DNA-based identification and molecular systematics of forensically important Sarcophagidae (Diptera)

Sarcophagid flies have many characteristics that make them ideal forensic indicators. However, their utility is severely limited because it is difficult or impossible to determine the species of a sarcophagid larva, and in many instances an adult specimen, based on anatomy. We developed a database of mitochondrial DNA sequence data that makes it possible to identify all sarcophagid species likely to be found feeding on a human corpse at an urban location in Canada or the USA. Analyses were based on a 783 base pair region of the gene for cytochrome oxidase subunit one (COI). The species analyzed, including some of no forensic importance that were included for purposes of phylogenetic comparisons, were members of the genera Sarcophaga, Peckia, Blaesoxipha, Rovinia, Wohlfahrtia, Brachicoma (all Sarcophagidae), and Musca (Muscidae).     

Differential Ability of Necrophagous Diptera to Colonize Concealed Resources: Empirical Evidence From a Field Experiment in Brazil

Field studies in forensic entomology seem to assume that a cadaver is a resource equally accessible to flies, irrespective of the species’ size, behavior, and sensorial capacity. We aimed to challenge this assumption by experimentally manipulating baited traps in order to test whether the accessibility to decomposing baits is related to the following: (i) the diversity of necrophagous dipterans; (ii) the body size of adults; and (iii) the female sexual maturity stage. The experiment was performed in a rainforest fragment in Northeastern Brazil, in an area characterized by high levels of homicides. Traps baited with decomposing chicken liver had three levels of access: easy (six openings on the trap), intermediate (three), and difficult (one). A total of 750 adults of Calliphoridae, Fanniidae, Muscidae, Phoridae, and Sarcophagidae were collected. Of the 18 species recorded, Megaselia scalaris was the most abundant (46.8%) followed by Lucilia eximia (29.7%) and Chrysomya megacephala (9.8%). The number of species increased significantly with the accessibility level, but overall abundance did not differ, as a consequence of the numerical dominance of M. scalaris. A strong female bias (>91%) was observed in all traps. For Calliphoridae specimens, 90% of the females caught in traps under intermediate and difficult access were sexually mature. By empirically demonstrating that limitation of access and exclusion of visual stimuli do not deter several dipteran species from reaching a substrate, we expand the knowledge on the factors that can shape the colonization of concealed human cadavers, including variables such as insect size and stage of sexual maturity.     

Post-mortem interval estimation based on insect evidence in a quasi-indoor habitat

Insects collected on indoor cadavers are frequently used for post-mortem interval (PMI) estimation. Buildings encountered during crime investigations vary according to temperatures inside, the extent of insect access restriction or sanitary conditions. This article reports the PMI oriented analyses of insect evidence sampled from the human cadaver in the atypical indoor habitat. The body was found in the uninhabited house, on the floor covered with rubbish, in the room with no doors and windows. Thermal conditions in the room were less variable than in the local weather station, however still much more variable compared to the typical indoor habitat, indicating the need for retrospective correction of temperature records from the station. Cadaver entomofauna was surprisingly diverse and abundant. We recorded several taxa usually not occurring on indoor cadavers, e.g. immature stages of Necrodes littoralis (Coleoptera: Silphidae) or Stearibia nigriceps (Diptera: Piophilidae). PMI was based on the age and the pre-appearance interval estimated for live puparium of S. nigriceps, giving the total interval of 37 (±7.4) days plus 4–20?days resulting from the absence of first colonizing specimens of the species. This estimate was corroborated with the age estimate for empty puparia of Sarcophaga argyrostoma (Diptera: Sarcophagidae) with traces of Nasonia sp. (Hymenoptera: Pteromalidae) eclosion. Other insects indicated shorter but consistent PMI. Difficulties and limitations of insect-based PMI estimations in unusual indoor habitats are discussed.     

