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Amat E, Gómez GF, López-Rubio A, Gómez-Piñerez LM, Albertino Rafael J. A short fragment of mitochondrial DNA for the taxonomic identification of blow flies (Diptera: Calliphoridae) in northwestern South America. JOURNAL OF MEDICAL ENTOMOLOGY 2023; 60:931-943. [PMID: 37467349 DOI: 10.1093/jme/tjad092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/08/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023]
Abstract
Blow flies are of medical, sanitary, veterinary, and forensic importance. Their accurate taxonomic identification is essential for their use in applied research. However, neotropical fauna has not been completely studied or described, and taxa identification without the required training is a difficult task. Additionally, the current morphological keys are not fitting to all extant taxa. Molecular-based approaches are widely used to overcome these issues, including the standard 5' COI barcode fragment (~650 base pairs [bp]) for identification at the species level. Here, a shorter sequence of 5' COI fragment (~342 bp) was assessed for the identification of 28 blow fly species inhabiting the northwest of South America. One tree-based (the generalized mixed Yule-coalescent-GMYC) and 3 distance-based approaches (automatic barcode gap discover - ABGD, the best close match - BCM, and the nearest neighbor - NN) analyses were performed. Noticeably, the amplification and sequencing of samples that had been preserved for up to 57 years were successful. The tree topology assigned 113 sequences to a specific taxon (70% effectiveness), while the distance approach assigned to 95 (59% effectiveness). The short fragment allowed the molecular identification of 19 species (60% of neotropical species except for the Lucilia species and Hemilucilia semidiaphana). According to these findings, the taxonomic and faunistic considerations of the blow fly fauna were provided. Overall, the short fragment approach constitutes an optimal species confirmation tool for the most common blow flies in northwestern South America.
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Affiliation(s)
- Eduardo Amat
- Grupo Bioforense, Facultad de Derecho y Ciencias Forenses, Tecnológico de Antioquia, Institución Universitaria, Calle 78B No. 72A-220, Medellín, Colombia
- Programa de Pós-graduação em Entomologia - Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, INPA, Manaus, Amazonas, Brazil
| | - Giovan F Gómez
- Grupo Bioforense, Facultad de Derecho y Ciencias Forenses, Tecnológico de Antioquia, Institución Universitaria, Calle 78B No. 72A-220, Medellín, Colombia
- Dirección Académica, Escuela de Pregrados, Universidad Nacional de Colombia Sede de La Paz, La Paz, Cesar, Colombia
| | - Andrés López-Rubio
- Grupo Bioforense, Facultad de Derecho y Ciencias Forenses, Tecnológico de Antioquia, Institución Universitaria, Calle 78B No. 72A-220, Medellín, Colombia
| | - Luz M Gómez-Piñerez
- Grupo Bioforense, Facultad de Derecho y Ciencias Forenses, Tecnológico de Antioquia, Institución Universitaria, Calle 78B No. 72A-220, Medellín, Colombia
| | - Jose Albertino Rafael
- Programa de Pós-graduação em Entomologia - Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, INPA, Manaus, Amazonas, Brazil
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Koroiva R, Santana DJ. Evaluation of partial 12S rRNA, 16S rRNA, COI and Cytb gene sequence datasets for potential single DNA barcode for hylids (Anura: Hylidae). AN ACAD BRAS CIENC 2022; 94:e20200825. [PMID: 36477987 DOI: 10.1590/0001-3765202220200825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 05/19/2021] [Indexed: 12/09/2022] Open
Abstract
We evaluated the extent of intraspecific and interspecific genetic distances and the effectiveness of predefined threshold values using the main genes for estimates of biodiversity and specimens' identification in anurans. Partial sequences of the mitochondrial genes for small (12S) and large (16S) ribosomal subunits, cytochrome c oxidase subunit I (COI) and Cytochrome b (Cytb) of the family Hylidae were downloaded from GenBank and curated for length, coverage, and potential contaminations. We performed analyses for all sequences of each gene and the same species present in these datasets by distance and tree (monophyly)-based evaluations. We also evaluated the ability to identify specimens using these datasets applying "nearest neighbor" (NN), "best close match" (BCM) and "BOLD ID" tests. Genetic distance thresholds were generated by the function 'threshVal' and "localMinima" from SPIDER package and traditional threshold values (1%, 3%, 6% and 10%) were also evaluated. Coding genes, especially COI, had a better identification capacity than non-coding genes on barcoding gap and monophyly analysis and NN, BCM, BOLD ID tests. Considering the multiple factors involved in global DNA barcoding evaluations, we present a critical assessment of the use of these genes for biodiversity estimation and specimens' identification in anurans (e.g. hylids).
