Monophyletic blowflies revealed by phylogenomics

Phylogenetic insights based on the first complete mitochondrial genome of Isomyia nebulosa (Diptera: Calliphoridae)

To investigate the phylogenetic position of Isomyia Walker, 1860, a genus that suffered from frequent revisions of the taxonomic status following the subfamily Rhiniinae (Diptera, Calliphoridae), we sequenced, assembled, annotated, and analyzed the first complete mitochondrial genome (mitogenome) of Isomyia nebulosa (Townsend, 1917) in this study. This mitogenome is 16,438 bp in length, with a standard set of 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and an A + T riched non-coding region without genetic rearrangement as most dipteran mitogenomes, but long intergenic nucleotides (IGNs) between trnQ and trnM are found. The phylogeny yielded by both Bayesian inference and maximum-likelihood analysis for all mitochondrial PCGs and rRNAs of 23 mitogenomes supports the monophyly of the family Calliphoridae and the subfamilies Calliphorinae, Chrysomyinae, and Luciliinae. In addition, I. nebulosa diverged anterior to the above-mentioned three calliphorid subfamilies with high genetic distances.

Genome-wide investigation and expression analysis of OSCA gene family in response to abiotic stress in alfalfa

Alfalfa is an excellent leguminous forage crop that is widely cultivated worldwide, but its yield and quality are often affected by drought and soil salinization. Hyperosmolality-gated calcium-permeable channel (OSCA) proteins are hyperosmotic calcium ion (Ca2+) receptors that play an essential role in regulating plant growth, development, and abiotic stress responses. However, no systematic analysis of the OSCA gene family has been conducted in alfalfa. In this study, a total of 14 OSCA genes were identified from the alfalfa genome and classified into three groups based on their sequence composition and phylogenetic relationships. Gene structure, conserved motifs and functional domain prediction showed that all MsOSCA genes had the same functional domain DUF221. Cis-acting element analysis showed that MsOSCA genes had many cis-regulatory elements in response to abiotic or biotic stresses and hormones. Tissue expression pattern analysis demonstrated that the MsOSCA genes had tissue-specific expression; for example, MsOSCA12 was only expressed in roots and leaves but not in stem and petiole tissues. Furthermore, RT-qPCR results indicated that the expression of MsOSCA genes was induced by abiotic stress (drought and salt) and hormones (JA, SA, and ABA). In particular, the expression levels of MsOSCA3, MsOSCA5, MsOSCA12 and MsOSCA13 were significantly increased under drought and salt stress, and MsOSCA7, MsOSCA10, MsOSCA12 and MsOSCA13 genes exhibited significant upregulation under plant hormone treatments, indicating that these genes play a positive role in drought, salt and hormone responses. Subcellular localization results showed that the MsOSCA3 protein was localized on the plasma membrane. This study provides a basis for understanding the biological information and further functional analysis of the MsOSCA gene family and provides candidate genes for stress resistance breeding in alfalfa.

Application of omics techniques in forensic entomology research

With the advent of the post-genome era, omics technologies have developed rapidly and are widely used, including in genomics, transcriptomics, proteomics, metabolomics, and microbiome research. These omics techniques are often based on comprehensive and systematic analysis of biological samples using high-throughput analysis methods and bioinformatics, to provide new insights into biological phenomena. Currently, omics techniques are gradually being applied to forensic entomology research and are useful in species identification, phylogenetics, screening for developmentally relevant differentially expressed genes, and the interpretation of behavioral characteristics of forensic-related species at the genetic level. These all provide valuable information for estimating the postmortem interval (PMI). This review mainly discusses the available omics techniques, summarizes the application of omics techniques in forensic entomology, and their future in the field.

The genome sequence of the Locust Fly, Stomorhina lunata (Fabricius, 1805)

We present a genome assembly from an individual female Stomorhina lunata (the Locust Fly; Arthropoda; Insecta; Diptera; Rhiniidae). The genome sequence is 728.1 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.49 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,358 protein coding genes.

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.

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.

The phylogeny and divergence times of leaf-mining flies (Diptera: Agromyzidae) from anchored phylogenomics

Leaf-mining flies (Diptera: Agromyzidae) are a diverse clade of phytophagous Diptera known largely for their economic impact as leaf- or stem-miners on vegetable and ornamental plants. Higher-level phylogenetic relationships of Agromyzidae have remained uncertain because of challenges in sampling of both taxa and characters for morphology and PCR-based Sanger-era molecular systematics. Here, we used hundreds of orthologous single-copy nuclear loci obtained from anchored hybrid enrichment (AHE) to reconstruct phylogenetic relationships among the major lineages of leaf-mining flies. The resulting phylogenetic trees are highly congruent and well-supported, except for a few deep nodes, when using different molecular data types and phylogenetic methods. Based on divergence time dating using a relaxed clock and model-based historical biogeography analysis, leaf-mining flies are shown to have diversified in multiple lineages since the early Paleocene, approximately 65 million years ago. Our study not only reveals a revised classification system of leaf-mining flies, but also provides a new phylogenetic framework to understand their macroevolution.

