DNA barcoding and the differentiation between North American and West European Phormia regina (Diptera, Calliphoridae, Chrysomyinae)

Domestic Filth Flies in New Haven, Connecticut: A Case Study on the Effects of Urbanization and Climate Change by Comparing Fly Populations after 78 Years

Simple Summary

Domestic filth fly population data were collected in the summers of 1942–1944 in the urban city of New Haven, Connecticut, during a polio epidemic. The current survey was completed 78 years later by setting out a weekly trap in the same region during June–September over a two-year period. Results indicate that the fly population has changed in the city, with 16 fewer species trapped overall, and there have been changes in the fly species trapped. Some species have increased in abundance, notably Lucilia coeruleiviridis, while numbers of the common Lucilia sericata have decreased, and Lucilia illustris was absent. Changes in land cover and climate were also assessed to show that the trap site has experienced significant habitat change, together with an increase in the average temperature and rainfall. Fly numbers were significantly affected by temperature and rainfall in both the 1940s and the current survey. The results of this study suggest the prolonged period of urbanization of the region is influencing the domestic filth fly population.

Abstract

Changes in common and widespread insect populations such as the domestic filth fly in urban cities are useful and relevant bioindicators for overall changes in the insect biomass. The current study surveyed necrophagous flies by placing a weekly trap from June–September over a two-year period in the city of New Haven, Connecticut, to compare data on fly abundance and diversity with data collected 78 years earlier. Climate and land cover changes were also assessed in combination with the fly population for each period. The survey results suggest the domestic filth fly population is now less diverse with decreased species richness and changes in the relative abundance of species. In both surveys, 95–96% of the population was composed of only three species. The current survey data indicate the numerical dominance of Lucilia sericata has decreased, the abundance of several species, notably Lucilia coeruleiviridis, has increased, and Lucilia illustris is absent. Species that showed a significant interaction with temperature in the 1940s survey have now increased in abundance, with several of the trapped species continuing to show an interaction with temperature and rainfall. Analysis of the land cover and climate data characterizes the trap site as a region exposed to a prolonged period of industrialization and urbanization, with only 7% of the land cover remaining undeveloped and over 50% impervious, coupled with an increase in temperature and rainfall. This study serves as a model for changes in domestic filth fly populations and other insects in similarly highly urbanized established cities.

Forensically relevant blow flies (Diptera: Calliphoridae) of Central Connecticut, USA

Connecticut and the Northeastern United States in general, lacks forensically relevant entomological survey data. To determine which forensically relevant calliphorid (blow flies, Diptera: Calliphoridae) and non-calliphorid species dominate Connecticut, 5 traps using pork bait were set out 7 times over a 2-year period to collect adult and immature specimens. Insects collected from human corpses in this region were also tabulated to collaborate the forensic relevance of trapped specimens. The survey identified a total of 8 species of blow flies of the Lucilia and Calliphora genera, 6 of which colonized the baits, and 5 of which have been found to colonize human corpses in the area. Non-calliphorid genera Sarcophaga and Muscina were also found to be colonizers of the baited traps but in relatively lower numbers. Trap sites differed significantly in the degree of urbanization which was determined by using GIS mapping to classify a 1 kilometer (km) radius around each site using land use and the percent of urban impervious surfaces. The 1 km radius revealed the highly fragmented nature of the immediate habitats of the trap sites and no habitat or seasonal preference was demonstrated by blow flies under these trap conditions. Temperature was the one variable which significantly affected the number of flies trapped and the colonizing species. All trapped species have been described previously as widespread and common in the United States and as synanthropic. Further research in this region should trap at the constantly changing extreme ends of the urban-rural gradient and in the colder temperatures of winter to explore the limits of the flexibility of these blow fly species.

