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

Grzywacz, Andrzej; Wyborska, Dominika; Piwczyński, Marcin

doi:10.1016/j.forsciint.2017.06.023

Cited by 22 publications

(22 citation statements)

References 57 publications

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“…For both databases, <70% of taxa were correctly assigned at both the genus and species level (Fig 1A). This result was lower than previously reported for flies (Diptera [15,20], beetles (Coleoptera [23]), butterflies and moths (Lepidoptera [24]), when searching against either or both of these databases. Six taxa were classified as being an ambiguous match ( i .…”

Section: Resultscontrasting

confidence: 63%

“…It is also possible that, given approximately 30% of the COI sequences obtained in this study were less than 430 bp, the discriminatory power needed to facilitate species-level identifications may have been diminished (reduced query length often negatively affects the ability to get a good match; S2 Table). Nevertheless, Grywacz and colleagues [20] examined the impact of barcode sequence length on identification success in Diptera. In their study, they applied a best match criteria with SpeciesIdentifier v1.8 using sequences in BOLD and GenBank relating to Dipteran Family (Fannidae), and obtained similar results when using fragments of 650 bp and 130 bp (96% and 94%, respectively).…”

Section: Resultsmentioning

confidence: 99%

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

2019

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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.

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Section: Resultscontrasting

confidence: 63%

Section: Resultsmentioning

confidence: 99%

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

2019

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“…Thus, we decided to complete the sequencing using the 1 × 300 bp conformation to obtain the most amount of data from a single amplicon. While 300 bp is shorter than the average length of most barcode sequences obtained in Meiklejohn et al [20] (297, 532, and 409 bp for COI , matK , and rbcL , respectively), studies encompassing a diverse range of taxa and barcode regions (e.g., COI , fishes, butterflies, wasps, flies, carnivores [49,50,51,52]; rbcL , land plants [48]) have shown that there is limited negative influence on the discrimination power when shorter portions of a barcode region are sequenced.…”

Section: Methodsmentioning

confidence: 96%

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

Boggs¹,

Scheible²,

Machado³

et al. 2019

Genes

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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.

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“…Obtained sequences were identified by comparison to sequences available in the NCBI database (National Center for Biotechnology Information, Bethesda, MD, USA) using the Basic Local Alignment Search Tool (BLAST) and BOLD v4 (Barcode of Life Data Systems) using BOLD Identification System [ 33 ]. All COI barcode sequences available for Fannia , including library of COI reference sequences available for forensically relevant Fanniidae [ 10 ], have been downloaded from BOLD database and supplemented with newly obtained data. DNA sequences were aligned using MAFFT v7 [ 34 ] and visually inspected and trimmed to a 658-bp long barcode fragment in Seaview 4.4.0 [ 35 ].…”

Section: Methodsmentioning

confidence: 99%

“…Under certain circumstances, species of Fanniidae may be utilized as forensic indicators [ 4 , 5 , 8 , 9 ]. However, the broad application of Fanniidae for medico-legal purposes is inhibited by the general difficulty of species identification in this family [ 10 ] and the absence of information linking females and immature stages to the more rigorously studied adult males.…”

Section: Introductionmentioning

confidence: 99%

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

Grzywacz

Jarmusz

Walczak

et al. 2021

Insects

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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.

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

Cited by 22 publications

References 57 publications

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

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

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

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

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