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de Bruyn M, Dalton DL, Mwale M, Ehlers K, Kotze A. Development and validation of a novel forensic STR multiplex assay for blue (Anthropoides paradiseus), wattled (Bugeranus carunculatus), and grey-crowned crane (Balearica regulorum). Forensic Sci Int Genet 2024; 73:103100. [PMID: 39067301 DOI: 10.1016/j.fsigen.2024.103100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/01/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
The blue crane (Anthropoides paradiseus), wattled crane (Bugeranus carunculatus), and grey-crowned crane (Balearica regulorum) are species of concern as their populations are declining and they face several threats including habitat loss, disturbance and illegal trade. In South Africa, these species are bred in captivity for trade purposes which is permitted and regulated globally under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Legal sustainable trade through captive breeding of endangered wildlife species such as cranes has been promoted to counteract the illegal trade of individuals from the wild. Captive breeding independent of wild populations may reduce the harvest pressures on wild bird populations which in turn benefit the recovery of exploited species. This approach is considered to be controversial by some individuals. Although captive breeding of endangered species, for both population sustainability and commercial purposes, is promoted to aid in conserving species, concerns have been raised with regards to breeding facilities being used for laundering of animals. To monitor the legal trade of cranes in South Africa a short tandem repeat (STR) assay following recommendations of the International Society for Forensic Genetics (ISFG) was developed and validated. An STR assay comprising of four multiplexes that include 16 STR markers and two gender determination markers was proven to be highly informative with average polymorphic information content (PIC) values of 0.806, 0.646 and 0.725 for A. paradiseus, B. regulorum and B. carunculatus respectively. In addition, the assay showed sufficient discriminatory power for parentage assignment of closely related individuals in all three species (A. paradiseus: PI = 1.7×10-24, PIsibs = 4.7×10-08, and B. carunculatus: PI = 1.4×10-19, PIsibs = 2.9×10-07 and B. regulorum: PI = 1.7×10-12, PIsibs = 5.0×10-05). Analysis of 251 samples suggested that the validated multiplex assay ensures reliability, reproducibility, and repeatability for applications in forensic case work where illegal trade of offspring is suspected through verifying parentage of captive birds in breeding facilities.
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Affiliation(s)
- Marli de Bruyn
- South African National Biodiversity Institute, Pretoria 0001, South Africa; Genetics Department, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Desiré Lee Dalton
- School of Health and Life Sciences, Teesside University, Middlesbrough TS1 3BX, United Kingdom.
| | - Monica Mwale
- South African National Biodiversity Institute, Pretoria 0001, South Africa
| | - Karen Ehlers
- Genetics Department, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
| | - Antoinette Kotze
- South African National Biodiversity Institute, Pretoria 0001, South Africa; Genetics Department, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
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2
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Baxter JR, Kotze A, de Bruyn M, Matlou K, Labuschagne K, Mwale M. DNA barcoding of southern African mammal species and construction of a reference library for forensic application. Genome 2024. [PMID: 38996389 DOI: 10.1139/gen-2023-0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of cytochrome c oxidase subunit 1 and cytochrome b sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94%-95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera.
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Affiliation(s)
- J R Baxter
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - A Kotze
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa
| | - M de Bruyn
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - K Matlou
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - K Labuschagne
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - M Mwale
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
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3
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Cooney GS, Köhler H, Chalopin C, Babian C. Discrimination of human and animal bloodstains using hyperspectral imaging. Forensic Sci Med Pathol 2024; 20:490-499. [PMID: 37721660 PMCID: PMC11297111 DOI: 10.1007/s12024-023-00689-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 09/19/2023]
Abstract
Blood is the most encountered type of biological evidence in violent crimes and contains pertinent information to a forensic investigation. The false presumption that blood encountered at a crime scene is human may not be realised until after costly and sample-consuming tests are performed. To address the question of blood origin, the novel application of visible-near infrared hyperspectral imaging (HSI) is used for the detection and discrimination of human and animal bloodstains. The HSI system used is a portable, non-contact, non-destructive method for the determination of blood origin. A support vector machine (SVM) binary classifier was trained for the discrimination of bloodstains of human (n = 20) and five animal species: pig (n = 20), mouse (n = 16), rat (n = 5), rabbit (n = 5), and cow (n = 20). On an independent test set, the SVM model achieved accuracy, precision, sensitivity, and specificity values of 96, 97, 95, and 96%, respectively. Segmented images of bloodstains aged over a period of two months were produced, allowing for the clear visualisation of the discrimination of human and animal bloodstains. The inclusion of such a system in a forensic investigation workflow not only removes ambiguity surrounding blood origin, but can potentially be used in tandem with HSI bloodstain age determination methods for rapid on-scene forensic analysis.
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Affiliation(s)
- Gary Sean Cooney
- Innovation Center Computer Assisted Surgery (ICCAS), Leipzig University, Leipzig, Germany
| | - Hannes Köhler
- Innovation Center Computer Assisted Surgery (ICCAS), Leipzig University, Leipzig, Germany
| | - Claire Chalopin
- Innovation Center Computer Assisted Surgery (ICCAS), Leipzig University, Leipzig, Germany
| | - Carsten Babian
- Institute for Legal Medicine, Leipzig University, Leipzig, Germany.
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4
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Scheible M, Stinson TL, Breen M, Callahan BJ, Thomas R, Meiklejohn KA. The development of non-destructive sampling methods of parchment skins for genetic species identification. PLoS One 2024; 19:e0299524. [PMID: 38507343 PMCID: PMC10954192 DOI: 10.1371/journal.pone.0299524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024] Open
Abstract
Parchment, the skins of animals prepared for use as writing surfaces, offers a valuable source of genetic information. Many have clearly defined provenance, allowing for the genetic findings to be evaluated in temporal and spatial context. While these documents can yield evidence of the animal sources, the DNA contained within these aged skins is often damaged and fragmented. Previously, genetic studies targeting parchment have used destructive sampling techniques and so the development and validation of non-destructive sampling methods would expand opportunities and facilitate testing of more precious documents, especially those with historical significance. Here we present genetic data obtained by non-destructive sampling of eight parchments spanning the 15th century to the modern day. We define a workflow for enriching the mitochondrial genome (mtGenome), generating next-generation sequencing reads to permit species identification, and providing interpretation guidance. Using sample replication, comparisons to destructively sampled controls, and by establishing authentication criteria, we were able to confidently assign full/near full mtGenome sequences to 56.3% of non-destructively sampled parchments, each with greater than 90% of the mtGenome reference covered. Six of eight parchments passed all four established thresholds with at least one non-destructive sample, highlighting promise for future studies.
