DNA barcoding allows identification of European Fanniidae (Diptera) of forensic interest

Molecular differentiation analysis of ten putative species of Fannia (Diptera: Fanniidae) collected in carrion-baited traps from Colombia

The genus Fannia is the most representative of the Fannidae family of true flies with worldwide distribution. Some species are attracted to decomposing materials and live vertebrate animals, which makes them important in forensics, medical and veterinary fields. However, identifying Fannia species can be difficult due to the high similarity in the external morphology of females and limited descriptions and morphological keys. Herein, molecular markers could provide a complementary tool for species identification. However, molecular identification has still limited application since databases contain few data for neotropical species of Fannia. This study assessed the potential of two molecular markers, the COI-3' region and internal transcribed spacer 2 (ITS2), to differentiate 10 putative species of the genus Fannia from Colombia using distance-based and tree-based approaches. The partial ITS2 and/or COI-3' regions allowed molecular diagnosis of six species, while pairs of species Fannia colazorrensis + F. dodgei and F. laclara + F. aburrae are conflicting. Although these results might suggest that conflicting pair species are conspecific, consistent morphological differences between males do not support this hypothesis. The lack of differentiation at the nuclear and mitochondrial molecular markers for the conflicting species may be due to incomplete evolutionary lineage separation, hybridization, or introgression events. In addition, sexual selection on male morphological traits before species-specific differences in molecular markers emerge may partially explain the results. Our study provides a valuable dataset to identify and confirm some Fannia species molecularly. Further, they could be used to associate females and immature stages with their conspecifics as a baseline to deep into their biology, ecology, distribution and potential applications in forensic and medico-veterinary entomology.

A survey of Wolbachia infection in brachyceran flies from Iran

Wolbachia is a maternally inherited intracellular bacterium that is considered to be the most plentiful endosymbiont found in arthropods. It reproductively manipulates its host to increase the chances of being transmitted to the insect progeny; and it is currently used as a means of suppressing disease vector populations or controlling vector-borne diseases. Studies of the dissemination and prevalence of Wolbachia among its arthropod hosts are important for its possible use as a biological control agent. The molecular identification of Wolbachia relies on different primers sets due to Wolbachia strain variation. Here, we screened for the presence of Wolbachia in a broad range of Brachycera fly species (Diptera), collected from different regions of Iran, using nine genetic markers (wsp, ftsZ, fbpA, gatB, CoxA, gltA, GroEL dnaA, and 16s rRNA), for detecting, assessing the sensitivity of primers for detection, and phylogeny of this bacterium. The overall incidence of Wolbachia among 22 species from six families was 27.3%. The most commonly positive fly species were Pollenia sp. and Hydrotaea armipes. However, the bacterium was not found in the most medically important flies or in potential human disease vectors, including Musca domestica, Sarcophaga spp., Calliphora vicinia, Lucilia sericata, and Chrysomya albiceps. The primer sets of 16s rRNA with 53.0% and gatB with 52.0% were the most sensitive primers for detecting Wolbachia. Blast search, phylogenetic, and MLST analysis of the different locus sequences of Wolbachia show that all the six distantly related fly species likely belonging to supergroup A. Our study showed some primer sets generated false negatives in many of the samples, emphasizing the importance of using different loci in detecting Wolbachia. The study provides the groundwork for future studies of a Wolbachia-based program for control of flies.

Geographical Distribution and Multimethod Species Identification of Forensically Important Necrophagous Flies on Hainan Island

Forensic entomology offers unique advantages for the minimum postmortem interval (PMImin) estimation of decomposed corpses in forensic investigations. Accurate species identification and up-to-date locality information are essential. Hainan Island has a tropical rainforest climate and a vast territory. In this study, the community structure of necrophagous flies on Hainan Island was investigated in detail according to geographical environment. The results showed that the dominant species included C. megacephala, S. peregrina, C. rufifacies, S. misera, H. ligurriens, S. sericea, S. cinerea, S. dux, C. pinguis, and M. domestica. Furthermore, C. rufifacies and C. villeneuvi were found only in the high-altitude areas of Wuzhi Mountain, while S. cinerea was distributed only in coastal areas; the latter is a representative species of Hainan Island and has not been reported before. Furthermore, a GenBank database of forensically important flies was established, whilst a high-resolution melt (HRM) curve analysis was applied to identify the common species of Hainan Island for the first time. This study enriches the database of forensically important flies in tropical rainforest regions.

