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

Chromosome-level genome assembly of Scathophaga stercoraria provides new insights into the evolutionary adaptations of dung flies

The yellow dung fly Scathophaga stercoraria is a widely distributed species in high-altitude regions of the Northern Hemisphere. It plays important roles as a decomposer, predator, and pollinator in the ecosystem. As a staple model organism, S. stercoraria serves as a standard test species for assessing the toxicity of drug residues in livestock dung and has been the focus of numerous studies. The genetic mechanisms underlying the ecological adaptability of S. stercoraria remain poorly understood. To fill the gap, we first assembled a high-quality chromosome-level genome of S. stercoraria, resulting in a final assembly size of 549.64 Mb, with a contig N50 of 4.06 Mb, and 92.53 % of the sequence anchored to six chromosomes. Gene family analysis revealed an expansion of Toll (Toll1), GNBP3, Cyp303a1, Cyp4d14, Cyp6g1, OR67d, and yolk protein genes in the S. stercoraria genome. Transcriptome analysis indicated that most genes in the trypsin and carboxypeptidase gene families are predominantly expressed during the larval stage, whereas the α-Amylase gene family is mainly expressed during the adult stage. Additionally, PGRP-SC is highly expressed during the larval stage, OBPs are primarily expressed during the adult stage, and yolk protein genes exhibit female-biased expression. Our study not only provides a new resource for the dung flies genomic pool, but also identifies the expression patterns of key ecologically adaptative genes and gene families at the developmental stages, which provides new insights into the ecological adaptive evolution of dung flies.

Phylogenomics resolves long-standing questions about the affinities of an endangered Corsican endemic fly

Recent studies on oestroidean Diptera (Brachycera) are providing a comprehensive and nuanced understanding of the evolutionary history of this remarkably diverse clade of holometabolous insects. The Oestroidea, which includes formidable pests such as various blowflies, botflies, and flesh flies that infest livestock, pets and humans, are mostly composed of beneficial species that act as scavengers or parasitoids on various pest insects. In our research, we used genomic methods to elucidate the phylogenetic position of Nesodexia corsicana Villeneuve, 1911 (Diptera: Calliphoridae), a mysterious oestroid species endemic to Corsica and characterized by distinctive morphological features that have puzzled taxonomists for years. Contrary to initial hypotheses, our results place Nesodexia Villeneuve, 1911 within the Calliphoridae subfamily Rhinophorinae, a small lineage of terrestrial isopod parasitoids. Through detailed morphological analysis of adults of both sexes and eggs, we uncovered significant insights consistent with our phylogenomic reconstruction. The unique morphological features of the species, coupled with its restricted and fragmented habitat, highlight its potential conservation importance. We delineated the area of occupancy for N. corsicana and assessed its "threatened" category using specific IUCN Red List criteria. In addition, we mapped the available habitat within its range and determined potential key biodiversity areas (KBA) triggered by N. corsicana. New potential KBAs are only partially covered by the Corsican Regional Park. Finally, we mapped the distribution of habitats on the island to assess the potential distribution of the species beyond its currently known geographic range.

Phylogenomic analysis of Tachinidae (Diptera: Calyptratae: Oestroidea): a transcriptomic approach to understanding the subfamily relationships

Tachinidae is the second most species-rich family of Diptera. It comprises four subfamilies, and all of its members have parasitoid habits. We present the first phylogenomic analysis of Tachinidae using transcriptomic data, based on 30 species. We constructed four datasets: three using translated data at the amino acid level (100% coverage, with 106 single-copy protein-coding genes; 75% coverage, with 1359 genes; and 50% coverage, with 1942 genes). The trees were estimated by analysing four matrices using maximum likelihood and maximum parsimony inferences, and only minor differences were found among them. Overall, our topologies are well resolved, with high node support. Polleniidae is corroborated as a sister group to Tachinidae. Within Tachinidae, our results confirm the hypothesis (Phasiinae + Dexiinae) + (Tachininae + Exoristinae). Phasiinae, Dexiinae and Exoristinae are recovered as monophyletic, and Tachininae as polyphyletic. Once again, the tribe Myiophasiini (Tachininae) composes a fifth lineage, clade sister to all the remaining Tachinidae. The Neotropical tribe Iceliini, formerly in Tachininae, is recovered within Exoristinae, sister to Winthemiini. In general, our results are congruent with recent phylogenetic studies that include tachinids, with the important confirmation of the subfamilial relationships and the existence of a fifth lineage of Tachinidae.

Phylogenetic relationships of the woodlouse flies (Diptera: Rhinophorinae) and the cluster flies (Diptera: Polleniidae)

