Utility of GenBank and the Barcode of Life Data Systems (BOLD) for the identification of forensically important Diptera from Belgium and France

Abstract Fly larvae living on dead corpses can be used to estimate post-mortem intervals. The identification of these flies is decisive in forensic casework and can be facilitated by using DNA barcodes provided that a representative and comprehensive reference library of DNA barcodes is available. We constructed a local (Belgium and France) reference library of 85 sequences of the COI DNA barcode fragment (mitochondrial cytochrome c oxidase subunit I gene), from 16 fly species of forensic interest (Calliphoridae, Muscidae, Fanniidae). This library was then used to evaluate the ability of two public libraries (GenBank and the Barcode of Life Data Systems – BOLD) to identify specimens from Belgian and French forensic cases. The public libraries indeed allow a correct identification of most specimens. Yet, some of the identifications remain ambiguous and some forensically important fly species are not, or insufficiently, represented in the reference libraries. Several search options offered by GenBank and BOLD can be used to further improve the identifications obtained from both libraries using DNA barcodes.

[1]  W. Bass,et al.  Insect Activity and Its Relationship to Decay Rates of Human Cadavers in East Tennessee , 1983 .

[2]  R. Cruickshank,et al.  The seven deadly sins of DNA barcoding , 2012, Molecular ecology resources.

[3]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[4]  Gaurav Vaidya,et al.  DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. , 2006, Systematic biology.

[5]  W R Mayr,et al.  ISFG: recommendations regarding the use of non-human (animal) DNA in forensic genetic investigations. , 2011, Forensic science international. Genetics.

[6]  Bruno Nevado,et al.  Comparative performances of DNA barcoding across insect orders , 2010, BMC Bioinformatics.

[7]  Carlo P. Campobasso,et al.  Best practice in forensic entomology—standards and guidelines , 2007, International Journal of Legal Medicine.

[8]  L. Boykin,et al.  Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification , 2012 .

[9]  T. Pape,et al.  DNA-based identification and molecular systematics of forensically important Sarcophagidae (Diptera). , 2001, Journal of forensic sciences.

[10]  Jifeng Cai,et al.  Identification of Forensically Important Sarcophagid Flies (Diptera: Sarcophagidae) in China, Based on COI and 16S rDNA Gene Sequences * , 2011, Journal of forensic sciences.

[11]  M. C. Espósito,et al.  Molecular phylogenetics of Oestroidea (Diptera: Calyptratae) with emphasis on Calliphoridae: insights into the inter-familial relationships and additional evidence for paraphyly among blowflies. , 2012, Molecular phylogenetics and evolution.

[12]  A. Lambert,et al.  ABGD, Automatic Barcode Gap Discovery for primary species delimitation , 2012, Molecular ecology.

[13]  A. Gunn,et al.  The ability of the blowflies Calliphora vomitoria (Linnaeus), Calliphora vicina (Rob-Desvoidy) and Lucilia sericata (Meigen) (Diptera: Calliphoridae) and the muscid flies Muscina stabulans (Fallén) and Muscina prolapsa (Harris) (Diptera: Muscidae) to colonise buried remains. , 2011, Forensic science international.

[14]  M. I. Marchenko Medicolegal relevance of cadaver entomofauna for the determination of the time of death. , 2001, Forensic science international.

[15]  Brian K. Schmidt,et al.  Project Description: DNA Barcodes of Bird Species in the National Museum of Natural History, Smithsonian Institution, USA , 2011, ZooKeys.

[16]  Xue-xin Chen,et al.  Utility of Multi-Gene Loci for Forensic Species Diagnosis of Blowflies , 2011, Journal of insect science.

[17]  T. Pape,et al.  The Muscoidea (Diptera: Calyptratae) are paraphyletic: Evidence from four mitochondrial and four nuclear genes. , 2008, Molecular phylogenetics and evolution.

[18]  R. Zehner,et al.  The use of COI barcodes for molecular identification of forensically important fly species in Germany , 2011, Parasitology Research.

[19]  D. Janzen,et al.  When species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths , 2011, BMC Ecology.

[20]  S. Adamowicz,et al.  DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits , 2012, BMC Ecology.