DNA-based and taxonomic identification of forensically important Sarcophagidae (Diptera) in southeastern Spain

Studying dipterans at the scene of a death can provide essential information for interpreting the evidence and help to reconstruct the events happened to a corpse in the past. Molecular tools have been employed for identification at specific levels in the cases of cryptic species or poorly conserved specimens. Identification of specimens is essential in forensic entomology since each species has a specific growth rate, which determines the calculation of the minimum post mortem interval (minPMI). In addition, phylogeographic reconstruction within a species can help to differentiate the haplotypes from a geographic area, thereby helping to clarify the possible relocation of a corpse. The morphological identification of Sarcophagidae species is often difficult, especially for the females. This is an important Diptera family since some of its species are among the first to reach a corpse, especially in warm areas. In this study, we compared the sarcophagids found in human corpses in forensic cases in Alicante (southeast of Spain) with specimens collected from baited traps in the same area and surrounding provinces. In total, 189 specimens were collected, comprising 72 from forensic cases and 117 from baited traps. Molecular identification was conducted by sequencing the cox1 mitochondrial gene and analyzing the sequences using ABGD, GMYC, and BIN species delimitation methods. The median joining algorithm in the PopART program was used to construct phylogeographic networks. Eight species in the family Sarcophagidae were identified. The most widely collected species were Sarcophaga argyrostoma and Sarcophaga tibialis. The haplotype networks obtained for these species did not indicate a clear geographic distribution of haplotypes. The S. argyrostoma samples from Alcoy were clearly isolated. The results demonstrated that this method is useful for identifying Sarcophagidae samples in forensic investigations and it can be employed for minPMI estimation.

Genetic diversity of Calliphora vicina (Diptera: Calliphoridae) in the Iberian Peninsula based on cox1, 16S and ITS2 sequences

The study of Diptera at the scene of a crime can provide essential information for the interpretation of evidence. Phylogeographic reconstruction could help differentiate haplotypes of a dipteran species in a geographical area, clarifying, for example, the details of a possible relocation of a corpse. In addition, inferring the ancestral areas of distribution helps to understand the current status of the species and its biogeographic history. One of the most important species in forensic entomology is Calliphora vicina Rovineau-Desvoidy, 1830 (Diptera: Calliphoridae). The aim of this work is to increase our knowledge of this species in the Iberian Peninsula using 464 specimens from Spain and Portugal. These samples were identified using morphological keys and by molecular methods using fragments of the cox1, 16S and ITS2 genes. The phylogeographic history of these populations was inferred from haplotype networks and the reconstruction of ancestral areas of distribution. The molecular results corroborated the morphological identifications of the samples. Phylogeographic networks showed no geographical structure, as haplotypes are shared among almost all populations. reconstruct ancestral state in phylogenies analyses showed a high rate of movement among populations, possibly related to human activity. These results suggest that this species had a very rapid and recent spatial and demographic expansion throughout the Iberian Peninsula.

Exogenous and endogenous microbiomes of wild-caught Phormia regina (Diptera: Calliphoridae) flies from a suburban farm by 16S rRNA gene sequencing

The black blow fly, Phormia regina (Meigen) (Diptera: Calliphoridae) is one of the most abundant carrion flies in North America. Calliphorids are important in agriculture and animal production, veterinary sciences, forensics and medical entomology. While the role of flies in the epidemiology of human and animal diseases is an active area of research, little is known about the microorganisms associated with these insects. We examined the diversity of wild-caught black blow fly endogenous (internal body) and exogenous (external body) microbial communities using 16S rRNA gene sequencing. Overall, 27 phyla, 171 families and 533 genera were detected, and diversity was significantly higher (P < 0.05) on external body surfaces. At the genus level, Dysgonomonas, Ignatzschineria, Acinetobacter, Vagococcus, Myroides, and Wohlfahrtiimonas were predominant. Cloning and sequencing of nearly full-length fragments of the 16S rRNA gene showed that some of the species identified are known to be pathogenic to humans, animals, and plants. Myroides odoratimimus and Acinetobacter radioresistens are well-known, multi-drug resistant bacteria. These results provide a snapshot of the microbial communities harbored by adult black blow flies and call for more comprehensive studies to better characterize the role these flies may play in the transmission of pathogenic microorganisms.

Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism

Lucilia (Diptera: Calliphoridae) is a genus of blowflies comprised largely of saprophagous and facultative parasites of livestock. Lucilia bufonivora, however, exhibits a unique form of obligate parasitism of amphibians, typically affecting wild hosts. The evolutionary route by which amphibian myiasis arose, however, is not well understood due to the low phylogenetic resolution in existing nuclear DNA phylogenies. Furthermore, the timing of when specificity for amphibian hosts arose in L. bufonivora is also unknown. In addition, this species was recently reported for the first time in North America (Canada) and, to date, no molecular studies have analysed the evolutionary relationships between individuals from Eastern and Western hemispheres. To provide broader insights into the evolution of the amphibian parasitic life history trait and to estimate when the trait first arose, a time-scaled phylogeny was inferred from a concatenated data set comprising mtDNA, nDNA and non-coding rDNA (COX1, per and ITS2 respectively). Specimens from Canada, the UK, Poland, Switzerland, the Netherlands and Germany were analysed, as well as individuals from its sister taxa, the saprophage Lucilia silvarum and a Nearctic species also implicated in amphibian myiasis, Lucilia elongata. Obligate amphibian parasitism appears to have arisen ~4 mya, likely as a result of niche displacement of a saprophagous/facultative parasite ancestor. Consistent paraphyly of L. bufonivora with respect to L. elongata across single-gene phylogenies and high mtDNA genetic distances between Nearctic and Palearctic individuals suggest on-going cryptic speciation facilitated by geographical isolation. These findings suggest that recent reports of L. bufonivora in the Nearctic do not constitute a recent introduction, but instead suggest that it remained unrecorded due to taxonomic confusion and low abundance. This is the first study to confirm the involvement of L. bufonivora in amphibian myiasis in Canada using DNA-based identification methods.

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Within Lucilia, a small genus of blowflies mostly comprised of carrion-breeding species, obligate parasitism for amphibians evolved around 4 mya.

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Geographic isolation between Nearctic and Palearctic lineages is facilitating on-going cryptic speciation of Lucilia bufonivora.

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First positive identification of L. bufonivora from two confirmed cases of amphibian myiasis in North America.

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding-based biomonitoring

This study summarizes results of a DNA barcoding campaign on German Diptera, involving analysis of 45,040 specimens. The resultant DNA barcode library includes records for 2,453 named species comprising a total of 5,200 barcode index numbers (BINs), including 2,700 COI haplotype clusters without species‐level assignment, so called “dark taxa.” Overall, 88 out of 117 families (75%) recorded from Germany were covered, representing more than 50% of the 9,544 known species of German Diptera. Until now, most of these families, especially the most diverse, have been taxonomically inaccessible. By contrast, within a few years this study provided an intermediate taxonomic system for half of the German Dipteran fauna, which will provide a useful foundation for subsequent detailed, integrative taxonomic studies. Using DNA extracts derived from bulk collections made by Malaise traps, we further demonstrate that species delineation using BINs and operational taxonomic units (OTUs) constitutes an effective method for biodiversity studies using DNA metabarcoding. As the reference libraries continue to grow, and gaps in the species catalogue are filled, BIN lists assembled by metabarcoding will provide greater taxonomic resolution. The present study has three main goals: (a) to provide a DNA barcode library for 5,200 BINs of Diptera; (b) to demonstrate, based on the example of bulk extractions from a Malaise trap experiment, that DNA barcode clusters, labelled with globally unique identifiers (such as OTUs and/or BINs), provide a pragmatic, accurate solution to the “taxonomic impediment”; and (c) to demonstrate that interim names based on BINs and OTUs obtained through metabarcoding provide an effective method for studies on species‐rich groups that are usually neglected in biodiversity research projects because of their unresolved taxonomy.