Phylogenetic relationships within the oestroid subclades Rhinophorinae (Calliphoridae) and Polleniidae were reconstructed for the first time, applying a Sanger sequencing approach using the two protein-coding nuclear markers CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase; 1794 bp) and MCS (molybdenum cofactor sulfurase; 2078 bp). Three genera of Polleniidae and nineteen genera of Rhinophorinae were analyzed together with a selection of taxa representing the major lineages of Oestroidea (non-rhinophorine Calliphoridae, Oestridae, Sarcophagidae, Tachinidae). The selected markers provide good resolution and moderate to strong support of the distal branches, but weak support for several deeper nodes. Polleniidae (cluster flies) emerge as monophyletic and their sister-group relationship to Tachinidae is confirmed. Morinia Robineau-Desvoidy as currently circumscribed emerges as paraphyletic with regard to Melanodexia Williston, and Pollenia Robineau-Desvoidy is the sister taxon of the Morinia-Melanodexia clade. We propose a classification with two subfamilies, Moriniinae Townsend (including Morinia, Melanodexia, and Alvamaja Rognes), and Polleniinae Brauer & Bergenstamm (including Pollenia, Dexopollenia Townsend, and Xanthotryxus Aldrich). Anthracomyza Malloch and Nesodexia Villeneuve are considered as Oestroidea incertae sedis pending further study. Rhinophorinae (woodlouse flies) emerge as monophyletic and sister to a clade composed of (Ameniinae + (Ameniinae + Phumosiinae)), and a tribal classification is proposed with the subfamily divided into Rhinophorini Robineau-Desvoidy, 1863 and Phytonini Robineau-Desvoidy, 1863 (the Stevenia-group and the Phyto-group of authors, respectively). Oxytachina Brauer & Bergenstamm, 1891, stat. rev. is resurrected to contain nine Afrotropical rhinophorine species currently assigned to genus Rhinomorinia Brauer & Bergenstamm, 1891: Oxytachina approximata (Crosskey, 1977) comb. nov., O. atra (Bischof, 1904) comb. nov., O. bisetosa (Crosskey, 1977) comb. nov., O. capensis (Brauer & Bergenstamm, 1893) comb. nov., O. scutellata (Crosskey, 1977) comb. nov., O. setitibia (Crosskey, 1977) comb. nov., O. verticalis (Crosskey, 1977) comb. nov., O. vittata Brauer & Bergenstamm, 1891, and O. xanthocephala (Bezzi, 1908) comb. nov.

First cladistic analysis of Toxotarsinae (Diptera: Calliphoridae), with insights on the evolution of the group and on the transformation series of some historically controversial characters

Toxotarsinae is a subfamily of Calliphoridae (Diptera: Calyptratae: Oestroidea) with 11 species currently distributed in three genera: Neta Shannon, 1926, Sarconesia Bigot, 1857, and Toxotarsus Macquart, 1851. All known species are endemic to South America, mostly restricted to areas with cooler temperatures-like high elevation areas of the Andean Cordillera-and lowlands and coastal regions in the subtropical and temperate parts of the continent. The classification of the subfamily has been somewhat controversial, with eleven, mostly monotypic nominal genera established to accommodate its species, mostly due to distinct interpretations of certain controversial characters by different authors. To provide a sound basis for a generic classification, we performed the first study aimed to understand the transformation series of those controversial characters and character states under a phylogenetic framework. Our maximum parsimony analyses, under both equal and implied weighting of characters and including all currently known species in the subfamily, retrieved two main clades of Toxotarsinae: the roraima group, composed of Sarconesia roraima (Townsend, 1935), Neta chilensis (Walker, 1836), and S. magellanica (Le Guillou, 1842), and the splendida group, composed of the remaining species of the subfamily. The position of S. magellanica varied, but the species was mostly recovered within the roraima group except in the analyses under implied weighting with k values between 1 and 6. Our results, which include an explicit interpretation of the transformation series associated with some characters and character states commonly used in Toxotarsinae systematics, suggest that both Sarconesia and Neta, along with other genera proposed in the past for species of the subfamily such as Sarconesiomima Lopes & Albuquerque, 1955, Chlorobrachycoma Townsend, 1918, Sarconesiopsis Townsend, 1918, and Roraimomusca Townsend, 1935, previously suggested to be synonyms of Sarconesia, do not properly reflect the evolution of lineages in the subfamily and should not be considered as valid nominal genera. Toxotarsus was the only genus consistently recovered as monophyletic and, based on the phylogenetic relationships recovered herein, we suggest including all known Toxotarsinae within this genus, with the roraima and splendida clades treated as species-groups. Finally, we discuss the characters commonly used to delimit the taxa subordinated to Toxotarsinae, such as the length of the first flagellomere, the position of the rays of the arista relative to the pedicel, the extension of the plumosity of the arista, and the number of postsutural acrostichal setae.

South African nose flies (Diptera, Calliphoridae, Rhiniinae): taxonomy, diversity, distribution and biology

Background

Rhiniinae (Diptera, Calliphoridae) is a taxon of nearly 400 known species, many of them termitophilous. Approximatelly 160 valid species in 16 genera are Afrotropical, with over 60 of them occurring in South Africa. The taxonomy of this group is outdated, as most studies of the South African taxa were conducted 40 to 70 years ago (mostly by Salvador Peris and Fritz Zumpt). Published information on their biology and ecology is also scarce.

New information

An annotated checklist of 73 species of Rhiniinae for South Africa was developed, based on the holdings of sixteen entomological collections in Africa, Europe and North America. Over 3,700 specimens were examined, revealing nine new species records for South Africa (Cosminaundulata Malloch, 1926, Isomyiacuthbertsoni (Curran, 1938), Rhyncomyabotswana Zumpt, 1974, R.tristis Séguy, 1933, Stomorhinaapta Curran, 1931, S.malobana (Lehrer, 2007), Thoraciteskirkspriggsi Kurahashi, 2001, Th.sarcophagoides Kurahashi, 2001 and Trichoberialanata (Villeneuve, 1920)). We propose one new combination Eurhyncomyiametzi (Zumpt, 1981) comb. nov. (= Rhyncomyametzi Zumpt, 1981)). Additionally, evidence is presented to remove Rhyncomyaviduella Villeneuve, 1927 stat. rev. from synonymy with Rhyncomyacassotis (Walker, 1849). Relevant novel biological and seasonality information, historical occurrence maps and high-definition photographs for each species are compiled.

