Complete tribal sampling reveals basal split in Muscidae (Diptera), confirms saprophagy as ancestral feeding mode, and reveals an evolutionary correlation between instar numbers and carnivory

Identification and distribution of some medico-veterinary important pathogens in muscid flies in two geographical regions of Türkiye

Some dipteran flies play an important role in the transmission of pathogens such as viruses, bacteria, fungi, protozoan and metazoan parasites in humans and other animals. Despite this importance, knowledge of the prevalence and molecular characteristics of some pathogens in flies is limited, and no data are available for Türkiye. In this study, we investigated the possible vector role of muscid fly species for the transmission of Enterocytozoon bieneusi Desportes (Chytridiopsida: Enterocytozoonidae), Encephalitozoon spp., Coxiella burnetii Derrick (Legionellales: Coxiellaceae) and Thelazia spp. using polymerase chain reaction (PCR) and sequence analysis. The flies were trapped in different animal-related places and surroundings from two different geographical regions of Türkiye including Central Anatolia and Middle Black Sea. According to the morphological keys, 850 (85%), 141 (14.1%) and 6 (0.6%) of the total of 1000 fly specimens identified as Musca domestica Linnaeus (Diptera: Muscidae), Stomoxys calcitrans Linnaeus (Diptera: Muscidae) and Musca autumnalis De Geer (Diptera: Muscidae), respectively. The other species including Haematobia irritans Linnaeus (Diptera: Muscidae), Muscina stabulans Fallén (Diptera: Muscidae) and Hydrotaea ignava Harris (Diptera: Muscidae) were each represented by a single specimen. Screening of the pathogens identified E. bieneusi only in M. domestica with a prevalence of 2.4%. Sequence analyses identified three known genotypes, Type IV, BEB6 and BEB8, and one novel genotype named AEUEb of E. bieneusi in M. domestica. Coxiella burnetii was detected in M. domestica and S. calcitrans with prevalences of 2.9% and 2.8%, respectively. The one specimen of H. ignava was also positive for C. burnetii. Encephalitozoon spp. and Thelazia spp. were not found in the examined specimens. Our results contribute to the current knowledge on the vector potential of muscid flies and their possible role in the transmission dynamics of certain pathogens, especially in regions where diseases are prevalent and affect public and animal health.

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.

Strongwellsea selandia and Strongwellsea gefion (Entomophthorales: Entomophthoraceae), two new species infecting adult flies from genus Helina (Diptera: Muscidae)

Two new species from the genus Strongwellsea (Entomophthorales: Entomophthoraceae) that infect adult flies from the genus Helina (Muscidae) are described: Strongwellsea selandia Eilenberg & Humber infecting adult Helina evecta (Harris), and Strongwellsea gefion Eilenberg & Humber infecting adult Helina reversio (Harris). The descriptions are based on pathobiological, phenotypical and genotypical characters. The new species differ from other described members from the genus Strongwellsea by a) pathobiology as revealed by natural host species, b) morphology of primary conidia, c) color of resting spores, and d) genotypical clustering based on analysis of ITS2. The two new species have only been documented from North Zealand, Denmark.

Ampliación de la distribución conocida de coleópteros, dípteros e himenópteros sarcosaprófagos (Arthropoda: Insecta) con potencial interés forense en la península ibérica

Con el objetivo de ampliar la distribución conocida y el conocimiento ecológico de las especies sarcosaprófagas con potencial interés forense en la península ibérica, se recopilan 758 nuevos registros correspondientes a 105 especies de coleópteros, dípteros e himenópteros en 43 provincias españolas y 4 distritos portugueses. Se registran un total de 89 primeras citas provinciales y se aportan numerosas localidades inéditas que permiten ampliar el rango de distribución conocido de la entomofauna sarcosaprófaga ibérica. Entre los resultados más relevantes destaca la expansión territorial de los dípteros alóctonos Chrysomya megacephala (Fabricius, 1794) y Hermetia illucens (Linnaeus, 1758) en la península ibérica. Además, se documentan hábitos sarcosaprófagos por primera vez en el formícido Hypoponera eduardi (Forel, 1894). Finalmente, se discuten los resultados ecológicos obtenidos en relación a las comunidades sarcosaprófagas y su potencial interés en estudios forenses.

Antennal and palpal sensilla of three predatory Lispe species (Diptera: Muscidae): an ultrastructural investigation

Antennae and maxillary palps are the most important chemical reception organs of flies. So far, the morphology of antennae and maxillary palps of flies of most feeding habits have been well described, except for that of relatively rare aquatic predatory species. This study describes sensilla on antennae and maxillary palps of three aquatic predatory Lispe species: Lispe longicollis, L. orientalis and L. pygmaea. Types, distribution, and density of sensilla are characterised via light and scanning electron microscopy. One type of mechanoreceptors is found on antennal scape. Mechanoreceptors (two subtypes) and one single pedicellar button (in L. pygmaea) are located on antennal pedicel. Four types of sensilla are discovered on antennal postpedicel: trichoid sensilla, basiconic sensilla (three subtypes), coeloconic sensilla and clavate sensilla. A unique character of these Lispe species is that the coeloconic sensilla are distributed sparsely on antennal postpedicel. Mechanoreceptors and basiconic sensilla are observed on the surface of maxillary palps in all three species. We demonstrated clear sexual dimorphism of the maxillary palps in some of the Lispe species, unlike most other Muscidae species, are larger in males than females. This, along with their courtship dance behaviour, suggest their function as both chemical signal receiver and visual signal conveyer, which is among the few records of a chemical reception organ act as a signal conveyer in insects.