[21]  N. Baeshen,et al.  Biological Identifications Through DNA Barcodes , 2012 .

[22]  Ana Rita Oliveira,et al.  Identification of sarcosaprophagous Diptera species through DNA barcoding in wildlife forensics. , 2013, Forensic science international.

[23]  D. Charabidze,et al.  La biologie des insectes nécrophages et leur utilisation pour dater le décès en entomologie médico-légale , 2012 .

[24]  S. Gaudieri,et al.  Mitochondrial DNA cytochrome oxidase I gene: potential for distinction between immature stages of some forensically important fly species (Diptera) in western Australia. , 2003, Forensic science international.

[25]  S. Ferrara,et al.  Use of Lucilia species for forensic investigations in Southern Europe. , 2008, Forensic science international.

[26]  J. Vian,et al.  Partial sequencing of the cytochrome oxydase b subunit gene I: a tool for the identification of European species of blow flies for postmortem interval estimation. , 2000, Journal of forensic sciences.

[27]  T. Backeljau,et al.  Identifying Insects with Incomplete DNA Barcode Libraries, African Fruit Flies (Diptera: Tephritidae) as a Test Case , 2012, PloS one.

[28]  C. Reiter,et al.  Effect of temperature on development of Liopygia (= Sarcophaga) argyrostoma (Robineau-Desvoidy) (Diptera: Sarcophagidae) and its forensic implications. , 2002, Journal of forensic sciences.

[29]  S. Donnellan,et al.  The utility of mitochondrial DNA sequences for the identification of forensically important blowflies (Diptera: Calliphoridae) in southeastern Australia. , 2001, Forensic science international.

[30]  F. Pereira,et al.  A Guide for Mitochondrial DNA Analysis in Non-Human Forensic Investigations , 2012 .

[31]  Alejandro A. Schäffer,et al.  Database indexing for production MegaBLAST searches , 2008, Bioinform..

[32]  W. Xinghua,et al.  The availability of 16SrDNA gene for identifying forensically important blowflies in China , 2010 .

[33]  M. Kimura A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[34]  J. Stevens,et al.  Application of DNA-based methods in forensic entomology. , 2008, Annual review of entomology.

[35]  S. Gaudieri,et al.  A global study of forensically significant calliphorids: implications for identification. , 2008, Forensic science international.

[36]  J D Wells,et al.  A DNA-based approach to the identification of insect species used for postmortem interval estimation and partial sequencing of the cytochrome oxydase b subunit gene I: a tool for the identification of European species of blow flies for postmortem interval estimation. , 2000, Journal of forensic sciences.

[37]  J. Vaňhara,et al.  The Muscidae (Diptera) of Central Europe , 2002 .

[38]  F. Sperling,et al.  A DNA-based approach to the identification of insect species used for postmortem interval estimation. , 1994, Journal of forensic sciences.

[39]  Lukas Wagner,et al.  A Greedy Algorithm for Aligning DNA Sequences , 2000, J. Comput. Biol..

[40]  R. Coquoz,et al.  DNA typing for identification of some species of Calliphoridae. An interest in forensic entomology. , 1999, Forensic science international.

[41]  A. Tagliabracci,et al.  DNA degradation and genetic analysis of empty puparia: genetic identification limits in forensic entomology. , 2010, Forensic science international.

[42]  Filipe Pereira,et al.  A Guide for Mitochondrial DNA Analysis in Non-Human Forensic Investigations~!2010-01-07~!2010-04-02~!2010-05-17~! , 2010 .

[43]  Jan Sauer,et al.  Genetic identification of forensically important flesh flies (Diptera: Sarcophagidae) , 2004, International Journal of Legal Medicine.

[44]  Jifeng Cai,et al.  Identification of forensically significant calliphorids based on mitochondrial DNA cytochrome oxidase I (COI) gene in China. , 2011, Forensic science international.

[45]  M. Dowton,et al.  DNA-based identification of forensically important Australian Sarcophagidae (Diptera) , 2009, International Journal of Legal Medicine.

[46]  S. Desmyter,et al.  COI sequence variability between Chrysomyinae of forensic interest. , 2009, Forensic science international. Genetics.