Synanthropic Flies-A Review Including How They Obtain Nutrients, along with Pathogens, Store Them in the Crop and Mechanisms of Transmission

An attempt has been made to provide a broad review of synanthropic flies and, not just a survey of their involvement in human pathogen transmission. It also emphasizes that the crop organ of calliphorids, sarcophagids, and muscids was an evolutionary development and has served and assisted non-blood feeding flies in obtaining food, as well as pathogens, prior to the origin of humans. Insects are believed to be present on earth about 400 million years ago (MYA). Thus, prior to the origin of primates, there was adequate time for these flies to become associated with various animals and to serve as important transmitters of pathogens associated with them prior to the advent of early hominids and modern humans. Through the process of fly crop regurgitation, numerous pathogens are still readily being made available to primates and other animals. Several studies using invertebrate-derived DNA = iDNA meta-techniques have been able to identify, not only the source the fly had fed on, but also if it had fed on their feces or the animal's body fluids. Since these flies are known to feed on both vertebrate fluids (i.e., from wounds, saliva, mucus, or tears), as well as those of other animals, and their feces, identification of the reservoir host, amplification hosts, and associated pathogens is essential in identifying emerging infectious diseases. New molecular tools, along with a focus on the crop, and what is in it, should provide a better understanding and development of whether these flies are involved in emerging infectious diseases. If so, epidemiological models in the future might be better at predicting future epidemics or pandemics.

Characterization and Comparative Analysis of Mitochondrial Genomes Among the Calliphoridae (Insecta: Diptera: Oestroidea) and Phylogenetic Implications

The Calliphoridae (blowflies) are significant for forensic science, veterinary management, medical science, and economic issues. However, the phylogenetic relationships within this family are poorly understood and controversial, and the status of the Calliphoridae has been a crucial problem for understanding the evolutionary relationships of the Oestroidea these years. In the present study, seven mitochondrial genomes (mitogenomes), including six calliphorid species and one Polleniidae species, were sequenced and annotated. Then a comparative mitochondrial genomic analysis among the Calliphoridae is presented. Additionally, the phylogenetic relationship of the Calliphoridae within the larger context of the other Oestroidea was reconstructed based on the mitogenomic datasets using maximum likelihood (ML) and Bayesian methods (BI). The results suggest that the gene arrangement, codon usage, and base composition are conserved within the calliphorid species. The phylogenetic analysis based on the mitogenomic dataset recovered the Calliphoridae as monophyletic and inferred the following topology within Oestroidea: (Oestridae (Sarcophagidae (Calliphoridae + (Polleniidae + (Mesembrinellidae + Tachinidae))))). Although the number of exemplar species is limited, further studies are required. Within the Calliphoridae, the Chrysomyinae were recovered as sister taxon to Luciliinae + Calliphorinae. Our analyses indicated that mitogenomic data have the potential for illuminating the phylogenetic relationships in the Oestroidea as well as for the classification of the Calliphoridae.

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.

