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.

Interactive Key for Third Instar Larvae of Neotropical Blow Flies (Insecta, Diptera, Calliphoridae): the Contribution of Computational Tools to Assist in Species Identification

Calliphoridae (Insecta, Diptera), popularly known as blow flies or carrion flies, as most are necrophagous comprises one of the most relevant families of insects on forensics. Currently, more than 1500 blow fly species are known, the majority of which can be found in the Old World. In the Neotropics, it is estimated that there are approximately 20 species of forensic importance. In view of the taxonomic impediment associated with the identification of immatures, in this study, we present an interactive identification key for third instar larvae of necrophagous Calliphoridae species. This key includes 12 Neotropical blow fly species of forensic importance, more than 70 pictures, schemes, and definitions glossary and is free to access.

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.

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.

Diversity of Necrophagous Flies (Diptera: Calliphoridae, Mesembrinellidae, and Sarcophagidae) in Anthropogenic and Preserved Environments of Five Different Phytophysiognomies in Northeastern Brazil

The present study investigated the potential association between the richness and abundance of species of the dipteran families Calliphoridae, Mesembrinellidae, and Sarcophagidae in anthropogenic and preserved environments of five phytophysiognomies (Cerrado, Amazon forest, Palm forest, marshland, and mangrove) that occur throughout the state of Maranhão, in northeastern Brazil. We sampled 90 sites (45 preserved and 45 anthropogenic areas) where we collected 26,036 specimens: 15,023 calliphorids (11 species), 231 mesembrinellids (one species), and 10,772 sarcophagids (52 species). Four environmental factors, canopy openness, temperature, leaf litter depth, and vegetation height, contributed most to the separation of preserved and anthropogenic sites in all five phytophysiognomies. Leaf litter depth was positively associated with the species richness of the calliphorids and mesembrinellids (C+ M group), while tree/shrub density, vegetation height, and temperature were associated negatively with the richness of the sarcophagids. Tree/shrub density and vegetation height were also associated negatively with abundance in both C+M and sarcophagid species. Overall, then, the structural characteristics of the environment affected the species richness and abundance, and deforestation may favor certain synanthropic species, leading to a decrease in the richness and abundance of the species that are adapted to preserved environments.

Prevalence Rate and Molecular Characteristics of Oestrus ovis L. (Diptera, Oestridae) in Sheep and Goats from Riyadh, Saudi Arabia

Heads of sheep (n = 600) and goats (n = 800) slaughtered at Al-Aziziah Abattoir in Riyadh, Saudi Arabia, were inspected for the presence of O. ovis larvae (L). Heads were split along the longitudinal axes, and larvae (L1, L2, and L3) were gathered. The infestation rate was significantly higher in goats (44.5%; 356/800) than that in sheep (22.3%; 134/600). Out of the 151 collected larvae from sheep, 0% were L1, 1.3% were L2, and 98.7% were L3. Out of the total of 468 larvae from goats, 0% were L1, 1.2% were L2, and 98.8% were L3. The infestation rate was significantly higher in males than that in females. Myiasis-causing larvae collected from Riyadh, Saudi Arabia, were authenticated as O. ovis, according to morphological characteristics. Polymerase chain reaction (PCR) amplification of a partial fragment (600 bp) of the mitochondrial cytochrome c oxidase subunit I (mtCOI) gene further confirmed the species. Phylogenetic analysis based on the partial mtCOI gene sequence demonstrated that 23 unique sequences showed high similarity based on nucleotide pairs of O. ovis accessions retrieved from GenBank.

Population Fluctuation, Influence of Abiotic Factors and the Height of Traps on the Abundance and Richness of Calliphoridae and Mesembrinellidae

Calliphoridae and Mesembrinellidae are relevant to environmental conservation, public health, and forensic entomology. Researches regarding the flight behavior and the influence of abiotic factors on these insects may assist the application of entomology sciences. This study aimed to analyze the population fluctuation of Calliphoridae and Mesembrinellidae, verifying the influence of environmental factors, trap height, and the anthropic effect in the Itaipu-Piratininga lagoon complex, Niterói (RJ). The collections were carried out monthly from September 2015 to August 2016, with fish bait (sardines) exposed for 48 h, totaling six traps, installed in three physiognomies (mangrove, ombrophilous forest, and restinga) at 1.5 and 2.5 m from the ground. Nine thousand seven hundred seventy-three individuals were captured, comprising two families, five genera and 11 species. Chrysomya megacephala (Fabricius, 1794) (Diptera: Calliphoridae) was the predominant species and Mesembrinella bellardiana (Aldrich, 1922) (Diptera: Mesembrinellidae) the least representative, indicating the low preservation level of this ecosystem. There was a weak, positive correlation between abundance of Chloroprocta idioidea (Robineau Desvoidy, 1830) (Diptera: Calliphoridae), Ch. megacephala, Chrysomya putoria (Wiedemann, 1818) (Diptera: Calliphoridae), and Lucilia cuprina (Wiedemann, 1830) (Diptera: Calliphoridae) with the temperature, as well as between the abundance of C. idioidea and Chrysomya albiceps (Wiedemann, 1819) (Diptera: Calliphoridae) with precipitation; however, there was no correlation between abundance and relative humidity. No significant influence of the trap height was observed. We stated a high influence of anthropic effects on the restinga and mangrove physiognomies, while the forest physiognomy still retains its preserved characteristics, with the dominance of forestall species.

