Say goodbye to tribes in the new house fly classification: A new molecular phylogenetic analysis and an updated biogeographical narrative for the Muscidae (Diptera)

Review of the endemic Neotropical genus Agenamyia Albuquerque (Diptera: Muscidae) with the description of new species from South America

Agenamyia Albuquerque, an endemic neotropical genus with two species, has been revised to include three new species: Agenamyia colombiana de Carvalho, Wolff & Fogaa sp. nov. from Envigado; Agenamyia maculata de Carvalho, Wolff & Fogaa sp. nov. from El Retiro; and Agenamyia timida de Carvalho, Wolff & Fogaa sp. nov. from Sopetrn, all localities in Antioquia, Colombia. This review presents an identification key for all species, including color images and illustrations of male and female terminalia. The distribution of all species is mapped and discussed.

Phylogeny and Evolutionary Timescale of Muscidae (Diptera: Calyptratae) Inferred from Mitochondrial Genomes

House flies (Muscidae) comprise the most species-rich family of the muscoid grade with over 5000 described species worldwide, and they are abundant in various terrestrial and aquatic ecosystems. The high number of species, varied appearances, complex feeding habits, and wide distributions have hindered researchers from understanding their phylogeny and evolutionary history. Here, we newly sequenced fifteen mitochondrial genomes and reconstructed the phylogenetic relationships and divergence time among eight subfamilies of Muscidae (Diptera). The best phylogenetic tree, which was inferred by IQ-Tree, recovered the monophyly for seven out of eight subfamilies (except for Mydaeinae). Based on phylogenetic analyses and morphological characteristics, we prefer the subfamily status of Azeliinae and Reinwardtiinae, and separate Stomoxyinae from Muscinae. Genus Helina Robineau-Desvoidy, 1830 was synonymized with Phaonia Robineau-Desvoidy, 1830. The divergence time estimation indicated Muscidae originated at 51.59 Ma (early Eocene). Most subfamilies had originated around 41 Ma. We provided a mtgenomic viewpoint on the phylogenetic relationships and divergence time estimation of Muscidae.

Phylogenetic Analyses Support the Monophyly of the Genus Lispe Latreille (Diptera: Muscidae) with Insights into Intrageneric Relationships

Lispe Latreille (Diptera: Muscidae) are a widespread group of predatory flies that inhabit semi-aquatic environments. Previous studies on this genus have mainly focused on morphological classification, so molecular data are entirely lacking, and there has been no attempt at a phylogenetic placement of the genus or the resolution of intragenic relationships. To address the phylogenetic placement of Lispe and to fill its gap in the Tree of Life Web Project, 58 Lispe spp. (covering 11 out of 13 acknowledged Lispe species groups) were selected to reconstruct a phylogeny using Maximum likelihood (ML) estimates, Maximum Parsimony (MP) analyses, and Bayesian inference (BI) based on two mitochondrial protein-coding genes (cytochrome c oxidase subunit I (COXI) and cytochrome b gene (CYTB)) and one nuclear gene (a fragment of the carbamoyl phosphate synthetase region of the CAD gene). The phylogenetic analyses indicated that the monophyletic Lispe is the sister group of the monophyletic Limnophora, together forming the tribe Limnophorini under the subfamily Coenosiinae. Three generic categories are proven obsolete: Chaetolispa Malloch, Lispacoenosia Snyder, and Xenolispa Malloch. Within the genus, the validity of 11 species groups is clarified by both molecular and morphological data. This study provides a sound basis for continuing intergeneric and intrageneric research into this fascinating and widespread genus.

Beyond canonical models: why a broader understanding of Diptera-microbiota interactions is essential for vector-borne disease control

Vector-borne diseases constitute a major global public health threat. The most significant arthropod disease vectors are predominantly comprised of members of the insect order Diptera (true flies), which have long been the focus of research into host-pathogen dynamics. Recent studies have revealed the underappreciated diversity and function of dipteran-associated gut microbial communities, with important implications for dipteran physiology, ecology, and pathogen transmission. However, the effective parameterization of these aspects into epidemiological models will require a comprehensive study of microbe-dipteran interactions across vectors and related species. Here, we synthesize recent research into microbial communities associated with major families of dipteran vectors and highlight the importance of development and expansion of experimentally tractable models across Diptera towards understanding the functional roles of the gut microbiota in modulating disease transmission. We then posit why further study of these and other dipteran insects is not only essential to a comprehensive understanding of how to integrate vector-microbiota interactions into existing epidemiological frameworks, but our understanding of the ecology and evolution of animal-microbe symbiosis more broadly.