A short fragment of mitochondrial DNA for the taxonomic identification of blow flies (Diptera: Calliphoridae) in northwestern South America

Blow flies are of medical, sanitary, veterinary, and forensic importance. Their accurate taxonomic identification is essential for their use in applied research. However, neotropical fauna has not been completely studied or described, and taxa identification without the required training is a difficult task. Additionally, the current morphological keys are not fitting to all extant taxa. Molecular-based approaches are widely used to overcome these issues, including the standard 5' COI barcode fragment (~650 base pairs [bp]) for identification at the species level. Here, a shorter sequence of 5' COI fragment (~342 bp) was assessed for the identification of 28 blow fly species inhabiting the northwest of South America. One tree-based (the generalized mixed Yule-coalescent-GMYC) and 3 distance-based approaches (automatic barcode gap discover - ABGD, the best close match - BCM, and the nearest neighbor - NN) analyses were performed. Noticeably, the amplification and sequencing of samples that had been preserved for up to 57 years were successful. The tree topology assigned 113 sequences to a specific taxon (70% effectiveness), while the distance approach assigned to 95 (59% effectiveness). The short fragment allowed the molecular identification of 19 species (60% of neotropical species except for the Lucilia species and Hemilucilia semidiaphana). According to these findings, the taxonomic and faunistic considerations of the blow fly fauna were provided. Overall, the short fragment approach constitutes an optimal species confirmation tool for the most common blow flies in northwestern South America.

Diptera (Dryomyzidae, Fanniidae, Muscidae, Piophilidae) Associated With Pig Carcasses in a Forest Habitat of Poland: Sex-Related Patterns of Visitation and Effectiveness of Sampling Methods

Our knowledge on many necrophilous dipterans was limited for a long time mainly due to taxonomic issues. Therefore, findings on the sex-related associations with pig carcasses in Dryomyzidae, Fanniidae, Muscidae, and Piophilidae are presented. Moreover, the effectiveness of pitfall traps and sweep nets in fly sampling were compared, since the correct method of collecting insects is critical for the development and application of entomological tools for forensic purposes. The trapped numbers of all species differed significantly in respect to both sexes. The sex ratios were strongly female-biased in most species of Muscidae and in Fanniidae. More females were also collected in Piophilidae, but the proportion of males was higher when compared to muscids. Within Dryomyzidae, the sex ratio differed according to species. Only Dryomyza flaveola (Fabricius, 1794) (Diptera: Dryomyzidae) and Muscina pascuorum (Meigen, 1826) (Diptera: Muscidae) had male-biased sex ratios. Differences in residency patterns between sexes in Stearibia nigriceps (Meigen, 1826) (Diptera: Piophilidae), Liopiophila varipes (Meigen, 1830) (Diptera: Piophilidae), and D. flaveola were statistically insignificant. All studied species were recorded for each sampling method. The effect of the sampling method on the number of individuals was statistically significant for all dipterans but Piophilidae. Pitfall traps outcompeted the aerial sweep net in representing Dryomyzidae and Muscidae, whereas both methods were almost equally effective in the collection of Piophilidae. A varied effectiveness of sampling methods was observed in Fanniidae. The sampling method significantly affected the determination of the appearance time of flies on carcasses, but the effect of species and sampling method was insignificant. Implications for forensic entomology are discussed.