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Affiliation(s)
- Ricardo Koroiva
- Universidade Federal da Paraíba, Departamento de Sistemática e Tecnologia, Centro de Ciências Exatas e da Natureza, Laboratório Multiusuário do Programa de Pós-Graduação em Ciências Biológicas/Zoologia, Castelo Branco, Campus Universitário, s/n, 58051900 João Pessoa, PB, Brazil.,Universidade Federal de Mato Grosso do Sul, Instituto de Biociências, Laboratório Mapinguari, Cidade Universitária, Avenida Costa e Silva, s/n, 79070900 Campo Grande, MS, Brazil
| | - Diego José Santana
- Universidade Federal de Mato Grosso do Sul, Instituto de Biociências, Laboratório Mapinguari, Cidade Universitária, Avenida Costa e Silva, s/n, 79070900 Campo Grande, MS, Brazil
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Khang TF, Mohd Puaad NAD, Teh SH, Mohamed Z. Random forests for predicting species identity of forensically important blow flies (Diptera: Calliphoridae) and flesh flies (Diptera: Sarcophagidae) using geometric morphometric data: Proof of concept. J Forensic Sci 2021; 66:960-970. [PMID: 33438785 DOI: 10.1111/1556-4029.14655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 11/26/2022]
Abstract
Wing shape variation has been shown to be useful for delineating forensically important fly species in two Diptera families: Calliphoridae and Sarcophagidae. Compared to DNA-based identification, the cost of geometric morphometric data acquisition and analysis is relatively much lower because the tools required are basic, and stable softwares are available. However, to date, an explicit demonstration of using wing geometric morphometric data for species identity prediction in these two families remains lacking. Here, geometric morphometric data from 19 homologous landmarks on the left wing of males from seven species of Calliphoridae (n = 55), and eight species of Sarcophagidae (n = 40) were obtained and processed using Generalized Procrustes Analysis. Allometric effect was removed by regressing centroid size (in log10 ) against the Procrustes coordinates. Subsequently, principal component analysis of the allometry-adjusted Procrustes variables was done, with the first 15 principal components used to train a random forests model for species prediction. Using a real test sample consisting of 33 male fly specimens collected around a human corpse at a crime scene, the estimated percentage of concordance between species identities predicted using the random forests model and those inferred using DNA-based identification was about 80.6% (approximate 95% confidence interval = [68.9%, 92.2%]). In contrast, baseline concordance using naive majority class prediction was 36.4%. The results provide proof of concept that geometric morphometric data has good potential to complement morphological and DNA-based identification of blow flies and flesh flies in forensic work.
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Affiliation(s)
- Tsung Fei Khang
- Institute of Mathematical Sciences, University of Malaya, Kuala Lumpur, Malaysia.,University of Malaya Centre for Data Analytics, University of Malaya, Kuala Lumpur, Malaysia
| | | | | | - Zulqarnain Mohamed
- Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia.,Institute of Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
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Koroiva R, Rodrigues LRR, Santana DJ. DNA barcoding for identification of anuran species in the central region of South America. PeerJ 2020; 8:e10189. [PMID: 33150083 PMCID: PMC7585382 DOI: 10.7717/peerj.10189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/24/2020] [Indexed: 11/20/2022] Open
Abstract
The use of COI barcodes for specimen identification and species discovery has been a useful molecular approach for the study of Anura. Here, we establish a comprehensive amphibian barcode reference database in a central area of South America, in particular for specimens collected in Mato Grosso do Sul state (Brazil), and to evaluate the applicability of the COI gene for species-level identification. Both distance- and tree-based methods were applied for assessing species boundaries and the accuracy of specimen identification was evaluated. A total of 204 mitochondrial COI barcode sequences were evaluated from 22 genera and 59 species (19 newly barcoded species). Our results indicate that morphological and molecular identifications converge for most species, however, some species may present cryptic species due to high intraspecific variation, and there is a high efficiency of specimen identification. Thus, we show that COI sequencing can be used to identify anuran species present in this region.
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Affiliation(s)
- Ricardo Koroiva
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | | | - Diego José Santana
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
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Pentinsaari M, Ratnasingham S, Miller SE, Hebert PDN. BOLD and GenBank revisited - Do identification errors arise in the lab or in the sequence libraries? PLoS One 2020; 15:e0231814. [PMID: 32298363 PMCID: PMC7162515 DOI: 10.1371/journal.pone.0231814] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 03/30/2020] [Indexed: 11/23/2022] Open
Abstract
Applications of biological knowledge, such as forensics, often require the determination of biological materials to a species level. As such, DNA-based approaches to identification, particularly DNA barcoding, are attracting increased interest. The capacity of DNA barcodes to assign newly encountered specimens to a species relies upon access to informatics platforms, such as BOLD and GenBank, which host libraries of reference sequences and support the comparison of new sequences to them. As parameterization of these libraries expands, DNA barcoding has the potential to make valuable contributions in diverse applied contexts. However, a recent publication called for caution after finding that both platforms performed poorly in identifying specimens of 17 common insect species. This study follows up on this concern by asking if the misidentifications reflected problems in the reference libraries or in the query sequences used to test them. Because this reanalysis revealed that missteps in acquiring and analyzing the query sequences were responsible for most misidentifications, a workflow is described to minimize such errors in future investigations. The present study also revealed the limitations imposed by the lack of a polished species-level taxonomy for many groups. In such cases, applications can be strengthened by mapping the geographic distributions of sequence-based species proxies rather than waiting for the maturation of formal taxonomic systems based on morphology.
