is typical of Diptera, containing all 37 genes usually present in bilaterian animals. We discovered inaccurate annotations of fly mt genomes previously deposited on GenBank and thus re-annotated all published mt genomes of Cyclorrhapha. These re-annotations were based on comparative analysis of homologous genes, and provide a statistical analysis of start and stop codon positions. We further detected two 18 bp of conserved intergenic sequences from tRNAGlu-tRNAPhe and ND1-tRNASer(UCN) across Cyclorrhapha, which are the mtTERM binding site motifs. Additionally, we compared automated annotation software MITOS with hand annotation method. Phylogenetic trees based on the mt genome data from Cyclorrhapha were inferred by Maximum-likelihood and Bayesian methods, strongly supported a close relationship between Sepsidae and the Tephritoidea.