The position of the Azeliinae in the Muscidae (Diptera) based on musculature of the male terminalia

The male genital and pregenital skeleton and musculature were studied in males of the following species of the Muscidae subfamily Azeliinae: Drymeia firthiana (Huckett, 1965), Drymeia longiseta Sorokina & Pont, 2015, Drymeia segnis (Holmgren, 1883), Thricops nigritellus (Zetterstedt, 1838), Thricops hirtulus (Zetterstedt, 1838), Hydrotaea dentipes (Fabricius, 1805), Muscina stabulans (Fallén, 1817), and Muscina levida (Harris, 1780). Descriptions and figures of the genital sclerites and muscles of D. firthiana and M. stabulans are given. A comparison was made between the genital segments and muscles of previously studied species of Mydaeinae and Muscinae and those of the Azeliinae. Based on the structure of the skeleton and muscles of syntergosternite VII + VIII and the phallapodeme muscles, significant differences were found between the subfamily Azeliinae and the subfamilies Mydaeinae and Muscinae. The basal position of the Azeliinae within the family Muscidae was confirmed. A comparison of the genital segments and muscles of the Muscidae with those of the Scathophagidae (Scathophaga stercoraria (Linnaeus, 1758)) and Anthomyiidae (Delia platura (Meigen, 1826)) was made. Tendencies in reduction of the pregenital segments and musculature, as well as of the phallapodeme muscles in the evolution of the Muscoidea have been revealed. The complete set of phallapodeme muscles in the Scathophagidae and Anthomyiidae corresponds to the basal state, and therefore the structure of the genital sclerites and muscles in the Muscidae shows a certain degree of reduction. The progressive changes in the Muscidae from the Azeliinae through the Mydaeinae to the Muscinae were traced.

Molecular Identification and Geometric Morphometric Analysis of Haematobosca aberrans (Diptera: Muscidae)

The genus Haematobosca Bezzi, 1907 (Diptera: Muscidae) contains haematophagous flies of veterinary importance. A new fly species of this genus was recognised from northern Thailand based on morphological characters and described as Haematobosca aberrans Pont, Duvallet & Changbunjong, 2020. In the present study, the mitochondrial cytochrome c oxidase I (COI) gene was used to confirm the morphological identification of H. aberrans. In addition, landmark-based geometric morphometrics was used to determine sexual dimorphism. The molecular analysis was conducted with 10 COI sequences. The results showed that all sequences were 100% identical. The sequence was not highly similar to reference sequences from GenBank and did not match any identified species from Barcode of Life Data Systems (BOLD). Phylogenetic analysis clearly differentiated this species from other species within the subfamily Stomoxyinae. For geometric morphometric analysis, a total of 16 wing pictures were analysed using the landmark-based approach. The results showed significant differences in wing shape between males and females, with a cross-validated classification score of 100%. The allometric analysis showed that wing shape has no correlation with size. Therefore, the COI gene is effective in species identification of H. aberrans, and geometric morphometrics is also effective in determining sexual dimorphism.

Comparative analysis of mitochondrial genomes among four species of muscid flies (Diptera: Muscidae) and its phylogenetic implications

Muscidae, commonly known as house flies and their close relatives, is one of the dipteran insects of recognized medical, veterinary, and ecological importance. Mitochondrial genomes (Mitogenomes) have been widely used for exploring phylogenetic analysis and taxonomic diagnosis due to the difficulty in distinguishing them morphologically. In this study, our complete mitogenomes of muscid flies were sequenced and aligned, which ranged from 15,117 bp (Synthesiomyia nudiseta) to 16,089 bp (Musca sorbens) in length, and contained a typical circular molecule comprising 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and a non-coding control region. The order and orientation of genes were identical with that from the ancestral insects. The phylogenetic analysis based on the mitochondrial genes indicated that the subfamily relationships within Muscidae were reconstructed as (Mydaeinae (Muscinae (Reinwardtiinae + Azeliinae))). Similar tree topologies were recovered from both Maximum Likelihood (ML) and Bayesian Inference (BI) analysis. Furthermore, we compared the phylogenetic analyses that were constructed using internal transcribed spacer 2 (ITS2), elongation factor-1α (EF-1α), 13 PCGs and 13 PCGs + ITS2 + EF-1α, respectively. Combined analysis of nuclear gene partitions improved support and resolution for resulting topologies but the positions of branches were obviously inconsistent due to limited species. More mitogenomes should be sequenced representing various taxonomic levels, especially close related species, which will enhance our understanding of phylogenetic relationships among muscids.