A molecular, morphological, and physiological comparison of English and German populations of Calliphora vicina (Diptera: Calliphoridae)

The bluebottle blow fly Calliphora vicina is a common species distributed throughout Europe that can play an important role as forensic evidence in crime investigations. Developmental rates of C. vicina from distinct populations from Germany and England were compared under different temperature regimes to explore the use of growth data from different geographical regions for local case work. Wing morphometrics and molecular analysis between these populations were also studied as indicators for biological differences. One colony each of German and English C. vicina were cultured at the Institute of Legal Medicine in Frankfurt, Germany. Three different temperature regimes were applied, two constant (16°C & 25°C) and one variable (17–26°C, room temperature = RT). At seven time points (600, 850, 1200, 1450, 1800, 2050, and 2400 accumulated degree hours), larval lengths were measured; additionally, the durations of the post feeding stage and intrapuparial metamorphosis were recorded. For the morphometric and molecular study, 184 females and 133 males from each C. vicina population (Germany n = 3, England n = 4) were sampled. Right wings were measured based on 19 landmarks and analyzed using canonical variates analysis and discriminant function analysis. DNA was isolated from three legs per specimen (n = 61) using 5% chelex. A 784 bp long fragment of the mitochondrial cytochrome b gene was sequenced; sequences were aligned and phylogenetically analyzed. Similar larval growth rates of C. vicina were found from different geographic populations at different temperatures during the major part of development. Nevertheless, because minor differences were found a wider range of temperatures and sampling more time points should be analyzed to obtain more information relevant for forensic case work. Wing shape variation showed a difference between the German and English populations (P<0.0001). However, separation between the seven German and English populations at the smaller geographic scale remained ambiguous. Molecular phylogenetic analysis by maximum likelihood method could not unambiguously separate the different geographic populations at a national (Germany vs England) or local level.

DNA Barcoding in Forensic Entomology - Establishing a DNA Reference Library of Potentially Forensic Relevant Arthropod Species

Throughout the years, DNA barcoding has gained in importance in forensic entomology as it leads to fast and reliable species determination. High-quality results, however, can only be achieved with a comprehensive DNA barcode reference database at hand. In collaboration with the Bavarian State Criminal Police Office, we have initiated at the Bavarian State Collection of Zoology the establishment of a reference library containing arthropods of potential forensic relevance to be used for DNA barcoding applications. CO1-5P' DNA barcode sequences of hundreds of arthropods were obtained via DNA extraction, PCR and Sanger Sequencing, leading to the establishment of a database containing 502 high-quality sequences which provide coverage for 88 arthropod species. Furthermore, we demonstrate an application example of this library using it as a backbone to a high throughput sequencing analysis of arthropod bulk samples collected from human corpses, which enabled the identification of 31 different arthropod Barcode Index Numbers.

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.

DNA-barcoding of forensically important blow flies (Diptera: Calliphoridae) in the Caribbean Region

Correct identification of forensically important insects, such as flies in the family Calliphoridae, is a crucial step for them to be used as evidence in legal investigations. Traditional identification based on morphology has been effective, but has some limitations when it comes to identifying immature stages of certain species. DNA-barcoding, using COI, has demonstrated potential for rapid and accurate identification of Calliphoridae, however, this gene does not reliably distinguish among some recently diverged species, raising questions about its use for delimitation of species of forensic importance. To facilitate DNA based identification of Calliphoridae in the Caribbean we developed a vouchered reference collection from across the region, and a DNA sequence database, and further added the nuclear ITS2 as a second marker to increase accuracy of identification through barcoding. We morphologically identified freshly collected specimens, did phylogenetic analyses and employed several species delimitation methods for a total of 468 individuals representing 19 described species. Our results show that combination of COI + ITS2 genes yields more accurate identification and diagnoses, and better agreement with morphological data, than the mitochondrial barcodes alone. All of our results from independent and concatenated trees and most of the species delimitation methods yield considerably higher diversity estimates than the distance based approach and morphology. Molecular data support at least 24 distinct clades within Calliphoridae in this study, recovering substantial geographic variation for Lucilia eximia, Lucilia retroversa, Lucilia rica and Chloroprocta idioidea, probably indicating several cryptic species. In sum, our study demonstrates the importance of employing a second nuclear marker for barcoding analyses and species delimitation of calliphorids, and the power of molecular data in combination with a complete reference database to enable identification of taxonomically and geographically diverse insects of forensic importance.