Annotated catalogue of the Tachinidae (Insecta, Diptera) of Chile

The Tachinidae (Diptera) of Chile are catalogued and information is given on distributions, name-bearing types, synonyms, nomenclatural issues, and pertinent literature. The history of tachinid collectors in Chile and authors who have contributed to the systematic knowledge of Chilean tachinids is extensively reviewed. The classification has been updated and 122 genera and 264 species are recognised in Chile. There is a significant amount of endemism with 28 genera and 100 species known only from Chile. There are also 113 species with distributions shared only between Chile and Argentina, particularly in the southern portions of these countries comprising Patagonia. The catalogue is based on examination of the original descriptions of all nominal species and all other references known to us containing relevant taxonomic and distributional information, for a total of approximately 450 references. Many of the name-bearing types and other Chilean specimens housed in collections were examined. Taxa are arranged hierarchically and alphabetically under the categories of subfamily, tribe, genus, subgenus (where recognised), and species. Nomenclatural information is provided for genus-group and species-group names, including lists of synonyms (mostly restricted to Neotropical taxa) and name-bearing type data. Species distributions are recorded by country within the New World and by larger geographical divisions in the Old World. Additional information is given in the form of notes and references under valid names at the level of tribe, genus, and species. Two genera are newly recorded from Chile: Chaetoepalpus Vimmer & Soukup, 1940 (Tachinini) (also newly recorded from Argentina) and Patelloa Townsend, 1916 (Goniini). Four species are newly recorded from Chile or other countries: Lyphaornata Aldrich, 1934 (Chile); Chaetoepalpuscoquilleti Vimmer & Soukup, 1940 (Argentina and Chile); Phytomypteraevanescens (Cortés, 1967) (Argentina); and Xanthobasisunicolor Aldrich, 1934 (Chile). Eight species previously recorded from Chile are deemed to have been misidentified or misrecorded from Chile (known distributions in parentheses): Archytasincertus (Macquart, 1851) (Argentina, Brazil, Paraguay, Uruguay); Archytasseminiger (Wiedemann, 1830) (Brazil, Colombia); Goniacrassicornis (Fabricius, 1794) (Brazil, Peru, Venezuela, Middle America, West Indies, Nearctic); Lespesiaandina (Bigot, 1888) (Cuba); Lespesiaarchippivora (Riley, 1871) (widespread Nearctic and most of Neotropical); Neoethillaignobilis (van der Wulp, 1890) (Mexico, United States); Siphona (Siphona) geniculata (De Geer, 1776) (Palaearctic, Nearctic [introduced]); and Winthemiaquadripustulata (Fabricius, 1794) (Palaearctic, Nearctic, Oriental]. As First Reviser we fix Paratheresiarufiventris Townsend, 1929 as the senior homonym and Sarcoprosenarufiventris Townsend, 1929 as the junior homonym when the two are placed together in Billaea Robineau-Desvoidy, 1830; and we fix Mayophoriniaangusta Townsend, 1927 as the senior homonym and Metarrhinomyiaangusta Townsend, 1927 as the junior homonym when the two are placed together in Myiopharus Brauer & Bergenstamm, 1889. New replacement names are proposed for eight preoccupied names of Neotropical species (country of type locality in parentheses): Billaearufescens O'Hara & Wood for Sarcoprosenarufiventris Townsend, 1929, preoccupied in the genus Billaea Robineau-Desvoidy, 1830 by Paratheresiarufiventris Townsend, 1929 (Peru), nom. nov.; Billaeatriquetrus O'Hara & Wood for Sarcoprosenatriangulifera Townsend, 1927, preoccupied in the genus Billaea Robineau-Desvoidy, 1830 by Dexiatriangulifera Zetterstedt, 1844 (Peru), nom. nov.; Eucelatorianudioculata O'Hara & Wood for Eucelatorioideanigripalpis Thompson, 1968, preoccupied in the genus Eucelatoria Townsend, 1909 by Chetolyganigripalpis Bigot, 1889 (Trinidad), nom. nov.; Eucelatoriaoblonga O'Hara & Wood for Urodexodeselongatum Cortés & Campos, 1974, preoccupied in the genus Eucelatoria Townsend, 1909 by Exoristaelongata van der Wulp, 1890 (Chile), nom. nov.; Lespesiathompsoni O'Hara & Wood for Sturmiopsoideaobscura Thompson, 1966, preoccupied in the genus Lespesia Robineau-Desvoidy, 1863 by Eurigasterobscurus Bigot, 1857 (Cuba), nom. nov.; Myiopharuscharapensis O'Hara & Wood for Metarrhinomyiaangusta Townsend, 1927, preoccupied in the genus Myiopharus Brauer & Bergenstamm, 1889 by Mayophoriniaangusta Townsend, 1927 (Peru), nom. nov.; Myiopharusincognitus O'Hara & Wood for Stenochaetaclaripalpis Thompson, 1968, preoccupied in the genus Myiopharus Brauer & Bergenstamm, 1889 by Neoxynopsoideaclaripalpis Thompson, 1968 (Trinidad), nom. nov.; and Myiopharusrufopalpus O'Hara & Wood for Paralispepalpalis Townsend, 1929, preoccupied in the genus Myiopharus Brauer & Bergenstamm, 1889 by Myioxynopspalpalis Townsend, 1927 (Peru), nom. nov. New type species fixations are made under the provisions of Article 70.3.2 of the ICZNCode for three genus-group names: Parafabricia Brauer & Bergenstamm, 1894 (synonym of Archytas Jaennicke, 1867), type species newly fixed as Parafabriciaperplexa Townsend, 1931; Tachinodes Brauer & Bergenstamm, 1889 (synonym of Archytas Jaennicke, 1867), type