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Affiliation(s)
- Melissa Scheible
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Timothy L. Stinson
- Department of English, College of Humanities and Social Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Benjamin J. Callahan
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Rachael Thomas
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Kelly A. Meiklejohn
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
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5
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Hatten CE, Fitriana YS, Prigge TL, Irham M, Sutrisno H, Abinawanto, Dingle C. Validation of methods for extraction of DNA and species identification from seized Helmeted Hornbill (Rhinoplax vigil) casques. FORENSIC SCIENCE INTERNATIONAL: ANIMALS AND ENVIRONMENTS 2022. [DOI: 10.1016/j.fsiae.2022.100058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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6
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Mitochondrial genes as strong molecular markers for species identification. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00393-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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7
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Mukantayev K, Kanayev D, Zhumabekova S, Shevtsov A, Tursunov K, Mukanov K, Ramankulov Y. Optimization of polymerase chain reaction for the identification of Roe deer, Saiga, and Siberian stag living in Kazakhstan. Vet World 2022; 15:2067-2071. [PMID: 36313838 PMCID: PMC9615498 DOI: 10.14202/vetworld.2022.2067-2071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
Background and Aim: One of the reasons for the decline in the number of wild species of artiodactyls is poaching and the illegal trading of animal products. Molecular genetic identification of animals from a biological sample effectively proves poaching cases and illegal trade of animal products. This study aimed to develop a polymerase chain reaction (PCR) test that allows for species identification of artiodactyl animals that are most often subject to poaching. Materials and Methods: Genomic DNA was extracted from meat and blood samples of animals killed by poachers using commercial kits. Three pairs of primers were designed and used to amplify the cytochrome b gene fragment of Roe deer, Saiga antelope, and Siberian stag. Results: The proposed protocol allows amplification of specific PCR products of 542 bp with Roe deer DNA, 587 bp with Saiga DNA, and 525 bp with Siberian stag DNA. Specificity analysis showed no cross activity with DNA from other animal species. The detection limit of PCR ranged from 15.6 pg to 1.9 pg of DNA in 25 mL of the reaction mixture. Conclusion: Sequencing the amplified products and subsequent comparison with the corresponding reference sequence showed a similarity ranging from 99.99% to 100%. The PCR based on the developed primers demonstrated high sensitivity and specificity when using DNA from homogeneous and heterogeneous animals.
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Affiliation(s)
- Kanatbek Mukantayev
- Laboratory of Immunochemistry and Immunobiotechnology, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Darkhan Kanayev
- Laboratory of Immunochemistry and Immunobiotechnology, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Sholpan Zhumabekova
- Laboratory of Immunochemistry and Immunobiotechnology, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Alexander Shevtsov
- Laboratory of Applied Genetics, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Kanat Tursunov
- Laboratory of Immunochemistry and Immunobiotechnology, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Kasim Mukanov
- Laboratory of Applied Genetics, National Center for Biotechnology, Nur-Sultan, Kazakhstan
| | - Yerlan Ramankulov
- Laboratory of Applied Genetics, National Center for Biotechnology, Nur-Sultan, Kazakhstan
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8
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Xu W, Xia J, Min S, Xiong Y. Fourier transform infrared spectroscopy and chemometrics for the discrimination of animal fur types. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 274:121034. [PMID: 35248857 DOI: 10.1016/j.saa.2022.121034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/02/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Rapid and reliable animal fur identification has remained a challenge for customs inspection. The accurate distinction between fur types has a significant meaning in implementing the correct tariff policy. A variety of analytical methods have been applied to work on distinguishing animal fur types, with tools of microscopy, molecular testing, mass spectrometry, Fourier transform infrared spectroscopy (FTIR), and Raman spectroscopy. In this research, the capability of attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) combined with pattern recognition methods was investigated for the discrimination of animal fur in six types. This work was to explore the non-destructive application of ATR-FTIR technique in discriminant analysis of animal fur. All spectra were collected by ATR-FTIR of the wavenumber ranging from 4000 to 650 cm-1. Data pretreatments included moving average smoothing and multiplicative scatter correction (MSC). Four supervised classification algorithms were chosen to categorize the types of fur: soft independent modeling of class analogy (SIMCA), principal component analysis linear discriminant analysis (PCA-LDA), partial least squares discriminant analysis (PLS-DA), least squares support vector machine (LS-SVM). PLS-DA and LS-SVM were both effective approaches, with a 100% classification accuracy rate. The accuracy of PCA-LDA and SIMCA was 98.33% and 99.44%, respectively. Furthermore, LS-SVM model obtained using Monte-Carlo sampling method also obtained 100% prediction accuracy, while all other methods produced misclassification. LS-SVM corrected the non-linearities for the animal fur FTIR data but also remarkably improved the prediction performance level. The results of this study revealed that the combination of ATR-FTIR and chemometrics has a huge potential for animal fur discrimination.
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Affiliation(s)
- Weixin Xu
- College of Science, China Agricultural University, Beijing 100193, PR China
| | - Jingjing Xia
- College of Science, China Agricultural University, Beijing 100193, PR China
| | - Shungeng Min
- College of Science, China Agricultural University, Beijing 100193, PR China.
| | - Yanmei Xiong
- College of Science, China Agricultural University, Beijing 100193, PR China.
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9
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Sekimoto Y, Tokai A, Aritaki M, Ando T, Masuda T. Objective discrimination of fur type based on electrophoresis optimized for fur‐hair proteins. Electrophoresis 2022; 43:1233-1241. [DOI: 10.1002/elps.202200002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/07/2022] [Accepted: 02/11/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Yuri Sekimoto
- Nissenken Quality Evaluation Center Taito‐ku Tokyo Japan
| | - Arisa Tokai
- Nissenken Quality Evaluation Center Taito‐ku Tokyo Japan
| | | | - Takeshi Ando
- Nissenken Quality Evaluation Center Taito‐ku Tokyo Japan
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology Faculty of Life Sciences Kumamoto University Chuo‐ku Kumamoto Japan
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10
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Kanthaswamy S, Brendel T, Cancela L, Andrade de Oliveira DA, Brenig B, Cons C, Crespi JA, Dajbychová M, Feldl A, Itoh T, Landi V, Martinez A, Natonek-Wisniewska M, Oldt RF, Radko A, Ramírez O, Rodellar C, Ruiz-Girón M, Schikorski D, Turba ME, Giovambatista G. An inter-laboratory study of DNA-based identity, parentage and species testing in animal forensic genetics. Forensic Sci Res 2021; 7:708-713. [PMID: 36817240 PMCID: PMC9930802 DOI: 10.1080/20961790.2021.1886679] [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] [Indexed: 10/20/2022] Open
Abstract
The probative value of animal forensic genetic evidence relies on laboratory accuracy and reliability. Inter-laboratory comparisons allow laboratories to evaluate their performance on specific tests and analyses and to continue to monitor their output. The International Society for Animal Genetics (ISAG) administered animal forensic comparison tests (AFCTs) in 2016 and 2018 to assess the limitations and capabilities of laboratories offering forensic identification, parentage and species determination services. The AFCTs revealed that analyses of low DNA template concentrations (≤300 pg/µL) constitute a significant challenge that has prevented many laboratories from reporting correct identification and parentage results. Moreover, a lack of familiarity with species testing protocols, interpretation guidelines and representative databases prevented over a quarter of the participating laboratories from submitting correct species determination results. Several laboratories showed improvement in their genotyping accuracy over time. However, the use of forensically validated standards, such as a standard forensic short tandem repeat (STR) kit, preferably with an allelic ladder, and stricter guidelines for STR typing, may have prevented some common issues from occurring, such as genotyping inaccuracies, missing data, elevated stutter products and loading errors. The AFCTs underscore the importance of conducting routine forensic comparison tests to allow laboratories to compare results from each other. Laboratories should keep improving their scientific and technical capabilities and continuously evaluate their personnel's proficiency in critical techniques such as low copy number (LCN) analysis and species testing. Although this is the first time that the ISAG has conducted comparison tests for forensic testing, findings from these AFCTs may serve as the foundation for continuous improvements of the overall quality of animal forensic genetic testing.