The Phylogenetic Relationships of the Fanniidae within the Muscoid Grade (Diptera: Calyptrata) Based on the Musculature of the Male Terminalia

Simple Summary

The Fanniidae is a small dipteran family in the muscoid grade of the Calyptrata. To resolve controversial issues of phylogeny, in addition to molecular analyses, the study of the muscles of the pregenital and genital segments of males can significantly help because they are considered to provide important information relating to the phylogenetic branching of the Cyclorrhapha. Here, the authors report on the structure of the sclerites and the muscles of terminal segments of three species of the Fanniidae. These structures are compared with other members of the muscoid grade, as well as the Oestroidea and Hippoboscoidea. In comparison with the majority of the Calyptrata, there is a significant reduction of the sclerites and muscles of the pregenital segments of the male genitalia of the Fanniidae. The presence of the lateral bacilliform sclerites, as well as the presence and position of the epandrial muscles of the Fanniidae as in primitive Muscidae and also in Tachina and Calliphora, is best interpreted as a plesiomorphic state, while the reductions are considered as derived relative to the ground plan of the Calyptrata.

Abstract

The abdominal and pregenital segments and the genitalia were studied in males of Fannia subpellucens (Zetterstedt, 1845), Fannia canicularis (Linnaeus, 1761) and Fannia incisurata (Zetterstedt, 1838). In comparison with the remaining members of the muscoid grade, in addition to the symmetry of the pregenital segments, significant reductions of the sclerites and musculature of the male terminalia have been observed in Fanniidae. The muscular structure of pregenital segments confirms that the fused pregenital ring is syntergosternite VI + VII + VIII. Symmetry and fusion, as well as the lower number of the sclerites and muscles of the pregenital segments and male genitalia of the Fanniidae, can be considered apomorphic character states. The presence of the lateral bacilliform sclerite, as well as the presence and position of the epandrial muscles M 26, three pairs of muscles M 19 and paired muscles M 18, can be considered as a plesiomorphic character state of the Fanniidae. The structure of the sclerites and muscles of the male abdominal segments and terminalia place the Fanniidae at the base of the muscoid grade and Oestroidea, as has been confirmed by recent molecular studies.

Development of Fannia pusio (Diptera: Fanniidae) Under Controlled Temperature Conditions and its Enforcement in the Estimate of the Post-mortem Interval (PMI)

Fannia pusio (Wiedemann, 1830) is a species belonging to the family Fanniidae, which is of great forensic, sanitary, and veterinary interest. The behavioral peculiarities of this species, depending on the temperature at which it is found, may provide additional information for future research. The application of entomology in the forensic field has focused especially on the early colonizing taxa of corpses that are in the initial stage of decomposition. However, species occurring at more advanced stages can contribute to further knowledge, as is the case with F. pusio. In addition, the species has the ability to colonize buried corpses that are inaccessible to larger dipterans. On the other hand, the sanitary and veterinary interest of this species is due to the performance of females as phoretic hosts of Dermatobia hominis eggs that cause myiasis in both animals and humans. In the current study, the behavior of F. pusio was observed at a temperature range of 5°C to 40°C. We found that its viability range is limited between 15°C and 35°C; above and below these temperatures, adults survive but oviposition does not take place. Data collected by statistical analysis were subsequently applied to calculate the post-mortem interval (PMI) using isomorphen and isomegalen diagrams. The results show a directly proportional relationship between growth rate and temperature increase. However, a slowdown in the growth of individuals was observed at extreme temperatures (5°C and 35°C). The results shown in this manuscript, together with the existing bibliography of other species, help to broaden the knowledge of F. pusio, which has not been studied in such depth until now.