species newly fixed as Juriniametallica Robineau-Desvoidy, 1830; and Willistonia Brauer & Bergenstamm, 1889 (synonym of Belvosia Robineau-Desvoidy, 1830), type species newly fixed as Willistoniaaldrichi Townsend, 1931. Lectotypes are designated for the following four nominal species, all described or possibly described from Chile: Echinomyiapygmaea Macquart, 1851 (a valid name in the genus Peleteria Robineau-Desvoidy, 1830); Goniachilensis Macquart, 1844 (a junior synonym of Goniapallens Wiedemann, 1830); Masiceraauriceps Macquart, 1844 (a valid name in the genus Lespesia Robineau-Desvoidy, 1863); and Prosopochoetanitidiventris Macquart, 1851 (a valid name in the genus Prosopochaeta Macquart, 1851). The following 27 new or revived combinations are proposed (distributions in parentheses): Blepharipezaandina Bigot, 1888 is moved to Lespesia Robineau-Desvoidy, 1863 as L.andina, nomen dubium (Cuba), comb. nov.; Camposodesevanescens Cortés, 1967 is moved to Phytomyptera Rondani, 1845 as P.evanescens (Argentina, Chile), comb. nov.; Ectophasiopsisypiranga Dios & Nihei, 2017 is moved to Trichopoda Berthold, 1827 and assigned to subgenus Galactomyia Townsend, 1908 as T. (G.) ypiranga (Argentina, Brazil), comb. nov.; Embiomyiaaustralis Aldrich, 1934 is moved to Steleoneura Stein, 1924 as S.australis (Argentina, Chile), comb. nov.; Eurigastermodestus Bigot, 1857 is moved to Lespesia as L.modesta (Cuba), comb. nov.; Eurigasterobscurus Bigot, 1857 is moved to Lespesia as L.obscura (Cuba), comb. nov.; Macropatelloatanumeana Townsend, 1931 is moved to Patelloa Townsend, 1916 as P.tanumeana (Argentina, Chile), comb. nov.; Masicerainsignis van der Wulp, 1882 is moved to Drino Robineau-Desvoidy, 1863 as D.insignis (Argentina, Chile), comb. nov.; Parasetigenahichinsi Cortés, 1967 is moved to Chetogena Rondani, 1856 as C.hichinsi (Chile), comb. nov.; Parasetigenaporteri Brèthes, 1920 and junior synonym Stomatotachinasplendida Townsend, 1931 are moved to Chetogena as C.porteri (Chile), both comb. nov.; Phoroceracalyptrata Aldrich, 1934 is moved to Admontia Brauer & Bergenstamm, 1889 as A.calyptrata (Argentina, Chile), comb. nov.; Poliopsauratus Campos, 1953 is moved to Admontia Brauer & Bergenstamm, 1889 as A.aurata (Chile), comb. nov.; Poliopsstriatus Aldrich, 1934 is moved to Admontia as A.striata (Argentina, Chile), comb. nov.; Ruiziellafrontosa Cortés, 1951 is moved to Chaetoepalpus Vimmer & Soukup, 1940 and placed in synonymy with C.coquilleti Vimmer & Soukup, 1940 (Argentina, Chile, Peru), comb. nov.; Ruiziellaluctuosa Cortés, 1951 is moved to Chaetoepalpus as C.luctuosus (Argentina, Chile), comb. nov.; Sarcoprosenaluteola Cortés & Campos, 1974 is moved to Billaea Robineau-Desvoidy, 1830 as B.luteola (Chile), comb. nov.; Sarcoprosenarufiventris Townsend, 1929 is moved to Billaea where it is a junior secondary homonym and is renamed B.rufescens O'Hara & Wood (Peru), comb. nov.; Sarcoprosenatriangulifera Townsend, 1927 is moved to Billaea where it is a junior secondary homonym and is renamed B.triquetrus O'Hara & Wood (Peru),comb. nov.; Saundersiaaurea Giglio-Tos, 1893 is moved to "Unplaced species of Tachinini" (Mexico), comb. nov.; Schistostephanaaurifrons Townsend, 1919 is moved to Billaea as B.aurifrons (Peru), comb. nov.; Siphoactiacharapensis Townsend, 1927 is moved to Clausicella Rondani, 1856 as C.charapensis (Peru), comb. nov.; Siphoactiaperegrina Cortés & Campos, 1971 is moved to Clausicella as C. peregrina (Chile), comb. nov.; Sturmiafestiva Cortés, 1944 is moved to Drino as D.festiva (Argentina, Chile), comb. nov.; Sturmiopsoideaobscura Thompson, 1966 is moved to Lespesia Robineau-Desvoidy, 1863, where it is a junior secondary homonym and is renamed L.thompsoni O'Hara & Wood (Trinidad), comb. nov.; Trichopodaarcuata Bigot, 1876 is returned to Trichopoda from Ectophasiopsis Townsend, 1915 and assigned to subgenus Galactomyia (Argentina, Chile), comb. revived; and Trichopodagradata Wiedemann, 1830 is returned to Trichopoda from Ectophasiopsis and assigned to subgenus Galactomyia (Argentina, Brazil, Uruguay), comb. revived. New or revived generic and specific synonymies are proposed for the following 14 names: Camposodes Cortés, 1967 with Phytomyptera Rondani, 1845, syn. nov.; Ectophasiopsis Townsend, 1915 with Trichopoda Berthold, 1827, subgenus Galactomyia Townsend, 1908, syn. nov.; Embiomyia Aldrich, 1934 with Steleoneura Stein, 1924, syn. nov.; Fabriciaandicola Bigot, 1888 with Peleteriarobusta (Wiedemann, 1830), syn. revived; Macropatelloa Townsend, 1931 with Patelloa Townsend, 1916, syn. nov.; Peleteriainca Curran, 1925 with Peleteriarobusta (Wiedemann, 1830), syn. revived; Poliops Aldrich, 1934 with Admontia Brauer & Bergenstamm, 1889, syn. nov.; Ruiziella Cortés, 1951 with Chaetoepalpus Vimmer & Soukup, 1940, syn. nov.; Ruiziellafrontosa Cortés, 1951 with Chaetoepalpuscoquilleti Vimmer & Soukup, 1940, syn. nov.; Sarcoprosena Townsend, 1927 with Billaea Robineau-Desvoidy, 1830, syn. nov.; Schistostephana Townsend, 1919 with Billaea, syn. nov.; Siphoactia Townsend, 1927 with Clausicella Rondani, 1856, syn. nov.; Stomatotachina Townsend, 1931 with Chetogena Rondani, 1856, syn. nov.; and Sturmiopsoidea Thompson, 1966 with Lespesia Robineau-Desvoidy, 1863, syn. nov.