First Report of Blaesoxipha plinthopyga (Diptera: Sarcophagidae) from a Human Corpse in the U.S.A. and a New State Geographic Record Based on Specimen Genotype

Carrion flies in the taxonomic family Sarcophagidae are often recovered from a human corpse. However, because such specimens are difficult to identify, the forensic literature on this taxon is quite limited compared with that of the commonly employed Calliphoridae. Faced with a sarcophagid larva that could not be identified microscopically from a death investigation in the state of Idaho, we generated cytochrome oxidase one DNA sequence data from the specimen. Comparison to a reference data set of forensically significant sarcophagids from Canada and the U.S.A. confirmed that this was the first discovery of Blaesoxipha plinthopyga in a human corpse in the U.S.A. and the first record of this species in Idaho. Because B. plinthopyga occurs from the Northern U.S.A. to the Neotropics, it is potentially useful for estimating time since death at many locations.     

Insect fauna visiting carrion in Southwest Virginia

Successional patterns of insect fauna on pig carcasses were studied in southwest Virginia. The objective was to identify and qualitatively assess the major taxa of forensic importance in this region. Studies were conducted in spring and summer 2001 and 2002, and fall 2002. Over 50 taxa were collected and identified. Phormia regina was the dominant fly species in the spring (>90%) and co-dominant with Phaenicia coeruleiviridis in the summer. Phaenicia sericata, Lucilia illustris, and Calliphora spp. were collected in spring and summer, but less frequently. Eleven species of Sarcophagidae also were collected with Sarcophaga utilis and Helicobia rapax the most common. In the fall, the dominant fly species were Calliphora vomitoria, L. illustris, and P. coeruleiviridis. The primary beetle species collected in spring and summer included three Staphylinidae (Creophilis maxillosus, Platydracus maculosus, and Aleochara lata) and three Silphidae (Oiceoptoma noveboracense, Necrodes surinamensis, and Necrophila americana). No beetles were collected in the fall.     

洛阳地区5种嗜尸性麻蝇分子鉴定研究

目的应用经典DNA条形码和28S r RNA基因鉴定洛阳地区5种常见嗜尸性麻蝇种属,评价其在常见嗜尸性麻蝇种属鉴定中应用的可行性。方法收集洛阳地区常见嗜尸性麻蝇类标本18只,经形态学分类鉴定后,Chelex-100法提取足部DNA,扩增并测序线粒体细胞色素C氧化酶亚基I(COI)和28S核糖体核糖核酸(28S r RNA)基因片段,BLAST比对后,与来自DNA条形码数据库(Barcode of Life Data,BOLD)的中国和韩国地区20条相应蝇种序列进行比对,用MEGA 7.0软件整理分析所得序列,计算碱基组成、种内及种间进化分歧率,并构建系统发育树。结果形态学鉴定18只嗜尸性麻蝇归于3属5种。每个样本获得COI和28S r RNA的扩增长度分别为646bp和721bp。在线BLAST比对结果显示样本COI序列相似度99%以上,邻近法构建发育树Bootstrap值为1 000,5种麻蝇可以较好聚类,与形态学鉴定结果一致。38个样本COI种内范围为0~0.022,棕尾别麻蝇、酱亚麻蝇和急钩(亚)麻蝇种间范围在0.057~0.090;赤尾麻蝇和红尾粪麻蝇种间范围在0~0.086。5种麻蝇的28S r RNA序列发育树显示,棕尾别麻蝇和急钩(亚)麻蝇明显各自聚类,其余3种成一类。结论对于本研究中的5种嗜尸性麻蝇,基于COI基因的DNA条形码可以有效区分棕尾别麻蝇、酱亚麻蝇和急钩(亚)麻蝇,28S r RNA基因只可以区分棕尾别麻蝇,二者可作为形态学鉴定之外的重要方法补充。     

DNA Barcoding Identifies all Immature Life Stages of a Forensically Important Flesh Fly (Diptera: Sarcophagidae)

Carrion‐breeding insects, such as flesh flies (Diptera: Sarcophagidae), can be used as evidence in forensic investigations. Despite their considerable forensic potential, their use has been limited because morphological species identification, at any life stage, is very challenging. This study investigated whether DNA could be extracted and cytochrome oxidase subunit I (COI) barcode sequences obtained for molecular identification of each immature life stage of the forensically important Australian flesh fly, Sarcophaga (Sarcorohdendorfia) impatiens (Walker). Genomic DNA extracts were prepared from all larval instars and puparia. Amplification of the barcoding region was successful from all extracts, but puparia amplicons were weak. All sequences were identified as S. impatiens with 99.95% confidence using the Barcoding of Life Database (BOLD). Importantly, crop removal was necessary to eliminate PCR inhibition for specimens from late second and early third instars. Similar results are expected for immatures of other carrion‐breeding species, enhancing the use of evidence from immature flies in forensic investigations.     