Seasonal and Geographic Variation in Biodiversity of Forensically Important Blow Flies (Diptera: Calliphoridae) in New Jersey, USA

Determining the time of colonization of human or other animal remains by blow flies (Diptera: Calliphoridae) can play an important role in criminal investigations. However, blow fly presence in a given area is strongly influenced by abiotic and biotic variables such as temperature and habitat. We wanted to assess the biodiversity of adult blow flies in New Jersey, USA, where very little is known about these taxa. Toward that end we collected adult blow flies biweekly from traps baited with bovine liver and placed across three regions in New Jersey over a 2-yr period (2011-2013). We collected and identified 9,257 adult calliphorids, comprising six genera and 12 species. Blow fly assemblages composed of these species varied by season, but community composition did not vary among regions within a given season. Three species, Lucilia coeruleiviridis (Macquart), Lucilia sericata (Meigen), and Phormia regina (Meigen) comprised 88.5% of all adult blow flies collected (42.6, 25.9, 20.0%, respectively). Combining all regions, the dominant species for both spring and summer was L. coeruleiviridis comprising 35.1% of all adults caught in spring and 64.1% in summer. P. regina was the dominant species in fall, totaling 40.1% of all adults caught and Calliphora vicina (Robineau-Desvoidy) was the dominant species for winter, totaling 44.8% of all adults caught. Our findings provide the first assessment of blow fly communities in New Jersey, and these results can be applied to surrounding states where data are severely lacking for forensic application.

Survey of the Genetic Diversity of Forensically Important Chrysomya (Diptera: Calliphoridae) from Egypt

Minimum postmortem interval estimations of a corpse using blow fly larvae in medicolegal investigations require correct identification and the application of appropriate developmental data of the identified fly species. Species identification of forensically relevant blow flies could be very difficult and time consuming when specimens are damaged or in the event of morphologically indistinguishable immature stages, which are most common at crime scenes. In response to this, an alternative, accurate determination of species may depend on sequencing and molecular techniques for identification. Chrysomyinae specimens (n = 158) belonging to three forensically important species [Chrysomya albiceps (Wiedemann), Chrysomya megacephala (F.), and Chrysomya marginalis (Wiedemann)] (Diptera: Calliphoridae) were collected from four locations in Egypt (Giza, Dayrout, Minya, and North Sinai) and sequenced across the mitochondrial cytochrome oxidase subunit I (COI) gene. Phylogenetic analyses using neighbor-joining, maximum likelihood and maximum parsimony methods resulted in the same topological structure and confirmed DNA based identification of all specimens. Interspecific divergence between pairs of species was 5.3% (C. marginalis-C. megacephala), 7% (C. albiceps-C. megacephala), and 8% (C. albiceps-C. marginalis). These divergences are sufficient to confirm the utility of cytochrome oxidase subunit I gene in the molecular identification of these flies in Egypt. Importantly, the maximum intraspecific divergence among individuals within a species was <1% and the least nucleotide divergence between species used for phylogenetic analysis was 3.6%. This study highlights the need for thorough and diverse sampling to capture all of the possible genetic diversity if DNA barcoding is to be used for molecular identification.

New developmental data for Cynomya mortuorum (L., 1761) in Belgium (Diptera: Calliphoridae)

The calliphorid Cynomya mortuorum (L., 1761) is a forensically important species mainly found in the Palearctic region. Knowledge about its biology and ecology is scarce. Thermal constants as well as developmental time were studied at constant and variable regimes of 5 average temperatures: 14, 16, 18, 20 and 22°C, respectively. Total developmental time varied between 15.82±0.40 days at 22°C and 28.67±2.38 days at 14°C, for the constant regime, and between 16.05±0.67 days at 22°C and 32.79±1.77 days at 14°C, for the variable regime. No significant differences were observed between ADD, and threshold at the constant (ADD: 277.39±14.78 DD; lower threshold: 4.72°C) and variable regimes (275.99±14.16 DD; lower threshold: 5.05°C).