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Affiliation(s)
- Sreetharan Kanthaswamy
- School of Mathematics and Natural Sciences, Arizona State University (ASU) at the West Campus, Glendale, AZ, USA,California National Primate Research Center, University of California, Davis, CA, USA,Evolutionary Biology Graduate Program, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Torsten Brendel
- Eurofins Genomics Europe Applied Genomics GmbH, Ebersberg, Germany
| | | | | | - Bertram Brenig
- Institute of Veterinary Medicine, University of Goettingen, Goettingen, Germany
| | - Carmen Cons
- Facultad de Veterinaria, Laboratorio de Genética Bioquímica (LAGENBIO), Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Julian A. Crespi
- Facultad de Ciencias Veterinarias UNLP, IGEVET – Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), La Plata, Argentina
| | | | - Andreas Feldl
- Eurofins Genomics Europe Applied Genomics GmbH, Ebersberg, Germany
| | - Tomohito Itoh
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan (LIAJ), Maebashi, Japan
| | - Vincenzo Landi
- Department of Veterinary Medicine, Animal Breeding and Genetics, University of Bari “Aldo Moro”, Valenzano, Italy
| | - Amparo Martinez
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, Córdoba, Spain
| | | | - Robert F. Oldt
- School of Mathematics and Natural Sciences, Arizona State University (ASU) at the West Campus, Glendale, AZ, USA,California National Primate Research Center, University of California, Davis, CA, USA,Evolutionary Biology Graduate Program, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Anna Radko
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | | | - Clementina Rodellar
- Facultad de Veterinaria, Laboratorio de Genética Bioquímica (LAGENBIO), Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Manuel Ruiz-Girón
- Laboratorio de Biología Molecular y Genómica, Hispalis Biolab S.L.U., Seville, Spain
| | | | | | - Guillermo Giovambatista
- Facultad de Ciencias Veterinarias UNLP, IGEVET – Instituto de Genética Veterinaria (UNLP-CONICET LA PLATA), La Plata, Argentina,CONTACT Guillermo Giovambatista
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11
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Kriangwanich W, Buddhachat K, Poommouang A, Chomdej S, Thitaram C, Kaewmong P, Kittiwattanawong K, Nganvongpanit K. Feasibility of melting fingerprint obtained from ISSR-HRM curves for marine mammal species identification. PeerJ 2021; 9:e11689. [PMID: 34239781 PMCID: PMC8237827 DOI: 10.7717/peerj.11689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/07/2021] [Indexed: 12/19/2022] Open
Abstract
Currently, species identification of stranded marine mammals mostly relies on morphological features, which has inherent challenges. The use of genetic information for marine mammal species identification remains limited, therefore, new approaches that can contribute to a better monitoring of stranded species are needed. In that context, the ISSR-HRM method we have proposed offers a new approach for marine mammal species identification. Consequently, new approaches need to be developed to identify individuals at the species level. Eight primers of the ISSR markers were chosen for HRM analysis resulting in ranges of accuracy of 56.78–75.50% and 52.14–75.93% in terms of precision, while a degree of sensitivity of more than 80% was recorded when each single primer was used. The ISSR-HRM primer combinations revealed a success rate of 100% in terms of discrimination for all marine mammals included in this study. Furthermore, ISSR-HRM analysis was successfully employed in determining marine mammal discrimination among varying marine mammal species. Thus, ISSR-HRM analysis could serve as an effective alternative tool in the species identification process. This option would offer researchers a heightened level of convenience in terms of its performance and success rate. It would also offer field practice to veterinarians, biologists and other field-related people a greater degree of ease with which they could interpret results when effectively classifying stranded marine mammals. However, further studies with more samples and with a broader geographical scope will be required involving distinct populations to account for the high degree of intraspecific variability in cetaceans and to demonstrate the range of applications of this approach.
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Affiliation(s)
- Wannapimol Kriangwanich
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Kittisak Buddhachat
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand.,Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Anocha Poommouang
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Siriwadee Chomdej
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Chatchote Thitaram
- Center of Elephant and Wildlife Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Korakot Nganvongpanit
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
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12
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Smart U, Cihlar JC, Budowle B. International Wildlife Trafficking: A perspective on the challenges and potential forensic genetics solutions. Forensic Sci Int Genet 2021; 54:102551. [PMID: 34134047 DOI: 10.1016/j.fsigen.2021.102551] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/29/2022]
Abstract
International wildlife trafficking (IWT) is a thriving and pervasive illegal enterprise that adversely affects modern societies. Yet, despite being globally recognized as a threat to biodiversity, national security, economy, and biosecurity, IWT remains largely unabated and is proliferating at an alarming rate. The increase in IWT is generally attributed to a lack of prioritization to curb wildlife crime through legal and scientific infrastructure. This review: (1) lays out the damaging scope and influence of IWT; (2) discusses the potential of DNA marker systems, barcodes, and emerging molecular technologies, such as long-read portable sequencing, to facilitate rapid, in situ identification of species and individuals; and (3) encourages initiatives that promote quality and innovation. Interdisciplinary collaboration promises to be one of the most effective ways forward to surmounting the complex scientific and legal challenges posed by IWT.
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Affiliation(s)
- Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA.
| | - Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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13
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Assessing illegal fishing and trade of Atlantic billfish and swordfish by DNA-based identification. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01190-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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14
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Abstract
Wildlife crime is on a massive scale by whatever metric is used. The illegal trade in wildlife and related products is leading to the decline and extinction of many iconic species from rhino to tigers. Almost all countries are signatures to CITES and therefore should enforce national legislation if alleged infringements of trade of wildlife occur. No country is immune from this illegal trade although countries like Australia have their own specific wildlife crimes. Australia is home to many reptilian, amphibian and avian species that are highly prized, predominantly as pets. Collection of protected species from the wild is illegal in all jurisdictions yet policing remote areas of the outback, where so much of the native endemic fauna and flora lives, is nearly impossible. The illegal international trade in these species is highlighted by two case studies provided in this review. A further case highlights the issues of each of the six states of Australia having separate legislation, which is compounded when wildlife crime can be inter-state crime. Australia is one of the few countries having an institute, based at the Australian Museum, with an accredited wildlife forensic science laboratory and therefore the capability to undertake forensic testing of seized samples. One way to reduce wildlife crime may be by educating those who buy illegally seized products that there is a direct connection between the dead animal from which it came and the devasting effect this purchase has on the environment.
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15
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Ewart KM, Johnson RN, Joseph L, Ogden R, Frankham GJ, Lo N. Phylogeography of the iconic Australian pink cockatoo, Lophochroa leadbeateri. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The pink cockatoo (Lophochroa leadbeateri; or Major Mitchell’s cockatoo) is one of Australia’s most iconic bird species. Two subspecies based on morphology are separated by a biogeographical divide, the Eyrean Barrier. Testing the genetic basis for this subspecies delineation, clarifying barriers to gene flow and identifying any cryptic genetic diversity will likely have important implications for conservation and management. Here, we used genome-wide single nucleotide polymorphisms (SNPs) and mitochondrial DNA data to conduct the first range-wide genetic assessment of the species. The aims were to investigate the phylogeography of the pink cockatoo, to characterize conservation units and to reassess subspecies boundaries. We found consistent but weak genetic structure between the two subspecies based on nuclear SNPs. However, phylogenetic analysis of nuclear SNPs and mitochondrial DNA sequence data did not recover reciprocally monophyletic groups, indicating incomplete evolutionary separation between the subspecies. Consequently, we have proposed that the two currently recognized subspecies be treated as separate management units rather than evolutionarily significant units. Given that poaching is suspected to be a threat to this species, we assessed the utility of our data for wildlife forensic applications. We demonstrated that a subspecies identification test could be designed using as few as 20 SNPs.