Seasonality of insect succession and pig carcass decomposition in a natural forest area in southeastern Brazil

In this study, successional patterns, relative abundance of larvae and adults of sarcosaprophagous insects, carcass decay, diversity and seasonality of species, and their potential as forensic indicators were studied. Four experiments were carried out in each season in a natural area of southeastern Brazil. Two pigs (Sus scrofa L.) were used in each experiment and were exposed to sunlight and shade, respectively. The Calliphoridae outnumbered the Sarcophagidae in specimens collected and reared from the carcasses. More insects were collected from carcasses exposed to the sun, while a larger number of specimens were reared from those in the shade. Temperature and rainfall influenced the stages of carcass decay and insect activity and abundance. Chrysomya albiceps was the most abundant species in all four experiments. The carcasses were used as a protein source and substratum for oviposition. The dark putrefaction and fermentation stages yielded more flies than the other stages. These results show that flies are important in carcass decay and are, therefore, also of forensic importance. Seven species can be considered valuable forensic indicators in Southeastern Brazil. However, only three species were useful as forensic indicators in wooded areas: P. intermutans, H. segmentaria, and H. semidiaphana.     

Some notes on the nocturnal larviposition by two species of Sarcophaga (Diptera: Sarcophagidae)

Experiments in the month of September 2005 were performed to study nocturnal larviposition by the flesh flies (Diptera: Sarcophagidae). Two species namely Sarcophaga albiceps Meigen and Sarcophaga hirtipes Wiedemann were observed to deposit their larvae during night time as well. Therefore, possibility of night larviposition by flesh flies should always be taken into consideration while determining age of maggots.     

A Preliminary Forensic Entomological Study of Beetles (Coleoptera) in Interior Alaska,USA*

Forensic entomology uses knowledge of arthropod ecology to help solve crimes. There has been no published forensic entomological research in Alaska. We used one piglet carcass split in half to create two carcass plots in Fairbanks (~64.8°N, subarctic) that were sampled over a period of 59 days in 2019. Four pitfall traps were placed around each carcass, and four similarly arranged pitfall traps were placed 40 m distant as controls. Traps were emptied approximately weekly covering the first four stages of decomposition. We focused on adults of the larger-bodied (>9 mm) families and subfamilies of Coleoptera: Staphylinidae (subfamily Staphylininae), Carabidae, and Silphidae. A total of 621 specimens were collected and processed: 29 staphylinines, 210 carabids, and 382 silphids. A one-way ANOVA showed no significant difference between the mean numbers of staphylinines or carabids caught in carcass versus control traps. Silphids showed significantly greater mean number of beetles caught in carcass traps relative to control traps. Four species of Silphidae were documented, but contrary to similar studies, the vast majority of specimens belonged to two species of Nicrophorus (N. vespilloides Herbst and N. investigator Zetterstedt). Each of the three target taxa showed a peak in the number of specimens collected during the bloat stage of decomposition despite the carabid peak being driven by a phytophagous species.     

DNA-based identification of forensically important Chrysomyinae (Diptera: Calliphoridae).

Identifying an insect specimen is an important first step in a forensic-entomological analysis. However, diagnostic morphological criteria are lacking for many species and life stages. We demonstrate a method for using mitochondrial DNA sequence data and phylogenetic analysis to identify any specimen of the blow fly subfamily Chrysomyinae likely to be collected from a human corpse within Canada or the USA. The reliability of the method was illustrated by analyzing specimens designed to mimic the information likely to be obtained from highly degraded specimens as well as specimens collected from widely separated geographic locations. Our sequence database may be suitable for another country provided the investigator knows the local fly fauna well enough to narrow the choice of chrysomyine species to those used in this study.     