DNA Barcoding Identifies Unknown Females and Larvae of Fannia R.-D. (Diptera: Fanniidae) from Carrion Succession Experiment and Case Report

Simple Summary

Insects are frequently attracted to animal and human cadavers, usually in large numbers. The practice of forensic entomology can utilize information regarding the identity and characteristics of insect assemblages on dead organisms to determine the time elapsed since death occurred. However, for insects to be used for forensic applications it is essential that species are identified correctly. Imprecise identification not only affects the forensic utility of insects but also results in an incomplete image of necrophagous entomofauna in general. The present state of knowledge on morphological diversity and taxonomy of necrophagous insects is still incomplete and identification of immature and female forms can be extremely difficult. In this study, we utilized molecular identification methods to link conspecific sexes and developmental stages of forensically important flies. We identified larvae and females of flies collected from animal and human cadavers which otherwise were morphologically unidentifiable. The present study fills a gap in taxonomy of flies and provides data facilitating application of new species as forensic indicators.

Abstract

Application of available keys to European Fanniidae did not facilitate unequivocal species identification for third instar larvae and females of Fannia Robineau-Desvoidy, 1830 collected during a study of arthropod succession on pig carrion. To link these samples to known species, we took the advantage of molecular identification methods and compared newly obtained cytochrome oxidase subunit I (COI) barcode sequences against sequences deposited in reference databases. As an outcome of the results obtained, we describe for the first time a third instar larva of Fannia nigra Malloch, 1910 and Fannia pallitibia (Rondani, 1866) and a female of Fannia collini d’Assis-Fonseca, 1966. We provide combinations of characters allowing for discrimination of described insects from other Fanniidae. We provide an update for the key by Rozkošný et al. 1997, which allows differentiation between females of F. collini and other species of Fanniidae. Additionally, we provide a case of a human cadaver discovered in Southern Poland and insect fauna associated with it as the first report of F. nigra larvae developing on a human body.

Wolbachia: A tool for livestock ectoparasite control

Ectoparasites and livestock-associated insects are a major concern throughout the world because of their economic and welfare impacts. Effective control is challenging and relies mainly on the use of chemical insecticides and acaricides. Wolbachia, an arthropod and nematode-infecting, maternally-transmitted endosymbiont is currently of widespread interest for use in novel strategies for the control of a range of arthropod-vectored human diseases and plant pests but to date has received only limited consideration for use in the control of diseases of veterinary concern. Here, we review the currently available information on Wolbachia in veterinary ectoparasites and disease vectors, consider the feasibility for use of Wolbachia in the control of livestock pests and diseases and highlight critical issues which need further investigation.

Identification of Forensically Important Flesh Flies Using the Cytochrome C Oxidase Subunits I and II Genes

Forensically important flesh flies (Diptera: Sarcophagidae) often are not morphologically distinguishable, especially at the immature stage. In addition, female flies are quite similar in general morphology, making accurate identifications difficult. DNA-based technologies, particularly mitochondrial DNA (mtDNA), have been used for species-level identification. The cytochrome oxidase subunits I and II (COI-COII) sequences of Iranian Sarcophagidae are still unavailable in GenBank. In this study as many as 648 (540 males and 106 females) fly specimens from family Sarcophagidae, representing 10 sarcophagid species, including eight forensically important species were collected from seven locations in five Iranian provinces. Of these, 150 male specimens were identified based on both morphology of male genitalia and DNA sequencing analysis. Sequence data from the COI-COII regions for 10 flesh fly species collected in Iran were generated for the first time. Digestion of COI-COII region by restriction enzymes RsaI, EcoRV, and HinfI provided distinct restriction fragment length polymorphism profiles among the species and can serve as molecular markers for species determination. Phylogenetic analysis represented that the COI-COII sequences are helpful for delimitation of sarcophagid species and implementation in forensic entomology. However, the application of the COI-COII fragment as a species identifier requires great caution and additional species and markers should be studied to ensure accurate species identification in the future.