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Affiliation(s)
- Kyle M Ewart
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Rebecca N Johnson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Leo Joseph
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, ACT, Australia
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Greta J Frankham
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
- Centre for Forensic Science, University of Technology Sydney, Broadway, NSW, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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Heinrich S, Leupen BT, Bruslund S, Owen A, Shepherd CR. A case for better international protection of the Sumatran Laughingthrush (Garrulax bicolor). Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2020.e01414] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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17
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Williams KM, Barkdull M, Fahmy M, Hekkala E, Siddall ME, Kvist S. Caught red handed: iDNA points to wild source for CITES-protected contraband leeches. EUR J WILDLIFE RES 2020. [DOI: 10.1007/s10344-020-01419-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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18
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Mori C, Matsumura S. Current issues for mammalian species identification in forensic science: a review. Int J Legal Med 2020; 135:3-12. [PMID: 32562039 DOI: 10.1007/s00414-020-02341-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/09/2020] [Indexed: 12/21/2022]
Abstract
Mammalian species identification is one of the important issues in forensic science. Determining the origins of non-human biological material found at crime scenes can increase the possibility of identifying the true culprit by narrowing down the range of suspects. Although many techniques based on mitochondrial DNA (mtDNA) have been developed, challenges remain to cost-effectively identify species from degraded samples containing a mixture of DNA from multiple species and to standardize procedures for mammalian species identification. This review evaluates the reliability and versatility of mtDNA-based techniques to reveal obstacles to the establishment of standard analytical methods, with a particular focus on DNA mixtures. When samples contain a mixture of DNA from multiple species, the interpretation of sequencing analysis results is difficult. Although DNA metabarcoding using next-generation sequencing (NGS) technologies can overcome the DNA mixture problem, DNA metabarcoding is not suitable for the type of small-scale analysis routinely performed by local forensic laboratories, primarily because it is costly and time-consuming. By contrast, fluorescent multiplex PCR analysis enables cost-effective and simultaneous species identification from suboptimal samples, although the number of identifiable species is currently limited in comparison with sequencing techniques. The advantages and limitations of current techniques presented in this review indicate that multiplex PCR analysis will continue to be important for mammalian species identification in forensic casework analysis. Further developments in multiplex PCR analysis that enable the identification of an increased number of species will play a key step for standardization efforts among forensic laboratories.
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Affiliation(s)
- Chikahiro Mori
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan. .,Forensic Science Laboratory, Gifu Prefectural Police Headquarters, 2-1-1 Yabutaminami, Gifu, 500-8501, Japan.
| | - Shuichi Matsumura
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
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19
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Du HY, Zhang XY, Dinh TD, Ma Y, Zong C, Li GL, Dahmer TD, Xu YC. Identification of hybrid green peafowl using mitochondrial and nuclear markers. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01159-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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Testing microsatellite loci for individual identification of captive African grey parrots (Psittacus erithacus): a molecular tool for parentage analysis that will aid in monitoring legal trade. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01127-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Vanek D, Rihova P, Ehler E, Dalihodova S, Stikarova R, Vankova L, Strnad Z. STRAND: A Cloud expert system for non-human DNA analysis. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Mariacher A, Garofalo L, Fanelli R, Lorenzini R, Fico R. A combined morphological and molecular approach for hair identification to comply with the European ban on dog and cat fur trade. PeerJ 2019; 7:e7955. [PMID: 31737444 PMCID: PMC6855206 DOI: 10.7717/peerj.7955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/27/2019] [Indexed: 11/20/2022] Open
Abstract
Animal furs are encountering more and more the detriment of public opinion, that is increasingly sensitive to animals, their welfare and protection. The feeling of outrage against animal suffering is particularly intense when cats and dogs are involved, since these are the most popular pets in Western countries. However, in some Asian countries breeding of dogs and cats for the fur industry is a common practice. These furs and their finished garments are often mislabelled in order to be imported and sold to unaware consumers in Western countries. The European Union has issued the Regulation 1523/2007, which bans the use and trade of dog and cat furs. The main purposes of the Regulation were to normalise the internal market and to address the concerns of European consumers about the risk of inadvertently buying products containing these species. The Regulation states that several analytical methods (microscopy, DNA testing and mass spectrometry) can be used to exclude dogs and cats as source species, but an official analytical protocol was not provided. In this paper, we report on the development of a reliable and affordable method for species identification in furs, based on a combined morphological and molecular approach. Our protocol provides an initial morphological analysis as a time and cost effective screening test. Only samples that are morphologically not excluded as canid/felid furs, based on few selected microscopic features, are then submitted to DNA testing. The application of this protocol on seized furs reached 92% identification of species. Our approach assists in identifying frauds and reinforcing the ban on dog and cat fur trade, allowing (1) rapid inexpensive recognition of fake furs, (2) exclusion of non-canid/non-felid furs through fast microscopic morphological screening, (3) overall cost reduction with lower number of samples to be submitted to DNA analysis, (4) analytical protocol to stand in court in case criminal sanctions are to be applied.
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Affiliation(s)
- Alessia Mariacher
- Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana, Grosseto, Italy
| | - Luisa Garofalo
- Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana, Rieti, Italy
| | - Rita Fanelli
- Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana, Rieti, Italy
| | - Rita Lorenzini
- Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana, Rieti, Italy
| | - Rosario Fico
- Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana, Grosseto, Italy
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23
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Araújo SBDE, Patricio GF, Simoni IC, Rivas EB, Fernandes MJB. Isoenzyme and molecular approach for authenticating and monitoring of animal cell lines. AN ACAD BRAS CIENC 2019; 91:e20180487. [PMID: 31618408 DOI: 10.1590/0001-3765201920180487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 02/05/2019] [Indexed: 11/21/2022] Open
Abstract
Authentication of cell lines is of paramount importance to validate the results from their use in biomedical research. Although isoenzyme polymorphism is the standard method, molecular methods based on mitochondrial DNA (mtDNA) have been developed to replace it. The aim of this study was the improvement of our isoenzyme electrophoretic analysis and the validation of one molecular technique targeted at mtDNA for the authentication of our animal cell lines. The combined method of cellular lysing through osmotic shock, followed by freezing-thawing in N2 to obtain isoenzyme extracts, and with 42 × 106 cells maintained the best efficiency. The superior electrophoretic conditions were PAGE run at 200 V. All cell lines had isoenzymatic mobility corresponding to their species to lactate dehydrogenase, malate-dehydrogenase, and glucose-6-phosphate dehydrogenase isoenzymes, and could be distinguished from each other. Two molecular techniques based on mtDNA were tested, one on the cytochrome b gene and other on cytochrome c oxidase I subunit gene. Due to difficulties in distinguishing all cell lines using only one these techniques, we merged the primers of two methods in such a way that there was a sufficient differentiation of all DNA fragments. The sequencing of these PCR products was also performed to validate these data.
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Affiliation(s)
- Shirley B DE Araújo
- Instituto Biológico, Av. Conselheiro Rodrigues Alves, 1252, 04014-900 São Paulo, SP, Brazil
| | - Giancarlo F Patricio
- Instituto Biológico, Av. Conselheiro Rodrigues Alves, 1252, 04014-900 São Paulo, SP, Brazil
| | - Isabela C Simoni
- Instituto Biológico, Av. Conselheiro Rodrigues Alves, 1252, 04014-900 São Paulo, SP, Brazil
| | - Eliana B Rivas
- Instituto Biológico, Av. Conselheiro Rodrigues Alves, 1252, 04014-900 São Paulo, SP, Brazil
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24
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Lan TM, Lin Y, Njaramba-Ngatia J, Guo XS, Li RG, Li HM, Kumar-Sahu S, Wang X, Yang XJ, Guo HB, Xu WH, Kristiansen K, Liu H, Xu YC. Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data. Genes (Basel) 2019; 10:E509. [PMID: 31284503 PMCID: PMC6679096 DOI: 10.3390/genes10070509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub.
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Affiliation(s)
- Tian Ming Lan
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yu Lin
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Ren Gui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Hai Meng Li
- BGI-Shenzhen, Shenzhen 518083, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sunil Kumar-Sahu
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xie Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiu Juan Yang
- Heilongjiang Provincial Museum, Harbin 150001, China
| | - Hua Bing Guo
- Forest Inventory and Planning Institute of Jilin Province, Changchun 130022, China
| | - Wen Hao Xu
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen 518083, China
| | - Huan Liu
- BGI-Shenzhen, Shenzhen 518083, China.