Use of Lucilia species for forensic investigations in Southern Europe

The aim of this study was to highlight the importance of evaluating entomological evidence in forensic investigations on a regional scale. To evaluate climatic, geographical and environmental influences on the selection of carrion-breeding fauna in Northern Italy and consequently on inferred forensic data (post-mortem intervals and post-mortem transfer), we present details of six indoor-outdoor cases. Results show that the most abundant species was Lucilia sericata, together with other fly species of entomo-forensic interest, belonging to the Calliphoridae and Sarcophagidae families. In particular, for the first time in Italy, we report finding Phormia regina, Lucilia ampullacea, Lucilia caesar and Sarcophaga (Pandelleana) protuberans on fresh cadavers. The active period of L. sericata in Northern Italy, according to previous findings in Southern Europe, revealing clearcut differences with phenologies in Northern Europe, has important consequences in estimating the period (season, months) of death in cases of long post-mortem intervals (several months or years) if empty puparia of this fly are found. According to our results, the distribution of L. sericata in areas with urban sprawl, like Northern Italian regions, cannot be used to evaluate post-mortem transfer from an urban area to a rural one.     

Identification of a corpse using autosomal and gonosomal STR markers

The identification of unidentified corpses poses an exceptional challenge in the field of forensic medicine, because visual traits are often unspecific. Forensic genetics offer a reliable means to determine the identity of a corpse unambiguously. In the process, Y and X chromosomal markers play an important role. Here, we report about a case out of the ordinary where a corpse was properly identified using forensic genetic methods.     

Mitochondrial DNA cytochrome oxidase I gene: potential for distinction between immature stages of some forensically important fly species (Diptera) in western Australia

Forensic entomology requires the fast and accurate identification of insects collected from a corpse for estimation of the postmortem interval (PMI). Identification of specimens is traditionally performed using morphological features of the insect. Morphological identification may be complicated however by the numerical diversity of species and physical similarity between different species, particularly in immature stages. In this study, sequencing was performed to study the mitochondrial DNA (mtDNA) as the prospective basis of a diagnostic technique. The sequencing focused on a section of the cytochrome oxidase I encoding region of mtDNA. Three species of calliphorid (blow flies) commonly associated with corpses in western Australia, Calliphora dubia, Chrysomya rufifacies and Lucilia sericata, in addition to specimens of Calliphora augur and Chrysomya megacephala were studied. Phylogenetic analysis of data revealed grouping of species according to genus. The DNA region sequenced allowed identification of all species, providing high support for separation on congeneric species. Low levels of variation between some species of the same genus however indicate that further sequencing is required to locate a region for development of a molecular-based technique for identification.     

PCR-RFLP identification of Diptera (Calliphoridae,Muscidae and Sarcophagidae)--a generally applicable method

A simple, rapid method using restriction fragment length polymorphisms (RFLPs) within the internal transcribed spacer (ITS) regions of the ribosomal DNA gene repeat allows identification of insects and other organisms. We used the method to identify the morphologically similar Diptera larvae that are important in forensic entomology for estimating the time and location of death. Polymerase chain reaction (PCR) was used to amplify a region from the 18S to the 28S rRNA genes. The ITS1 and ITS2 regions provided variation between species and homogeneity within species, with the exception of Cochliomya macellaria. Combinations of the restriction enzymes DdeI, HinfI and Sau3AI provided diagnostic bands for identification of the ten species from three families of Diptera (Calliphoridae, Muscidae and Sarcophagidae).     

STR and SNP analysis of human DNA from Lucilia sericata larvae's gut contents

Importance of forensic entomology becomes inevitable when come across some incident where corpse is unidentifiable and lot of maggots or other insects are present. The most common application of forensic entomology is to use insects for the identification of specimens or human remains. DNA analysis recovered from a larva's gut contents can be used to identify a missing body. The obtained human STR and SNP profile support the association of a maggot to a specific patients or corpse. Main aim of this research was the identification of human DNA from gut contents of third instar maggots (larvae of Lucilia sericata) placed on diabetic patient's wounds for treatment purpose. Maggots (8–15) were taken from each diabetic patients (no. of the patients 8) and DNA was extracted from the gut contents manually by using Qiagen tissue protocol. Agarose gel electrophoresis was performed and the total size of DNA was seen using UV transilluminator. PCR amplification, STRs and SNPs profiling was then performed using PCR 9700 and AmpFLSTR Identifiler and SnaPshot Multiplex Kit (Applied Biosystems) respectively. The results were analyzed on ABI 310. SNP profiles were good and identifiable compared to the STRs where amplification was poor and the peaks were low. This may be the fact of the enzymatic activity present in the gut of the larvae which cause tremendous reduction in DNA size and thus yield. The results of this study reveals that it is possible to obtain a complete human profile using STRs and SNPs even if DNA is recovered from gut contents of maggots.     