Assessment of BOLD and GenBank - Their accuracy and reliability for the identification of biological materials

Taxonomic identification of biological materials can be achieved through DNA barcoding, where an unknown "barcode" sequence is compared to a reference database. In many disciplines, obtaining accurate taxonomic identifications can be imperative (e.g., evolutionary biology, food regulatory compliance, forensics). The Barcode of Life DataSystems (BOLD) and GenBank are the main public repositories of DNA barcode sequences. In this study, an assessment of the accuracy and reliability of sequences in these databases was performed. To achieve this, 1) curated reference materials for plants, macro-fungi and insects were obtained from national collections, 2) relevant barcode sequences (rbcL, matK, trnH-psbA, ITS and COI) from these reference samples were generated and used for searching against both databases, and 3) optimal search parameters were determined that ensure the best match to the known species in either database. While GenBank outperformed BOLD for species-level identification of insect taxa (53% and 35%, respectively), both databases performed comparably for plants and macro-fungi (~81% and ~57%, respectively). Results illustrated that using a multi-locus barcode approach increased identification success. This study outlines the utility of the BLAST search tool in GenBank and the BOLD identification engine for taxonomic identifications and identifies some precautions needed when using public sequence repositories in applied scientific disciplines.

Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation?

In forensic geology casework, sample size typically limits routine characterization of material using bulk approaches. To address this, DNA-based characterization of biological taxa has received attention, as the taxa present can be useful for sample-to-sample comparisons and source attribution. In our initial work, low biodiversity was captured when DNA barcodes were Sanger-sequenced from plant and insect fragments isolated from 10 forensic-type surface soils. Considering some forensic laboratories now have access to massively parallel sequencing platforms, we assessed whether biological taxa present in the same surface soils could be better characterized using DNA metabarcoding. To achieve this, plant and animal barcodes were amplified and sequenced on an Illumina MiniSeq for three different DNA sample types (n = 50): individual fragments used in our initial study, and 250 and 100 mg of bulk soil (from the 10 sites used in the initial study). A total of 572 unique target barcode sequences passed quality filtering and were used in downstream statistical analyses: 54, 321, and 285 for individual fragments, 100 mg, and 250 mg bulk soil samples, respectively. Plant barcodes permitted some spatial separation of sample sites in non-metric multidimensional scaling plots; better separation was obtained for samples prepared from bulk soil. This study confirmed that bulk soil DNA metabarcoding is a better approach for characterizing biological taxa present in surface soils, which could supplement traditional geologic examinations.

Thermal requirements for the development of immature stages of Fannia canicularis (Linnaeus) (Diptera: Fanniidae)

Entomological material may be used to estimate the time since death occurred (minimum post-mortem interval, mPMI) in forensically obscure cases. The method commonly used to calculate mPMI is the application of a thermal summation model. Little is known about the thermal requirements of Fanniidae. To fill this gap, the influence of temperature on the development time of Fannia canicularis (Linnaeus), a cosmopolitan species with the potential to be used in forensic entomology, was studied. An experiment was performed under nine ambient temperatures. The thermal summation constants (k) and developmental zeros (T_min) of this species were calculated for six developmental events: hatching, first ecdysis, second ecdysis, wandering, pupariation, and eclosion. Data were primarily analysed with two linear models, and then, since the relationship between temperature and development rate is curvilinear close to the lower and higher developmental thresholds, the relationship was also modelled using three nonlinear models. A fourth nonlinear model was also used to estimate the intrinsic optimum temperature of F. canicularis, at which the population size is maximal and the mortality is the lowest. At 33 °C, larvae did not hatch from eggs, and thus changes in larval body length were analysed at the eight remaining temperatures. Fannia canicularis development from egg to eclosion required a mean ± SE of 481.73 ± 9.89 degree-days above a lower threshold temperature of 4.64 ± 0.19 °C. At the lowest experimental temperature tested, 10 °C, F. canicularis successfully completed all developmental events, although ca. 30% of wandering larvae proceeded to the inactive stage instead of pupariation. Results obtained from nonlinear models were not satisfactory and did not allow us to consider them as reliable from a biological point of view.

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.