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
| | - Yan Chun Xu
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China.
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25
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Moore MK, Frazier K. Humans Are Animals, Too: Critical Commonalities and Differences Between Human and Wildlife Forensic Genetics. J Forensic Sci 2019; 64:1603-1621. [DOI: 10.1111/1556-4029.14066] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/10/2019] [Accepted: 04/08/2019] [Indexed: 12/31/2022]
Affiliation(s)
- M. Katherine Moore
- Forensic Laboratory Conservation Biology Division Northwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration 219 Fort Johnson Road Charleston SC29412
| | - Kim Frazier
- Wyoming Game and Fish Wildlife Forensic and Fish Health Laboratory 1212 South Adams Street Laramie WY 82070
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26
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Dinh TD, Ngatia JN, Cui LY, Ma Y, Dhamer TD, Xu YC. Influence of pairwise genetic distance computation and reference sample size on the reliability of species identification using Cyt b and COI gene fragments in a group of native passerines. Forensic Sci Int Genet 2019; 40:85-95. [PMID: 30780122 DOI: 10.1016/j.fsigen.2019.02.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/23/2019] [Accepted: 02/12/2019] [Indexed: 01/09/2023]
Abstract
Species identification is fundamental to wildlife forensic practice. The desirability of molecular genetic methods is increasing rapidly. The sequence of a marker, rather than its particular diagnostic nucleotides, provides greater safety through comparisons between intra- and inter-specific pairwise genetic distances. However, it has not been well described how reliability of species assignment is influenced by distance computing methods and reference sample sizes. In this study, the influences were tested using 12 species from 4 genera of passerine birds and the sequences of partial Cytochrome b (Cyt b) and Cytochrome Oxidase subunit I (COI) genes. Results showed that different substitution types have different outcomes of pairwise genetic distance estimation and this influences the risk of false inclusion and exclusion. Transition (Ts) is the most effective substitution type to reveal optimal species resolution for both Cyt b and COI gene fragments no matter whether K2P and p-distance are used. Sample size required to accurately estimate pairwise distance is essentially determined by the genetic diversity of a species in reference to a given strictness of predefined acceptable accuracy. These findings suggest that for future forensic work on birds by use of Cyt b and COI gene fragments, transition should be used exclusively for marker validation and identification practice when targeting closely related species. Meanwhile, the reference database should sufficiently represent overall genetic diversity of the species. The minimum sample size should be estimated based on existing knowledge of genetic diversity. Special caution should be used for species assignment when only several reference data are available for animals that are considered likely to have high genetic diversity.
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Affiliation(s)
- Thi Dao Dinh
- College of Wildlife Resources, Northeast Forestry University, China
| | | | - Liang Yu Cui
- College of Wildlife Resources, Northeast Forestry University, China
| | - Yue Ma
- College of Wildlife Resources, Northeast Forestry University, China; State Forestry and Grassland Administration Detecting Center of Wildlife of China, China
| | | | - Yan Chun Xu
- College of Wildlife Resources, Northeast Forestry University, China; State Forestry and Grassland Administration Detecting Center of Wildlife of China, China; State Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization of China, China.
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27
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Conte J, Potoczniak MJ, Mower C, Tobe SS. ELEquant: a developmental framework and validation of forensic and conservation real-time PCR assays. Mol Biol Rep 2019; 46:2093-2100. [PMID: 30721419 DOI: 10.1007/s11033-019-04660-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/28/2019] [Indexed: 11/28/2022]
Abstract
A framework for the development and validation of a qPCR assay for species identification and DNA quantification for conservation and forensic purposes is presented. Elephants are commonly poached for their ivory tusks, which is the primary driving force behind their endangered status. In addition to poaching and trade, habitat loss due to logging and mining has also resulted in loss of elephants. Crimes against animals can be deterred and/or further prosecution sought through testing with forensic genetic techniques. The creation of novel genetic assays can greatly impact wildlife forensic science investigations in identifying the species. Molecular genetic techniques can help enforce conservation efforts; however, they must be properly developed and validated to be of evidentiary quality for court systems. African and Asian elephant buccal cells were used as model in this work. The assay provides a method to differentiate biological fluids of both genera of elephants simultaneously. It can be used for identification of elephant derived products and presents valuable quantification for optimized further testing, such as microsatellite detection.
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Affiliation(s)
- Jillian Conte
- Department of Biological and Physical Sciences, Keystone College, One College Green, La Plume, PA, 18440, USA. .,Department of Biological Sciences, University of the Sciences, Philadelphia, PA, USA.
| | - Margret J Potoczniak
- Department of Chemistry, Physics and Forensic Science, Arcadia University, 450 S. Easton Road, Glenside, PA, 19038, USA
| | - Courtney Mower
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE, USA.,ARP Sciences, LLC, Rockville, MD, USA
| | - Shanan S Tobe
- Department of Chemistry, Physics and Forensic Science, Arcadia University, 450 S. Easton Road, Glenside, PA, 19038, USA.,College of Science and Engineering, Flinders University, Adelaide, SA, 5042, Australia
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28
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Kumar V, Chandra K, Kundu S, Tyagi K, Amin Laskar B, Singha D, Chakraborty R, Pakrashi A. Utility of mitochondrial DNA in wildlife forensic science: reliable identification of confiscated materials from Eastern India. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1561216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kailash Chandra
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Kaomud Tyagi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Boni Amin Laskar
- Zoological Survey of India, Freshwater Biology Regional Centre (FBRC), Hyderabad, India
| | - Devkant Singha
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Rajasree Chakraborty
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Avas Pakrashi
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
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29
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Santos C, Pereira F. Identification of plant species using variable length chloroplast DNA sequences. Forensic Sci Int Genet 2018; 36:1-12. [PMID: 29870882 DOI: 10.1016/j.fsigen.2018.05.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 05/10/2018] [Accepted: 05/28/2018] [Indexed: 02/07/2023]
Abstract
The correct identification of species in the highly divergent group of plants is crucial for several forensic investigations. Previous works had difficulties in the establishment of a rapid and robust method for the identification of plants. For instance, DNA barcoding requires the analysis of two or three different genomic regions to attain reasonable levels of discrimination. Therefore, new methods for the molecular identification of plants are clearly needed. Here we tested the utility of variable-length sequences in the chloroplast DNA (cpDNA) as a way to identify plant species. The SPInDel (Species Identification by Insertions/Deletions) approach targets hypervariable genomic regions that contain multiple insertions/deletions (indels) and length variability, which are found interspersed with highly conserved regions. The combination of fragment lengths defines a unique numeric profile for each species, allowing its identification. We analysed more than 44,000 sequences retrieved from public databases belonging to 206 different plant families. Four target regions were identified as suitable for the SPInDel concept: atpF-atpH, psbA-trnH, trnL CD and trnL GH. When considered alone, the discrimination power of each region was low, varying from 5.18% (trnL GH) to 42.54% (trnL CD). However, the discrimination power reached more than 90% when the length of some of these regions is combined. We also observed low diversity in intraspecific data sets for all target regions, suggesting they can be used for identification purposes. Our results demonstrate the utility of the SPInDel concept for the identification of plants.
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Affiliation(s)
- Chiara Santos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n 4450-208, Matosinhos, Portugal; Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
| | - Filipe Pereira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n 4450-208, Matosinhos, Portugal.