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.

Museomics and phylogenomics with protein-encoding ultraconserved elements illuminate the evolution of life history and phallic morphology of flesh flies (Diptera: Sarcophagidae)

BACKGROUND

The common name of the Flesh flies (Sarcophagidae) usually relates them with organisms feeding on decomposing organic matter, although the biology of one of the largest radiations among insects also includes predation, coprophagy, and even kleptoparasitism. The question of whether the ancestor of all sarcophagids was a predator or a decomposer, or in association to which host have sarcophagids evolved, has thus always piqued the curiosity of flesh fly specialists. Such curiosity has often been hindered by both the impossibility of having a well-supported phylogeny of Sarcophagidae and its sister group to trace live habits and the scarcity of information on the biology of the group. Using a phylogenomic dataset of protein-encoding ultraconserved elements from representatives of all three subfamilies of Sarcophagidae as ingroup and a large Calyptratae outgroup, a robust phylogenetic framework and timescale are generated to understand flesh fly systematics and the evolution of their life histories.

RESULTS

The evolutionary history for Sarcophagidae reconstructed here differs considerably from previous hypotheses. Within subfamily Sarcophaginae, a group of predatory flies, including genera Lepidodexia and Boettcheria, emerged as sister-group to the rest of Sarcophaginae. The genera Oxysarcodexia, Ravinia, and Tricharaea, long considered archaic and early-branching coprophagous and sarcosaprophagous lineages, were found nested well within the Sarcophaginae as sister-group to the sarcosaprophagous Microcerella. Predation on invertebrates is suggested as the ancestral and dominant strategy throughout the early evolution of flesh flies. Several transitions from predation to sarcosaprophagy and coprophagy occur across the sarcophagid phylogenetic tree, in contrast with almost no transitions from sarcosaprophagy or coprophagy to predatory habits. Regarding the morphological evolution of flesh flies, there might be a concerted evolution of male genitalia traits, such as the phallotrema position and the juxta, or the vesica and the folding of the phallotrema. One diversification rate shift was inferred in the evolution of sarcophagids, which is related to the origin of genus Sarcophaga.

CONCLUSIONS

This study has a significant impact on understanding sarcophagid evolution and highlights the importance of having a robust phylogenetic framework to reconstruct the ancestral character state of biological and morphological characters. I discuss the evolution of life histories of the family in relation to their hosts or substrates and outline how sarcosaprophagy, coprophagy, and kleptoparasitism behavior on various hosts may have evolved from predation on invertebrates. This study provides a phylogenetic framework for further physiological and comparative genomic work between predatory, sarcosaprophagous, coprophagous, and kleptoparasitic lineages, which could also have significant implications for the evolution of diverse life histories in other Diptera.

Evolutionary profile of the family Calliphoridae, with notes on the origin of myiasis

The family Calliphoridae is a group of heterogenous calyptrate flies with a worldwide distribution including species of ecological, veterinary, medical, and forensic importance. Notorious for their parasitic habits, the larvae of many blowflies are characterised - like some other dipteran larvae - by their ability to develop in animal flesh. When parasitism affects a living host, it is termed "myiasis". This has led the Calliphoridae to be considered as a pivotal family in its relationship with a man. Nevertheless, even after more than 50 years of research, the phylogenetic relationships among calliphorid subfamilies together with the evolutionary origin of myiasis remain unclear. In order to elucidate these problems, we constructed three phylogenetic trees by using nucleotide sequence data from cytochrome oxidase subunit one (COI), representing a mitochondrial conservative gene, and nuclear 28S subunit of ribosomal RNA gene (28S rRNA) in order to interpret the evolutionary profile of myiasis in the family Calliphoridae. The sequenced data represented species associated with ectoparasitic life-styles, either saprophagy or facultative and obligate parasitism. A total number of 50 accessions were collected for 28S rRNA, 56 for COI, and 38 for combined sequences phylogeny. Molecular Evolutionary Genetics Analysis (MEGA) software was used to align 2197 nucleotide positions of 28S rRNA and 1500 nucleotide positions of COI with a gap opening penalties and gap extension penalties equalling 20 and 0.1 respectively. The results reveal the non-monophyly of the family Calliphoridae despite the stable monophyletic status of the Chrysomyinae, Luciliinae, and Auchmeromyiinae. Also, our findings recommend ranking the Toxotarsinae as a separate family. Furthermore, comparative analysis of the phylogenetic trees shows that the habit of obligatory myiasis originated independently more than five times. This strengthens our hypothesis that the origin of eating fresh meat is a case of convergent evolution that has taken place after speciation events millions of years ago. Finally, estimating the divergence dates between lineages from molecular sequences provides a better chance of understanding their evolutionary biology.

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.