Faunistic Analysis of the Families Calliphoridae and Mesembrinellidae (Diptera) at Jardim Botânico do Rio de Janeiro, Brazil

Flies of the family Calliphoridae play a variety of ecological roles. They carry various pathogens and cause myiasis in humans and livestock, but they are useful to forensic entomology and in larval therapy. Mesembrinellidae flies, formerly classified in the family Calliphoridae, are good bioindicators of human interference in natural environments. In this study, we carried out an inventory of the Calliphoridae and Mesembrinellidae at four collecting sites within the Jardim Botânico do Rio de Janeiro. Eight traps were set, four in the arboretum (sites A and B), where the public is allowed to visit, and four at an Atlantic Forest fragment (sites C and D), open only to researchers. From July 2014 to June 2015, a total of 35,890 calliphorid flies were captured in 10 species and 145 Mesembrinellidea in 3. The greatest number of flies was found at site A and diversity was higher at site C. Chrysomya megacephala (Wiedemann) (Diptera: Calliphoridae) was the most prevalent species, being present at all sites. Mesembrinella bellardiana (Aldrich) (Diptera: Mesembrinellidae), Laneella nigripes (Guimarães) (Diptera: Mesembrinellidae), and Huascaromusca purpurata (Aldrich) (Diptera: Mesembrinellidae) were present at sites C and D, which indicates a preservation of the area because they are asynanthropic species. There were significant differences between sites A and D and sites B and D.

DNA Barcodes for Forensically Important Fly Species in Brazil

Here, we analyze 248 DNA barcode sequences of 35 fly species of forensic importance in Brazil. DNA barcoding can be effectively used for specimen identification of these species, allowing the unambiguous identification of 31 species, an overall success rate of 88%. Our results show a high rate of success for molecular identification using DNA barcoding sequences and open new perspectives for immature species identification, a subject on which limited forensic investigations exist in Tropical regions. We also address the implications of building a robust forensic DNA barcode database. A geographic bias is recognized for the COI dataset available for forensically important fly species in Brazil, with concentration of sequences from specimens collected mainly in sites located in the Cerrado, Mata Atlântica, and Pampa biomes.

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.

Checklist and distribution maps of the blow flies of Venezuela (Diptera, Calliphoridae, Mesembrinellidae)

A checklist of the 39 species of blow flies (Calliphoridae and Mesembrinellidae) so far known to occur in Venezuela is provided, based on a thorough literature review and the examination of ca. 500 specimens deposited in the main entomological collections of the country. Data from the literature and museum collections were used to generate distribution maps for 37 species. Three species are recorded from Venezuela for the first time: Chrysomya putoria (Wiedemann, 1830), Mesembrinella spicata Aldrich, 1925 and Mesembrinella umbrosa Aldrich, 1922.

The blowflies of the Madeira Archipelago: species diversity, distribution and identification (Diptera, Calliphoridaes. l.)

Knowledge on the taxonomic diversity and distribution of blowflies from the Madeira Archipelago is updated. New and interesting findings are reported for poorly studied islands and islets of this archipelago, together with a brief analysis of the diversity of Macaronesian Calliphoridae s. l. Seven blowfly species were collected during this study, including the first records of Calliphora vicina Robineau-Desvoidy, 1830, Chrysomya albiceps (Wiedemann, 1819), Lucilia sericata (Meigen, 1826), Pollenia rudis (Fabricius, 1794) and Stomorhina lunata (Fabricius, 1805) from Porto Santo, and of Calliphora vicina, Lucilia sericata and Stomorhina lunata from Desertas Islands. The presence of Calliphora loewi Enderlein, 1903 in Madeira Laurisilva forest is discussed and its first instar larva is redescribed, revealing important differences in relation to its original description. An identification key to the adult Madeiran blowflies is provided for the first time.