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30
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Garofalo L, Mariacher A, Fanelli R, Fico R, Lorenzini R. Hindering the illegal trade in dog and cat furs through a DNA-based protocol for species identification. PeerJ 2018; 6:e4902. [PMID: 29888130 PMCID: PMC5993017 DOI: 10.7717/peerj.4902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/15/2018] [Indexed: 11/20/2022] Open
Abstract
In Western countries dogs and cats are the most popular pets, and people are increasingly opposed to their rearing for the fur industry. In 2007, a Regulation of the European Union (EU) banned the use and trade of dog and cat furs, but an official analytical protocol to identify them as source species was not provided, and violations of law are still frequent in all Member States. In this paper we report on the development and validation of a simple and affordable DNA method for species detection in furs to use as an effective tool to combat illegal trade in fur products. A set of mitochondrial primers was designed for amplification of partial cytochrome b, control region and ND1 gene in highly degraded samples, like furs and pelts. Our amplification workflow involved the use of a non-specific primer pair to perform a first test to identify the species through sequencing, then the application of species-specific primer pairs to use in singleplex end-point PCRs as confirmation tests. The advantage of this two-step procedure is twofold: on the one hand it minimises the possibility of negative test results from degraded samples, since failure of amplification with a first set of primers can be offset by successful amplification of the second, and on the other it adds confidence and reliability to final authentication of species. All designed primers were validated on a reference collection of tissue samples, obtaining solid results in terms of specificity, sensitivity, repeatability and reproducibility. Application of the protocol on real caseworks from seized furs yielded successful results also from old and dyed furs, suggesting that age and chemical staining do not necessarily affect positive amplifications. Major pros of this approach are: (1) sensitive and informative primer sets for detection of species; (2) short PCR amplicons for the analysis of poor quality DNA; (3) binding primers that avoid contamination from human DNA; (4) user-friendly protocol for any laboratory equipped for analysis of low-copy-number DNA. Our molecular procedure proved to be a good starting point for enforcing the EU Regulation against dog and cat fur trade in forensic contexts where source attribution is essential to the assignment of responsibilities.
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Affiliation(s)
- Luisa Garofalo
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana "M. Aleandri", Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Rieti, Italy
| | - Alessia Mariacher
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana "M. Aleandri", Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Grosseto, Italy
| | - Rita Fanelli
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana "M. Aleandri", Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Rieti, Italy
| | - Rosario Fico
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana "M. Aleandri", Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Grosseto, Italy
| | - Rita Lorenzini
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana "M. Aleandri", Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Rieti, Italy
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31
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Kumar V, Sharma N, Singal K, Sharma A. A Wildlife Forensic Study for the Species Identification of Indian Blackbuck through Forensically Informative Nucleotide Sequencing (FINS). ACTA ACUST UNITED AC 2018. [DOI: 10.13005/bbra/2621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Identification of exhibits obtained in wildlife cases usually presents challenging tasks for the forensic science investigators. This study describes a casework, where a degraded tissue sample was recovered from pathology department LUVAS University Hisar, Haryana to resolve the identity of the questioned sample. The mitochondrial DNA region of the questioned sample was amplified and sequenced using universal primers of cytochrome b gene to determine the forensically informative nucleotide sites to find the species identity. The obtained sequencing results were compared with the most homologous sequences extracting from NCBI-GenBank database and a phylogenetic tree was done with the aligned sequences to determine the species identity with strong bootstrap support. The informative sites generated revealed that the degree of sequence similarity showed maximum homology (100%) with the sequence obtained from the database. Based on the FINS analysis the recovered sample related to Antilope cervicapra (family Bovidae).
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Affiliation(s)
- Vikas Kumar
- Department of Genetics (Forensic Science), Maharshi Dayanand University, Rohtak Haryana, India
| | - Neelkamal Sharma
- Department of Genetics (Forensic Science), Maharshi Dayanand University, Rohtak Haryana, India
| | - Kusum Singal
- Department of Genetics (Forensic Science), Maharshi Dayanand University, Rohtak Haryana, India
| | - Arun Sharma
- Department of Genetics (Forensic Science), Maharshi Dayanand University, Rohtak Haryana, India
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Differentiation of human blood from animal blood using Raman spectroscopy: A survey of forensically relevant species. Forensic Sci Int 2018; 282:204-210. [DOI: 10.1016/j.forsciint.2017.11.033] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/04/2017] [Accepted: 11/20/2017] [Indexed: 01/20/2023]
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Kumar V, Sharma N, Sharma A. DNA barcoding of the Indian blackbuck (Antilope cervicapra) and their correlation with other closely related species. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2017. [DOI: 10.1186/s41935-017-0034-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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34
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Izadpanah M, Mohebali N, Elyasi Gorji Z, Farzaneh P, Vakhshiteh F, Shahzadeh Fazeli SA. Simple and fast multiplex PCR method for detection of species origin in meat products. Journal of Food Science and Technology 2017; 55:698-703. [PMID: 29391634 DOI: 10.1007/s13197-017-2980-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 11/24/2022]
Abstract
Identification of animal species is one of the major concerns in food regulatory control and quality assurance system. Different approaches have been used for species identification in animal origin of feedstuff. This study aimed to develop a multiplex PCR approach to detect the origin of meat and meat products. Specific primers were designed based on the conserved region of mitochondrial Cytochrome C Oxidase subunit I (COX1) gene. This method could successfully distinguish the origin of the pig, camel, sheep, donkey, goat, cow, and chicken in one single reaction. Since PCR products derived from each species represent unique molecular weight, the amplified products could be identified by electrophoresis and analyzed based on their size. Due to the synchronized amplification of segments within a single PCR reaction, multiplex PCR is considered to be a simple, fast, and inexpensive technique that can be applied for identification of meat products in food industries. Nowadays, this technique has been considered as a practical method to identify the species origin, which could further applied for animal feedstuffs identification.
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Affiliation(s)
- Mehrnaz Izadpanah
- 1Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
- 2School of Advance Technologies in Medicine, Tehran University of Medical Science, Tehran, Iran
| | - Nazanin Mohebali
- 1Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Zahra Elyasi Gorji
- 1Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Parvaneh Farzaneh
- 1Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Faezeh Vakhshiteh
- 1Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Seyed Abolhassan Shahzadeh Fazeli
- 1Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
- 3Department of Molecular and Cellular Biology, Faculty of Basic Sciences and Advanced Technologies in biology, University of Science and Culture, Tehran, Iran
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Lalitha R, Chandavar VR. Intraspecific variations in Cyt b and D-loop sequences of Testudine species, Lissemys punctata from south Karnataka. J Adv Res 2017; 9:87-95. [PMID: 30046490 PMCID: PMC6057446 DOI: 10.1016/j.jare.2017.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/21/2017] [Accepted: 10/23/2017] [Indexed: 11/17/2022] Open
Abstract
The freshwater Testudine species have gained importance in recent years, as most of their population is threatened due to exploitation for delicacy and pet trade. In this regard, Lissemys punctata, a freshwater terrapin, predominantly distributed in Asian countries has gained its significance for the study. A pilot study report on mitochondrial markers (Cyt b and D-loop) conducted on L. punctata species from southern Karnataka, India was presented in this investigation. A complete region spanning 1.14 kb and ∼1 kb was amplified by HotStart PCR and sequenced by Sanger sequencing. The Cyt b sequence revealed 85 substitution sites, no indels and 17 parsimony informative sites, whereas D-loop showed 189 variable sites, 51 parsimony informative sites with 5′ functional domains TAS, CSB-F, CSBs (1, 2, 3) preceding tandem repeat at 3′ end. Current data highlights the intraspecific variations in these target regions and variations validated using suitable evolutionary models points out that the overall point mutations observed in the region are transitions leading to no structural and functional alterations. The mitochondrial data generated uncover the genetic diversity within species and conservationist can utilize the data to estimate the effective population size or for forensic identification of animal or its seizures during unlawful trade activities.