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.

Strongwellsea tigrinae and Strongwellsea acerosa (Entomophthorales: Entomophthoraceae), two new species infecting dipteran hosts from the genus Coenosia (Muscidae)

Two new species from the genus Strongwellsea (Entomophthorales: Entomophthoraceae) are described: Strongwellsea tigrinae from adult Coenosia tigrina (Diptera: Muscidae) and Strongwellsea acerosa from adult Coenosia testacea. The descriptions are based on pathobiological, phenotypical and genotypical characters. Further, the circumscription of the genus Strongwellsea is emended. Our findings suggest that Strongwellsea harbors a high number of species, of which now only five have been described.

Wing morphometrics for the identification of Nearctic and Palaearctic Piophilidae (Diptera) of forensic relevance

The Piophilidae (Diptera) are a family comprising about 80 species, several of them of high economic and forensic relevance. An unequivocal species identification is crucial for designing effective control measures or to provide reliable estimations of the minimum post mortem interval. However, the identification may sometimes not be possible, either because the diagnostic morphological characters are not easily observable or very fragile, or because of a poor DNA quality and/or unavailability of reference molecular signatures. In the recent years, the use of wing morphometric techniques has emerged as a powerful tool for the identification of different families of forensically important Diptera. The present study applies, for the first time, this technique to the identification of 11 Piophilidae species of forensic relevance in the Nearctic and Palaearctic regions, as well as to the discrimination of sexes, distinct geographical populations and, in the case of the dimorphic species Prochyliza nigrimana (Meigen), seasonal morphs. Wing shape variation was analysed using 14 landmarks located at wing vein junctions and a cross-variation analysis was used to test the reliability of identifications. The present results demonstrate that wing shape can be used to identify most species with relatively high success, whereas cross-validation analyses indicated that discrimination between sexes, populations or morphs was less effective, even if significant differences were observed in every comparison. We conclude that wing morphometrics can be a powerful identification tool that might be used in combination with other methods in order to achieve accurate and reliable species identifications-independently of the sex, geographic origin or colour variation of the samples-even with those piophilid species that have been object of frequent misidentifications.

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.

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.

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.

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.

Application of DNA barcoding for identifying forensically relevant Diptera from northern Thailand

In recent decades, forensic entomology has become a useful tool in criminal investigations all over the world. Species-specific identification of flies plays an important role in this field and is obligatory for accurate calculation of the post-mortem interval. However, not all important colonizers of a corpse can be identified by common morphological keys. Due to similar morphology and the lack of keys for some taxa, especially for immature stages, DNA barcoding has become more popular during the last recent years. This development is particularly important for countries like Thailand, in which forensic entomology is a newly developing research area and which faces several challenges such as a high biodiversity of fly species. The most commonly used barcoding region in forensic entomology, the mitochondrial cytochrome oxidase subunit 1 (coI) gene, as well as a 1000-bp-long region of the 28S nuclear rRNA gene, was used to analyze and establish the molecular barcodes of 13 different species of flies of forensic relevance in northern Thailand.

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.

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

House flies are one of the best known groups of flies and comprise about 5000 species worldwide. Despite over a century of intensive taxonomic research on these flies, classification of the Muscidae is still poorly resolved. Here we brought together the most diverse molecular dataset ever examined for the Muscidae, with 142 species in 67 genera representing all tribes and all biogeographic regions. Four protein coding genes were analyzed: mitochondrial CO1 and nuclear AATS, CAD (region 4) and EF1-α. Maximum likelihood and Bayesian approaches were used to analyze five different partitioning schemes for the alignment. We also used Bayes factors to test monophyly of the traditionally accepted tribes and subfamilies. Most subfamilial taxa were not recovered in our analyses, and accordingly monophyly was rejected by Bayes factor tests. Our analysis consistently found three main clades of Muscidae and so we propose a new classification with only three subfamilies without tribes. Additionally, we provide the first timeframe for the diversification of all major lineages of house flies and examine contemporary biogeographic hypotheses in light of this timeframe. We conclude that the muscid radiation began in the Paleocene to Eocene and is congruent with the final stages of the breakup of Gondwana, which resulted in the complete separation of Antarctica, Australia, and South America. With this newly proposed classification and better understanding of the timing of evolutionary events, we provide new perspectives for integrating morphological and ecological evolutionary understanding of house flies, their taxonomy, phylogeny, and biogeography.