Testing the Accuracy of Vegetation-Based Ecoregions for Predicting the Species Composition of Blow Flies (Diptera: Calliphoridae)

To properly define ecoregions, specific criteria such as geology, climate, or species composition (e.g., the presence of endemic species) must be taken into account to understand distribution patterns and resolve ecological biogeography questions. Since the studies on insects in Baja California are scarce, and no fine-scale ecoregions based on the region's entomofauna is available, this study was designed to test whether the ecoregions based on vegetation can be used for insects, such as Calliphoridae. Nine collecting sites distributed along five ecoregions were selected, between latitudes 29.6° and 32.0°N. In each site, three baited traps were used to collect blow flies from August 2017 to June 2019 during summer, winter, and spring. A total of 30,307 individuals of blow flies distributed in six genera and 13 species were collected. The most abundant species were Cochliomyia macellaria (Fabricius), Phormia regina (Meigen), and Chrysomya rufifacies (Macquart). The composition of the Calliphoridae community was different between the localities and three general groups have been distinguished, based on the species composition similarity (ANOSIM) results: Gulf-Desert, Mountains, and Pacific-Center. The vegetation-based ecoregions only reflect the blow fly species' distributions to a certain extent, meaning that care must be taken when undertaking ecological biogeographical studies using regionalization based on organisms other than the focal taxa because vegetation does not always reflect fauna species composition.

Three-dimensional characterization of first instar horse and rhinoceros stomach bot fly larvae (Oestridae: Gasterophilinae: Gasterophilus, Gyrostigma): novel morphology and evolutionary implications

Larval characters are of importance in systematic and evolutionary studies of Diptera but lag behind characters of adults due to difficulties in obtaining relevant information. Larvae of stomach bot flies are obligate parasites completing development exclusively in the alimentary tract of equids and rhinoceroses. They possess diversified morphological adaptations, providing remarkable examples to further our understanding of larval evolution. Herein, three-dimensional structures of first instar Gasterophilus pecorum and Gyrostigma rhinocerontis are compared using confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM). We suggest CLSM has a large potential for exploiting cryptic character systems of micro fly larvae, as spectral range and intensity of autofluorescence emitted by sclerotized structures and soft tissues are distinct, presenting a high-contrast mechanism for multistructural visualization with non-destructive sample preparation. Five new potential synapomorphies are proposed to corroborate the sister-group Gasterophilus and Gyrostigma. The upward curving mouth-hooks of first instar Gasterophilus and Gyrostigma are distinctive in Cyclorrhapha and possibly serve to facilitate the larval subcutaneous migration within the host. Three types of mouthhooks are recognized in first instar Oestridae, with the gently curved and gradually tapered type optimized as the ancestral state, from which the gasterophiline and hypodermatine types evolved independently.

A phylogenomic study of Steganinae fruit flies (Diptera: Drosophilidae): strong gene tree heterogeneity and evidence for monophyly

BACKGROUND

The Drosophilidae family is traditionally divided into two subfamilies: Drosophilinae and Steganinae. This division is based on morphological characters, and the two subfamilies have been treated as monophyletic in most of the literature, but some molecular phylogenies have suggested Steganinae to be paraphyletic. To test the paraphyletic-Steganinae hypothesis, here, we used genomic sequences of eight Drosophilidae (three Steganinae and five Drosophilinae) and two Ephydridae (outgroup) species and inferred the phylogeny for the group based on a dataset of 1,028 orthologous genes present in all species (> 1,000,000 bp). This dataset includes three genera that broke the monophyly of the subfamilies in previous works. To investigate possible biases introduced by small sample sizes and automatic gene annotation, we used the same methods to infer species trees from a set of 10 manually annotated genes that are commonly used in phylogenetics.

RESULTS

Most of the 1,028 gene trees depicted Steganinae as paraphyletic with distinct topologies, but the most common topology depicted it as monophyletic (43.7% of the gene trees). Despite the high levels of gene tree heterogeneity observed, species tree inference in ASTRAL, in PhyloNet, and with the concatenation approach strongly supported the monophyly of both subfamilies for the 1,028-gene dataset. However, when using the concatenation approach to infer a species tree from the smaller set of 10 genes, we recovered Steganinae as a paraphyletic group. The pattern of gene tree heterogeneity was asymmetrical and thus could not be explained solely by incomplete lineage sorting (ILS).

CONCLUSIONS

Steganinae was clearly a monophyletic group in the dataset that we analyzed. In addition to ILS, gene tree discordance was possibly the result of introgression, suggesting complex branching processes during the early evolution of Drosophilidae with short speciation intervals and gene flow. Our study highlights the importance of genomic data in elucidating contentious phylogenetic relationships and suggests that phylogenetic inference for drosophilids based on small molecular datasets should be performed cautiously. Finally, we suggest an approach for the correction and cleaning of BUSCO-derived genomic datasets that will be useful to other researchers planning to use this tool for phylogenomic studies.

The world Polleniidae (Diptera, Oestroidea): key to genera and checklist of species

A key to the world genera and a checklist of the world species for the family Polleniidae, including distributions, are provided. The following taxonomic and nomenclatural changes are proposed: Nitellia hermoniella Lehrer, 2007 = Pollenia mediterranea Grunin, 1966, syn. nov., Pollenia bentalia Lehrer, 2007 = Pollenia semicinerea Villeneuve, 1911, syn. nov., Dasypoda angustifrons Jacentkovský, 1941 = Pollenia tenuiforceps Séguy, 1928, syn. nov.; Anthracomyza Malloch, 1928, resurrected name (monotypic; type species Anthracomyia atratula Malloch) is considered a valid name and tentatively assigned to Polleniidae, giving Anthracomyza atratula (Malloch, 1927) as a resurrected combination; Morinia crassitarsis (Villeneuve, 1936), stat. rev. is considered a valid species, and Micronitellia Enderlein, 1936, stat. nov. is considered an available name.