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Affiliation(s)
- Mikko Pentinsaari
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | - Scott E. Miller
- National Museum of Natural History, Smithsonian Institution, Washington, DC, United States of America
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
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Vilela DS, Koroiva R, Cordero-Rivera A, Guillermo-Ferreira R. A further study on Franciscobasis Machado & Bedê, 2016 (Odonata: Coenagrionidae), a newly described genus from Minas Gerais, Brazil. PLoS One 2019; 14:e0223241. [PMID: 31593578 PMCID: PMC6782088 DOI: 10.1371/journal.pone.0223241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/17/2019] [Indexed: 11/21/2022] Open
Abstract
The genus Franciscobasis Machado & Bedê, 2016 is endemic to the Serra da Canastra National Park in Minas Gerais state, Brazil. Two species of Franciscobasis were described simultaneously with the genus description: F. franciscoi and F. sonia, the latter described only from females. Through morphological and molecular analysis, we investigated if F. sonia may represent the young female of F. franciscoi. Resulting data did not present adequate differences between females to characterize them as different species. Therefore, we suggest that F. sonia is a junior synonym of F. franciscoi, and the female of F. franciscoi goes through a complex ontogenetic color change.
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Affiliation(s)
- Diogo Silva Vilela
- Graduate Program in Entomology, Department of Biology, University of São Paulo (USP), Ribeirão Preto, Brazil
- Laboratory of Ecological Studies on Ethology and Evolution (LESTES), Department of Hydrobiology, Federal University of São Carlos, São Carlos, Brazil
| | - Ricardo Koroiva
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Adolfo Cordero-Rivera
- ECOEVO Lab, Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Pontevedra, Spain
| | - Rhainer Guillermo-Ferreira
- Laboratory of Ecological Studies on Ethology and Evolution (LESTES), Department of Hydrobiology, Federal University of São Carlos, São Carlos, Brazil
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Heo CC, Rahimi R, Mengual X, M Isa MS, Zainal S, Khofar PN, Nazni WA. Eristalinus arvorum (Fabricius, 1787) (Diptera: Syrphidae) in Human Skull: A New Fly Species of Forensic Importance. J Forensic Sci 2019; 65:276-282. [PMID: 31305956 DOI: 10.1111/1556-4029.14128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/25/2019] [Accepted: 06/25/2019] [Indexed: 11/30/2022]
Abstract
A body of an unknown adult female was found within a shallow burial ground in Malaysia whereas the skull was exposed and visible on the ground. During autopsy examination, nine insect larvae were recovered from the interior of the human skull and subsequently preserved in 70% ethanol. The larvae were greyish in appearance, each with a posterior elongated breathing tube. A week after the autopsy, more larvae were collected at the burial site, and some of them were reared into adults. Adult specimens and larvae from the skull and from the burial site were sequenced to obtain DNA barcodes. Results showed all adult flies reared from the burial site, as well as the larvae collected from the skull were identified as Eristalinus arvorum (Fabricius, 1787) (Diptera: Syrphidae). Here, we report the colonization of E. arvorum larvae on a human corpse for the first time.
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Affiliation(s)
- Chong Chin Heo
- Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, 47000 Sungai Buloh, Selangor, Malaysia.,Institute of Pathology, Laboratory & Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, 47000 Sungai Buloh, Selangor, Malaysia
| | - Razuin Rahimi
- Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, 47000 Sungai Buloh, Selangor, Malaysia.,Department of Forensic Medicine, Hospital Sungai Buloh, Selangor, Malaysia
| | - Ximo Mengual
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz-Institut für Biodiversität der Tiere, Adenauerallee 160, D-53113, Bonn, Germany
| | - Mohd Shahirul M Isa
- Faculty of Applied Science, Universiti Teknologi MARA, 40450 Shah Alam, Selangor, Malaysia
| | - Syameem Zainal
- Faculty of Applied Science, Universiti Teknologi MARA, 40450 Shah Alam, Selangor, Malaysia
| | - Putri Nabihah Khofar
- Faculty of Applied Science, Universiti Teknologi MARA, 40450 Shah Alam, Selangor, Malaysia
| | - Wasi Ahmad Nazni
- Division of Medical Entomology, Institute for Medical Research, Jalan Pahang, Kuala Lumpur, Malaysia
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