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      The uses of Chrysomya megacephala (Fabricius, 1794) (Diptera: Calliphoridae) in forensic entomology

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          ABSTRACT

          Chrysomya megacephala (Fabricius, 1794) occurs on every continent and is closely associated with carrion and decaying material in human environments. Its abilities to find dead bodies and carry pathogens give it a prominence in human affairs that may involve prosecution or litigation, and therefore forensic entomologists. The identification, geographical distribution and biology of the species are reviewed to provide a background for approaches that four branches of forensic entomology (urban, stored-product, medico-criminal and environmental) might take to investigations involving this fly.

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          DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success.

          Rudolf Meier, Kwong Shiyang, Gaurav Vaidya … (2006)
          DNA barcoding and DNA taxonomy have recently been proposed as solutions to the crisis of taxonomy and received significant attention from scientific journals, grant agencies, natural history museums, and mainstream media. Here, we test two key claims of molecular taxonomy using 1333 mitochondrial COI sequences for 449 species of Diptera. We investigate whether sequences can be used for species identification ("DNA barcoding") and find a relatively low success rate (< 70%) based on tree-based and newly proposed species identification criteria. Misidentifications are due to wide overlap between intra- and interspecific genetic variability, which causes 6.5% of all query sequences to have allospecific or a mixture of allo- and conspecific (3.6%) best-matching barcodes. Even when two COI sequences are identical, there is a 6% chance that they belong to different species. We also find that 21% of all species lack unique barcodes when consensus sequences of all conspecific sequences are used. Lastly, we test whether DNA sequences yield an unambiguous species-level taxonomy when sequence profiles are assembled based on pairwise distance thresholds. We find many sequence triplets for which two of the three pairwise distances remain below the threshold, whereas the third exceeds it; i.e., it is impossible to consistently delimit species based on pairwise distances. Furthermore, for species profiles based on a 3% threshold, only 47% of all profiles are consistent with currently accepted species limits, 20% contain more than one species, and 33% only some sequences from one species; i.e., adopting such a DNA taxonomy would require the redescription of a large proportion of the known species, thus worsening the taxonomic impediment. We conclude with an outlook on the prospects of obtaining complete barcode databases and the future use of DNA sequences in a modern integrative taxonomy.
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            Testing the reliability of genetic methods of species identification via simulation.

            Howard Ross, Sumathi Murugan, Wai Lok Sibon Li (2008)
            Although genetic methods of species identification, especially DNA barcoding, are strongly debated, tests of these methods have been restricted to a few empirical cases for pragmatic reasons. Here we use simulation to test the performance of methods based on sequence comparison (BLAST and genetic distance) and tree topology over a wide range of evolutionary scenarios. Sequences were simulated on a range of gene trees spanning almost three orders of magnitude in tree depth and in coalescent depth; that is, deep or shallow trees with deep or shallow coalescences. When the query's conspecific sequences were included in the reference alignment, the rate of positive identification was related to the degree to which different species were genetically differentiated. The BLAST, distance, and liberal tree-based methods returned higher rates of correct identification than did the strict tree-based requirement that the query was within, but not sister to, a single-species clade. Under this more conservative approach, ambiguous outcomes occurred in inverse proportion to the number of reference sequences per species. When the query's conspecific sequences were not in the reference alignment, only the strict tree-based approach was relatively immune to making false-positive identifications. Thresholds affected the rates at which false-positive identifications were made when the query's species was unrepresented in the reference alignment but did not otherwise influence outcomes. A conservative approach using the strict tree-based method should be used initially in large-scale identification systems, with effort made to maximize sequence sampling within species. Once the genetic variation within a taxonomic group is well characterized and the taxonomy resolved, then the choice of method used should be dictated by considerations of computational efficiency. The requirement for extensive genetic sampling may render these techniques inappropriate in some circumstances.
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              POY version 4: phylogenetic analysis using dynamic homologies

              Andrés Varón, Le Vinh, Ward C Wheeler (2010)
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                Author and article information

                Journal
                Journal ID (nlm-ta): Forensic Sci Res
                Journal ID (iso-abbrev): Forensic Sci Res
                Journal ID (publisher-id): TFSR
                Journal ID (publisher-id): tfsr20
                Title: Forensic sciences research
                Publisher: Taylor & Francis
                ISSN (Print): 2096-1790
                ISSN (Electronic): 2471-1411
                Publication date Collection: 2018
                Publication date (Electronic): 21 March 2018
                Volume: 3
                Issue: 1 , Special Issue on Forensic Entomology
                Pages: 2-15
                Affiliations
                Southern African Forensic Entomology Research Laboratory, Department of Zoology and Entomology, Rhodes University , Grahamstown, South Africa
                Author notes
                Author information
                http://orcid.org/0000-0003-2961-2628
                http://orcid.org/0000-0002-4335-5667
                Article
                Publisher ID: 1426136
                DOI: 10.1080/20961790.2018.1426136
                PMC ID: 6197084
                PubMed ID: 30483647
                SO-VID: 6f4aa095-5e39-4561-ba9b-e4746e91e968
                Copyright © © 2018 The Author(s). Published by Taylor & Francis Group on behalf of the Academy of Forensic Science.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 06 September 2017
                Date accepted : 08 January 2018
                Page count
                Figures: 2, Tables: 3, References: 173, Pages: 14
                Funding
                Funded by: Rhodes University 10.13039/501100001333
                Award ID: 37201
                Rhodes University [grant number 37201].
                Categories
                Subject: Review

                Keywords: forensic sciences,forensic entomology,chrysomya megacephala,morphology,taxonomy,biogeography,life cycle,ecology
                Data availability:
                Keywords: forensic sciences, forensic entomology, chrysomya megacephala, morphology, taxonomy, biogeography, life cycle, ecology

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