Characterization and Identification of Puparia of Hydrotaea Robineau-Desvoidy, 1830 (Diptera: Muscidae) From Forensic and Archaeological Contexts

Flies and beetles are the main components of the entomofauna colonizing a body after death. Following the recognition of constant and predictable colonization patterns and the knowledge about the dependence of the insect development to temperature, a new discipline, forensic entomology, has provided information useful to reconstruct criminal events. Funerary archaeoentomology has also applied the same rationale in archaeological contexts. Puparia represent a large fraction of the insect remains that can be found associated with a cadaver, especially when the body is mummified or in the advanced stages of decomposition. Puparium identification is still a problematic topic due to the lack of identification keys and, in several cases, a lack of diagnostic feature descriptions. Here, we focus the attention on some Hydrotaea Robineau-Desvoidy (Diptera, Muscidae) puparia from forensic and archaeological contexts. Puparia of Hydrotaea capensis (Wiedemann), Hydrotaea ignava (Harris), Hydrotaea aenescens (Wiedemann), Hydrotaea similis Meade, Hydrotaea pilipes Stein, and Hydrotaea dentipes (Fabricius) are here detailed and illustrated. Posterior spiracles, anal plate, and intersegmental spines have been considered as good diagnostic characters for the identification of these puparia.

The complete mitochondrial genome of Graphomya rufitibia (Diptera: Muscidae)

Graphomya rufitibia (Diptera: Muscidae) was distributed worldwide. In this study, the complete mitogenome of G. rufitibia was sequenced and annotated, and the full-length was a 15,374 bp fragment, consisting of A (40.64%), G (8.96%), T (36.80%), and C (13.59%). The mitogenome is composed of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding AT-rich region. Most PCGs used the canonical putative codon to start and stop, 21 tRNAs are folded into the classic clover-leaf structure, with the one exception of tRNA-Ser (AGN). A total length of 11,182 bp encoding 3727 amino acids, and account for 72.7% of the whole mitogenome. Phylogenetic analyses showed that G. rufitibia belongs to family Mydaeinae.

Identification of Muscidae (Diptera) of medico-legal importance by means of wing measurements

Cadavers attract numerous species and genera of Muscidae, both regular elements of carrion insect assemblages, and accidental visitors. Identification of adult Muscidae may be considered difficult, particularly by non-experts. Since species identification is a vital first step in the analysis of entomological material in any forensic entomology orientated experiment and real cases, various alternative methods of species identification have been proposed. We investigated possibility of semiautomated identification by means of wing measurements as an alternative for classic morphology and DNA-based approaches. We examined genus-level identification success for 790 specimens representing 13 genera of the most common European cadavers visiting Muscidae. We found 99.8% of examined specimens correctly identified to the genus-level. Without error, the following were identified: Azelia, Eudasyphora, Graphomya, Hydrotaea, Musca, Muscina, Mydaea, Neomyia, Polietes, Stomoxys and Thricops. Genus-level misidentifications were found only in Helina and Phaonia. Discrimination of examined material on the species level within Hydrotaea (318 specimens representing eight species) and Muscina (163 specimens representing four species) showed lower, yet still high average identification success, 97.2 and 98.8%, respectively. Our results revealed relatively high success in both genus and species identification of Muscidae of medico-legal importance. Semiautomated identification by means of wing measurements can be used by non-experts and does not require sophisticated equipment. This method will facilitate the identification of forensically relevant muscids in comparison to more difficult and more time-consuming identification approaches based on taxonomic keys or DNA-based methods. However, for unambiguous identification of some taxa, we recommend complementary use of identification keys.

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.