Identification of forensically important sarcophagid flies (Diptera: Sarcophagidae) in China, based on COI and 16S rDNA gene sequences

Insects attracted to cadavers may provide important indications of the postmortem interval (PMI). However, use of the flesh flies (Diptera: Sarcophagidae) for PMI estimation is limited as the species are often not morphologically distinct, especially as immatures. In this study, 23 forensically important flesh flies were collected from 13 locations in 10 Chinese provinces. Then, a 278-bp segment of the cytochrome oxidase subunits one (COI) gene and a 289-bp segment of the 16S rDNA gene of all specimens were successfully sequenced. Phylogenetic analysis of the sequenced segments showed that all sarcophagid specimens were properly assigned into four species (Boerttcherisca peregrina [Robineau-Desvoidy, 1830], Helicophagella melanura [Meigen, 1826], Parasarcophaga albiceps [Meigen, 1826], and Parasarcophaga dux [Thompson, 1869]) with relatively strong supporting values, thus indicating that the COI and 16S rDNA regions are suitable for identification of sarcophagid species. The difference between intraspecific threshold and interspecific divergence confirmed the potential of the two regions for sarcophagid species identification.     

Shells and Bones: A Forensic Medicine Study of the Association of Terrestrial Snail Allopeas micra with Buried Human Remains in Brazil

Little is known regarding the scavenger fauna associated with buried human corpses, particularly in clandestine burials. We report the presence of 20 shells of the terrestrial snail Allopeas micra, within hollow bones of human remains buried for 5 years, during the process of collecting DNA material. The fact that a large number of shells of A. micra had been found in the corpse and in the crime scene supports the assumption that there was no attempt to remove the corpse from the area where the crime occurred. Despite this, our observations cannot be used to estimate the postmortem interval because there is no precise knowledge about the development of this species. This is the first record of a terrestrial snail associated with a human corpse and its role in this forensic medicine case.     

Application of HRM-PCR (high resolution melting PCR) for identification of forensically important Coleoptera species

Precise estimation time of death is one of key task of forensic entomology. Especially interesting is Coleofauna present at all stages of cadaver decomposition. The morphological identification of Coleoptera species from varying life stages to species level is time-consuming and needs highly qualified entomologists. Among different molecular methods of species identification very promising is high-resolution melting PCR. It allows fast single-tube assignment of analyzed sample to species based on amplicon melting profile. The object of this study were different specimens of Coleoptera collected at pig cadavers in Łomna (central Poland) during 2012 - 2014. Specimes were identified to species by experts of corresponding Coleoptera families. From 120 collected specimens belonging to four families and twelve species HRM-PCR correctly identified specimens belonging to three families and eight species.     

Validation of cytochrome b sequence analysis as a method of species identification

One of the stages of dealing with biological material submitted to forensic laboratories is species identification. The aim of the present work was to validate and assess the possibility of applying sequence analysis of the region coding cytochrome b as a method of species identification in the field of forensic science. DNA originating from individuals from major phyla of vertebrates was isolated by the organic method from various specimens. Extracted DNA was subjected to PCR and direct cycle sequencing using a universal pair of primers. The validation process, performed according to TWGDAM recommendations, revealed that the technique is a very sensitive and reliable method of species identification allowing analysis of tiny amounts of material and also degraded material, and can be useful in the field of forensic genetics. The case example presented here, concerning the determination of species origin of biological evidence collected from fatal road accident, confirms that analysis can be carried out even when there is no reference sample, and the sequences obtained can be assessed through analysis of their similarity to sequences for cytochrome b present in DNA databases.