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Affiliation(s)
- R Lalitha
- Molecular Endocrinology Laboratory, Department of Biotechnology, Yuvaraja's College, A Constituent Autonomous College of University of Mysore, Mysore 570005, India
| | - V R Chandavar
- Molecular Endocrinology Laboratory, Department of Biotechnology, Yuvaraja's College, A Constituent Autonomous College of University of Mysore, Mysore 570005, India
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Solazzo C. Follow-up on the characterization of peptidic markers in hair and fur for the identification of common North American species. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1375-1384. [PMID: 28600869 DOI: 10.1002/rcm.7923] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/06/2017] [Accepted: 06/06/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Species identification of hair is routinely done by microscopic analysis. Following previous studies that used protein analysis to characterize species markers in hair and wool, the present work aims at covering a larger number of species and to ultimately offer a method for rapid hair identification in forensics and archaeology. METHODS Hair is mostly made of alpha-keratins; these proteins have only been sequenced in a handful of species and most animal families are under-represented. Using a methodology developed for the characterization of peptidic markers in tissues such as bone (peptide mass fingerprinting or PMF) and commonly applied on collagen, hair from common North American fur-bearing species was analyzed by MALDI-TOF-MS to obtain peptidic profiles. RESULTS Alpha-keratin peptides that are typically dominant on peptide mass profiles of hair were chosen as markers. Matching peaks were identified for each species tested and compared to known sequences from related organisms whenever possible. The markers were used to create a flowchart to narrow down identification to the family level. CONCLUSIONS The methodology was developed on a limited numbers of markers chosen for their variability and reliability on the peptide mass fingerprint. In the absence of genetic sequences, this strategy is a quick way to compare species from a common geographic origin. The work presented here was focused on North American species but could be applied to other animal families.
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Affiliation(s)
- Caroline Solazzo
- Museum Conservation Institute, Museum Support Center, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD, 20746, USA
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37
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Budowle B, Schmedes SE, Wendt FR. Increasing the reach of forensic genetics with massively parallel sequencing. Forensic Sci Med Pathol 2017. [DOI: 10.1007/s12024-017-9882-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Lopez-Oceja A, Nuñez C, Baeta M, Gamarra D, de Pancorbo MM. Species identification in meat products: A new screening method based on high resolution melting analysis of cyt b gene. Food Chem 2017; 237:701-706. [PMID: 28764056 DOI: 10.1016/j.foodchem.2017.06.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 05/26/2017] [Accepted: 06/01/2017] [Indexed: 10/19/2022]
Abstract
Meat adulteration by substitution with lower value products and/or mislabeling involves economic, health, quality and socio-religious issues. Therefore, identification and traceability of meat species has become an important subject to detect possible fraudulent practices. In the present study the development of a high resolution melt (HRM) screening method for the identification of eight common meat species is reported. Samples from Bos taurus, Ovis aries, Sus scrofa domestica, Equus caballus, Oryctolagus cuniculus, Gallus gallus domesticus, Meleagris gallopavo and Coturnix coturnix were analyzed through the amplification of a 148 bp fragment from the cyt b gene with a universal primer pair in HRM analyses. Melting profiles from each species, as well as from several DNA mixtures of these species and blind samples, allowed a successful species differentiation. The results demonstrated that the HRM method here proposed is a fast, reliable, and low-cost screening technique.
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Affiliation(s)
- A Lopez-Oceja
- BIOMICS Research Group, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz 01006, Spain
| | - C Nuñez
- BIOMICS Research Group, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz 01006, Spain
| | - M Baeta
- BIOMICS Research Group, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz 01006, Spain
| | - D Gamarra
- BIOMICS Research Group, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz 01006, Spain
| | - M M de Pancorbo
- BIOMICS Research Group, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz 01006, Spain.
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Suntrarachun S, Chanhome L, Sumontha M. Phylogenetic analysis of the king cobra, Ophiophagus hannah in Thailand based on mitochondrial DNA sequences. ASIAN BIOMED 2017. [DOI: 10.5372/1905-7415.0802.289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Abstract
Background: Snakes possess adaptive characteristics of morphology that may result in incorrect reconstruction of phylogeny. Molecular approaches have become the major source of new information for advancing our understanding of evolutionary, genetic relationships, and species identification.
Objective: We studied DNA sequences of Ophiophagus hannah in different parts of Thailand and compared them with those of O. hannah from other countries.
Materials and Methods: We studied the mitochondrial NADH dehydrogenase subunit 2 (ND2) and control region (CR) sequences of 12 individuals O. hannah from different localities across Thailand. Phylogenetic analysis of DNA sequences were compared to the published sequences of O. hannah deposited in NCBI GenBank database from other countries.
Results: O. hannah could be categorized into 2 Clades, 5 haplotypes, and 4 localities based on 43 different nucleotide positions from the 736 bp of ND2 and 673 bp of CR. Clade A was haplotype A from southern Thailand. Clade B consisted of haplotypes B, C, D, and E. Haplotype B and C came from northern Thailand. Haplotype D came from western Thailand, while haplotype E was O. hannah from central Thailand. The DNA sequences of Clade B were similar to the sequences of O. hannah in Myanmar and southern China that are already deposited in NCBI GenBank database.
Conclusion: We found a different genotype of O. hannah from southern Thailand and suggest that this may be a new species of O. hannah.
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Affiliation(s)
- Sunutcha Suntrarachun
- Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok 10330, Thailand
| | - Lawan Chanhome
- Queen Saovabha Memorial Institute, The Thai Red Cross Society, Bangkok 10330, Thailand
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Rębała K, Rabtsava AA, Kotova SA, Kipen VN, Zhurina NV, Gandzha AI, Tsybovsky IS. STR Profiling for Discrimination between Wild and Domestic Swine Specimens and between Main Breeds of Domestic Pigs Reared in Belarus. PLoS One 2016; 11:e0166563. [PMID: 27851802 PMCID: PMC5112791 DOI: 10.1371/journal.pone.0166563] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/30/2016] [Indexed: 12/04/2022] Open
Abstract
A panel comprising 16 short tandem repeats (STRs) and a gender-specific amelogenin marker was worked out and tested for robustness in discrimination between wild and domestic swine subspecies encountered in Europe, between regional populations of wild boars and between main breeds of domestic pigs reared in Belarus. The STR dataset comprised 310 wild boars, inhabiting all administrative regions of Belarus, and 313 domestic pigs, representing three local and three cosmopolitan lines. Additionally, a total of 835 wild boars were genotyped for the presence of melanocortin 1 receptor (MC1R) alleles specific for domestic pigs. Correctness of assignment of STR profiles to appropriate populations was measured by log-likelihood ratios (log-LRs). All samples were correctly identified as wild boars or domestic pigs with average log-LR of 42.4 (LR = 2.6×1018). On the other hand, as many as 50 out of 835 (6.0%) genotyped wild boars from Belarus possessed MC1R alleles specific to domestic pigs, demonstrating supremacy of our STR profiling system over traditional differentiation between wild boars and domestic pigs, based on single binary markers. Mean log-LRs for allocation of wild boars to their regions of origin and of domestic pigs to appropriate breeds were 2.3 (LR = 9.7) and 13.4 (LR = 6.6×105), respectively. Our results demonstrate the developed STR profiling system to be a highly efficient tool for differentiation between wild and domestic swine subspecies and between diverse breeds of domestic pigs as well as for verification of genetic identity of porcine specimens for the purpose of forensic investigations of wildlife crimes, assurance of veterinary public health, parentage control in animal husbandry, food safety management and traceability of livestock products.