The world woodlouse flies (Diptera, Rhinophoridae)

The world Rhinophoridae are catalogued, recognising 33 genera and 177 species. Nomenclatural information is provided for all genus-group and species-group names, including lists of synonyms and name-bearing type data. Species distributions are recorded by country. A key to the world genera is presented. Four new genera are erected to accommodate five new species, which do not fit within any of the current generic concepts in Rhinophoridae, according to the results of a morphology-based phylogenetic analysis: Marshallicona Cerretti & Pape with type species Marshallicona quitu Cerretti & Pape, gen. et sp. nov. (Ecuador); Maurhinophora Cerretti & Pape with type species Maurhinophora indoceanica Cerretti & Pape, gen. et sp. nov. (Mauritius); Neotarsina Cerretti & Pape with type species Neotarsina caraibica Cerretti & Pape, gen. et sp. nov. (Trinidad and Tobago) and Neotarsina andina Cerretti & Pape, sp. nov. (Peru); Kinabalumyia Cerretti & Pape with type species Kinabalumyia pinax Cerretti & Pape, gen. et sp. nov. (Malaysia, Sabah). The genus Aporeomyia Pape & Shima (type species Aporeomyia antennalis Pape & Shima), originally assigned to Tachinidae, is here reassigned to Rhinophoridae based on a reassessment of the homologies of the male terminalia. The following five species-group names, which were previously treated as junior synonyms or nomina dubia, are recognised as valid species names: Acompomintho caucasica (Villeneuve, 1908), stat. rev. [from nomen dubium to valid species]; Acompomintho sinensis (Villeneuve, 1936), stat. rev. [from nomen dubium to valid species]; Stevenia bertei (Rondani, 1865), stat. rev. [from nomen dubium to valid species]; Stevenia sardoa Villeneuve, 1920, stat. rev. [from junior synonym of Rhinophora deceptoria Loew, 1847 to valid species]; Stevenia subalbida (Villeneuve, 1911), stat. rev. [from junior synonym of Rhinophora deceptoria Loew, 1847 to valid species]. Reversal of precedence is invoked for the following case of subjective synonymy to promote stability in nomenclature: Rhinophora lepida (Meigen, 1824), nomen protectum, and Musca parcus Harris, 1780: 144, nomen oblitum. New generic and specific synonymies are proposed for the following two names: Mimodexia Rohdendorf, 1935, junior synonym of Tromodesia Rondani, 1856, syn. nov. and Ptilocheta tacchetti Rondani, 1865, junior synonym of Stevenia obscuripennis (Loew, 1847), syn. nov. The following new combinations are proposed: Acompomintho sinensis (Villeneuve, 1936), comb. nov. [transferred from Tricogena Robineau-Desvoidy, 1830]; Tromodesia guzari (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia intermedia (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia lindneriana (Rohdendorf, 1961), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia magnifica (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia obscurior (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia pallidissima (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935]; Tromodesia setiventris (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935] and Tromodesia shachrudi (Rohdendorf, 1935), comb. nov. [transferred from Mimodexia Rohdendorf, 1935].

Diptera of Canada

The Canadian Diptera fauna is updated. Numbers of species currently known from Canada, total Barcode Index Numbers (BINs), and estimated numbers of undescribed or unrecorded species are provided for each family. An overview of recent changes in the systematics and Canadian faunistics of major groups is provided as well as some general information on biology and life history. A total of 116 families and 9620 described species of Canadian Diptera are reported, representing more than a 36% increase in species numbers since the last comparable assessment by JF McAlpine et al. (1979). Almost 30,000 BINs have so far been obtained from flies in Canada. Estimates of additional number of species remaining to be documented in the country range from 5200 to 20,400.

Molecular phylogeny and evolution of world Tachinidae (Diptera)

We reconstructed phylogenetic relationships within the diverse parasitoid fly family Tachinidae using four nuclear loci (7800 bp) and including an exceptionally large sample of more than 500 taxa from around the world. The position of the earthworm-parasitizing Polleniinae (Calliphoridae s.l.) as sister to Tachinidae is strongly supported. Our analyses recovered each of the four tachinid subfamilies and most recognized tribes, with some important exceptions in the Dexiinae and Tachininae. Most notably, the tachinine tribes Macquartiini and Myiophasiini form a clade sister to all other Tachinidae, and a clade of Palpostomatini is reconstructed as sister to Dexiinae + Phasiinae. Although most nodes are well-supported, relationships within several lineages that appear to have undergone rapid episodes of diversification (basal Dexiinae and Tachininae, Blondeliini) were poorly resolved. Reconstructions of host use evolution are equivocal, but generally support the hypothesis that the ancestral host of tachinids was a beetle and that subsequent host shifts to caterpillars may coincide with accelerated diversification. Evolutionary reconstructions of reproductive strategy using alternative methods were incongruent, however it is most likely that ancestral tachinids possessed unincubated, thick shelled eggs from which incubated eggs evolved repeatedly, potentially expanding available host niches. These results provide a broad foundation for understanding the phylogeny and evolution of this important family of parasitoid insects. We hope it will serve as a framework to be used in concert with morphology and other sources of evidence to revise the higher taxonomic classification of Tachinidae and further explore their evolutionary history and diversification.