Larval morphology of the avian parasitic genus Passeromyia: playing hide and seek with a parastomal bar

The enigmatic larvae of the Old World genus Passeromyia Rodhain & Villeneuve, 1915 (Diptera: Muscidae) inhabit the nests of birds as saprophages or as haematophagous agents of myiasis among nestlings. Using light microscopy, confocal laser scanning microscopy and scanning electron microscopy, we provide the first morphological descriptions of the first, second and third instar of P. longicornis (Macquart, 1851) (Diptera: Muscidae), the first and third instar of P. indecora (Walker, 1858) (Diptera: Muscidae), and we revise the larval morphology of P. heterochaeta (Villenueve, 1915) (Diptera: Muscidae) and P. steini Pont, 1970 (Diptera: Muscidae). We provide a key to the third instar of examined species (excluding P. steini and P. veitchi Bezzi, 1928 (Diptera: Muscidae)). Examination of the cephaloskeleton revealed paired rod-like sclerites, named 'rami', between the lateral arms of the intermediate sclerite in the second and third instar larva. We reveal parastomal bars fused apically with the intermediate sclerite, the absence of which has so far been considered as apomorphic for second and third instar muscid larvae. Examination of additional material suggests that modified parastomal bars are not exclusive features of Passeromyia but occur widespread in the Muscidae, and rami may occur widespread in the Cyclorrhapha.

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.

An updated catalogue of true flies (Insecta: Diptera) from northern Pakistan

We present the first comprehensive catalogue of true flies from the northernmost territories of Pakistan, including Azad Jammu & Kashmir and Gilgit-Baltistan. In the current inventory, 64 genera and 153 species in 16 families are being documented. The total number of known species has been updated based on the availability of taxonomic literatures from Pakistan. In 2007, Insect Fauna of Azad Jammu & Kashmir was updated and it lists only 16 known species in order Diptera where as there is no such documented information so far available on the dipterous fauna of Gilgit-Baltistan. However, during the last few decades, relatively a few studies have been conducted on some major group of flies, i.e., Syrphidae, Sepsidae, Calliphoridae, and Tephritidae from Azad Kashmir and Gilgit-Baltistan. Among these, Syrphidae represents 53 species which is the highest number of species recorded, followed by Sepsidae and Calliphoridae with 20 and 18 species, respectively. The present diversity does not reflect the true species account in the northern areas; the important biogeographic area that exhibits a very heterogeneous fauna, not only because of the high mountains with valleys (the Hindu Kush and Karakoram ranges of the Western Himalayas) but also the junction points of the world’s two largest zoogeographical regions (the Oriental and Palaearctic). Some common families, i.e., Stratiomyidae, Asilidae, Bombyliidae, Muscidae, Conopidae, Pipinculidae, Tachinidae, and some other families which are common in high mountainous regions of northern Pakistan still need to be explored in the future studies. The complete locality data for each valid species are presented as the baseline for future studies from northern areas of Pakistan, i.e., Azad Jammu & Kashmir and Gilgit-Baltistan.

Chrysomya pinguis (Walker) (Diptera: Calliphoridae), blow fly of forensic importance: A review of bionomics and forensic entomology appraisal

Role of blow flies as the entomological evidence used in forensic investigations has risen dramatically worldwide. As the diverse habitats of Thailand suitably endowed with biodiversity of insects, blow flies of forensic importance need investigation in their bionomics, which are further applied in forensic investigations. Chrysomya pinguis (Walker, 1858) (Diptera: Calliphoridae) make up one of the most common blow fly species found associated with the human corpses and/or death scenes in several countries of the Asia continent. Given the major species as forensically important, this review is performed by the need for gathering information of C. pinguis from literature search in the future application in the regions where this species exists. This review deals with morphology, current knowledge on bionomics and forensic entomology involvement. Important morphological characteristics of egg, larva, puparium and adult were highlighted with illustration and/or micrographs. Search pertaining to molecular analysis used for fly identification and developmental rate of larvae were included. Furthermore, we outline potential issues and challenges of C. pinguis research that necessitate forensic applications in the future.

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.