[47]  A. Martínez-Sánchez,et al.  Larval morphology, development and forensic importance of Synthesiomyia nudiseta (Diptera: Muscidae) in Europe: a rare species or just overlooked? , 2012, Bulletin of Entomological Research.

[48]  J. Stevens,et al.  Paraphyly in Hawaiian hybrid blowfly populations and the evolutionary history of anthropophilic species , 2002, Insect molecular biology.

[49]  J. Wells,et al.  Validation of a DNA-based method for identifying Chrysomyinae (Diptera: Calliphoridae) used in a death investigation , 2006, International Journal of Legal Medicine.

[50]  G. Sonet,et al.  Why is the molecular identification of the forensically important blowfly species Lucilia caesar and L. illustris (family Calliphoridae) so problematic? , 2012, Forensic science international.

[51]  M. Pancorbo,et al.  DNA typing of Diptera collected from human corpses in Portugal. , 2009, Forensic science international.

[52]  M. Gouy,et al.  Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation. , 2006, Molecular phylogenetics and evolution.

[53]  G. Sonet,et al.  Identification of forensically important Sarcophaga species (Diptera: Sarcophagidae) using the mitochondrial COI gene , 2013, International Journal of Legal Medicine.

[54]  J. Stevens,et al.  Phylogenetic analysis of forensically important Lucilia flies based on cytochrome oxidase I sequence: a cautionary tale for forensic species determination , 2007, International Journal of Legal Medicine.

[55]  Michael Balke,et al.  The Effect of Geographical Scale of Sampling on DNA Barcoding , 2012, Systematic biology.

[56]  H. Magalon,et al.  DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae) , 2007, Proceedings of the Royal Society B: Biological Sciences.

[57]  M. Haase,et al.  Pitfalls in comparisons of genetic distances: a case study of the avian family Acrocephalidae. , 2012, Molecular phylogenetics and evolution.

[58]  M. Dowton,et al.  DNA Barcoding Identifies all Immature Life Stages of a Forensically Important Flesh Fly (Diptera: Sarcophagidae) , 2013, Journal of forensic sciences.

[59]  F. Sperling,et al.  DNA-based identification of forensically important Chrysomyinae (Diptera: Calliphoridae). , 2001, Forensic science international.

[60]  M. Nei,et al.  MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. , 2011, Molecular biology and evolution.

[61]  A. Serrano,et al.  Carrion flies of forensic interest: a study of seasonal community composition and succession in Lisbon, Portugal , 2012, Medical and veterinary entomology.

[62]  P. Hebert,et al.  bold: The Barcode of Life Data System (http://www.barcodinglife.org) , 2007, Molecular ecology notes.

[63]  Rob Ogden,et al.  Validation of the barcoding gene COI for use in forensic genetic species identification. , 2007, Forensic science international.

[64]  Chung Hyun Park,et al.  Using the Developmental Gene Bicoid to Identify Species of Forensically Important Blowflies (Diptera: Calliphoridae) , 2013, BioMed research international.

[65]  Jifeng Cai,et al.  The availability of 16S rRNA for the identification of forensically important flies (Diptera: Muscidae) in China. , 2010, Tropical biomedicine.

[66]  Emmanuel Paradis,et al.  pegas: an R package for population genetics with an integrated-modular approach , 2010, Bioinform..

[67]  X. Wang,et al.  Identification of the forensically important sarcophagid flies Boerttcherisca peregrina, Parasarcophaga albiceps and Parasarcophaga dux (Diptera: Sarcophagidae) based on COII gene in China. , 2010, Tropical biomedicine.

[68]  M. Villet,et al.  Models of development for blowfly sister species Chrysomya chloropyga and Chrysomya putoria , 2009, Medical and veterinary entomology.

[69]  F. Sperling,et al.  Molecular phylogeny of Chrysomya albiceps and C. rufifacies (Diptera: Calliphoridae). , 1999, Journal of medical entomology.

[70]  I. Joseph,et al.  The use of insects in forensic investigations: An overview on the scope of forensic entomology , 2011, Journal of forensic dental sciences.