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Affiliation(s)
- Krzysztof Rębała
- Department of Forensic Medicine, Medical University of Gdansk, Gdansk, Poland
- * E-mail:
| | - Alina A. Rabtsava
- Scientific and Practical Centre of the State Committee of Forensic Expertises, Minsk, Belarus
| | - Svetlana A. Kotova
- Scientific and Practical Centre of the State Committee of Forensic Expertises, Minsk, Belarus
| | - Viachaslau N. Kipen
- Scientific and Practical Centre of the State Committee of Forensic Expertises, Minsk, Belarus
| | - Natalja V. Zhurina
- Scientific and Practical Centre of the National Academy of Sciences on Animal Husbandry, Zhodino, Belarus
| | - Alla I. Gandzha
- Scientific and Practical Centre of the National Academy of Sciences on Animal Husbandry, Zhodino, Belarus
| | - Iosif S. Tsybovsky
- Scientific and Practical Centre of the State Committee of Forensic Expertises, Minsk, Belarus
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41
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Coutu AN, Lee-Thorp J, Collins MJ, Lane PJ. Mapping the Elephants of the 19th Century East African Ivory Trade with a Multi-Isotope Approach. PLoS One 2016; 11:e0163606. [PMID: 27760152 PMCID: PMC5070863 DOI: 10.1371/journal.pone.0163606] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/12/2016] [Indexed: 11/18/2022] Open
Abstract
East African elephants have been hunted for their ivory for millennia but the nineteenth century witnessed strongly escalating demand from Europe and North America. It has been suggested that one consequence was that by the 1880s elephant herds along the coast had become scarce, and to meet demand, trade caravans trekked farther into interior regions of East Africa, extending the extraction frontier. The steady decimation of elephant populations coupled with the extension of trade networks have also been claimed to have triggered significant ecological and socio-economic changes that left lasting legacies across the region. To explore the feasibility of using an isotopic approach to uncover a ‘moving frontier’ of elephant extraction, we constructed a baseline isotope data set (δ13C, δ15N, δ18O and 87Sr/86Sr) for historic East African elephants known to have come from three distinct regions (coastal, Rift Valley, and inland Lakes). Using the isotope results with other climate data and geographical mapping tools, it was possible to characterise elephants from different habitats across the region. This baseline data set was then used to provenance elephant ivory of unknown geographical provenance that was exported from East Africa during the late nineteenth and early twentieth centuries to determine its likely origin. This produced a better understanding of historic elephant geography in the region, and the data have the potential to be used to provenance older archaeological ivories, and to inform contemporary elephant conservation strategies.
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Affiliation(s)
- Ashley N. Coutu
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
- Department of Archaeology, University of Cape Town, Rondebosch, South Africa
- * E-mail:
| | - Julia Lee-Thorp
- Research Laboratory for Archaeology, University of Oxford, Oxford, United Kingdom
| | - Matthew J. Collins
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Paul J. Lane
- Department of Archaeology and Ancient History, Uppsala University, Uppsala, Sweden
- School of Geography, Archaeology & Environmental Science, University of the Witwatersrand, South Africa
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42
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Hadas L, Hermon D, Bar-Gal GK. Before they are gone - improving gazelle protection using wildlife forensic genetics. Forensic Sci Int Genet 2016; 24:51-54. [PMID: 27294679 DOI: 10.1016/j.fsigen.2016.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 05/04/2016] [Accepted: 05/29/2016] [Indexed: 11/25/2022]
Abstract
Throughout their habitats gazelles (genus Gazella) face immediate threats due to anthropogenic effects and natural environmental changes. Excessive poaching plays a major role in their populations decline. Three unique populations of gazelles currently live in Israel: mountain gazelle (Gazella gazella), Dorcas gazelle (Gazella Dorcas) and acacia gazelle (Gazella arabica acacia). Ongoing habitat degradation and constant pressure from illegal hunting has caused a continuous decrease in the last 10 years, stressing the need for drastic measures to prevent species extinction. Wildlife forensic science assists enforcement agencies in the escalating arms race against poachers. Wildlife forensic genetic tests being implemented in our laboratory offer both species and individual identification, which rely on two mitochondrial genes (12S rRNA and 16S rRNA) and nine nuclear Short Tandem Repeats (STR), respectively. The current study, presents a poaching case in which mitochondrial DNA-based species identification revealed the presence of mountain gazelle DNA on the seized items. Subsequently, STR markers linked the suspect to more than one gazelle, increasing the severity of the criminal charges.
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Affiliation(s)
- Lia Hadas
- The Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Dalia Hermon
- DNA and Forensic Biology Laboratory, Division of Identification and Forensic Science (DIFS), Israel Police, National H.Q., Jerusalem, Israel
| | - Gila Kahila Bar-Gal
- The Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel.
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Lopez-Oceja A, Gamarra D, Borragan S, Jiménez-Moreno S, de Pancorbo MM. New cyt b gene universal primer set for forensic analysis. Forensic Sci Int Genet 2016; 23:159-165. [PMID: 27206224 DOI: 10.1016/j.fsigen.2016.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 11/28/2022]
Abstract
Analysis of mitochondrial DNA, and in particular the cytochrome b gene (cyt b), has become an essential tool for species identification in routine forensic practice. In cases of degraded samples, where the DNA is fractionated, universal primers that are highly efficient for the amplification of the target region are necessary. Therefore, in the present study a new universal cyt b primer set with high species identification capabilities, even in samples with highly degraded DNA, has been developed. In order to achieve this objective, the primers were designed following the alignment of complete sequences of the cyt b from 751 species from the Class of Mammalia listed in GenBank. A highly variable region of 148bp flanked by highly conserved sequences was chosen for placing the primers. The effectiveness of the new pair of primers was examined in 63 animal species belonging to 38 Families from 14 Orders and 5 Classes (Mammalia, Aves, Reptilia, Actinopterygii, and Malacostraca). Species determination was possible in all cases, which shows that the fragment analyzed provided a high capability for species identification. Furthermore, to ensure the efficiency of the 148bp fragment, the intraspecific variability was analyzed by calculating the concordance between individuals with the BLAST tool from the NCBI (National Center for Biotechnological Information). The intraspecific concordance levels were superior to 97% in all species. Likewise, the phylogenetic information from the selected fragment was confirmed by obtaining the phylogenetic tree from the sequences of the species analyzed. Evidence of the high power of phylogenetic discrimination of the analyzed fragment of the cyt b was obtained, as 93.75% of the species were grouped within their corresponding Orders. Finally, the analysis of 40 degraded samples with small-size DNA fragments showed that the new pair of primers permits identifying the species, even when the DNA is highly degraded as it is very common in forensic samples.
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Affiliation(s)
- A Lopez-Oceja
- BIOMICS Research Group, University of the Basque Country, UPV/EHU, 01006, Vitoria-Gasteiz, Spain
| | - D Gamarra
- BIOMICS Research Group, University of the Basque Country, UPV/EHU, 01006, Vitoria-Gasteiz, Spain
| | - S Borragan
- Parque de la Naturaleza de Cabárceno, 39693, Obregón, Cantabria, Spain
| | - S Jiménez-Moreno
- Area of Forensic and Legal Medicine, Pathology and Surgery Dept., Miguel Hernández University of Elche, 03550, Elche, Alicante, Spain
| | - M M de Pancorbo
- BIOMICS Research Group, University of the Basque Country, UPV/EHU, 01006, Vitoria-Gasteiz, Spain.
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44
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Ogden R, Linacre A. Wildlife forensic science: A review of genetic geographic origin assignment. Forensic Sci Int Genet 2015; 18:152-9. [DOI: 10.1016/j.fsigen.2015.02.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 02/12/2015] [Accepted: 02/24/2015] [Indexed: 10/23/2022]
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High-resolution melting of 12S rRNA and cytochrome b DNA sequences for discrimination of species within distinct European animal families. PLoS One 2014; 9:e115575. [PMID: 25531439 PMCID: PMC4274031 DOI: 10.1371/journal.pone.0115575] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/29/2014] [Indexed: 11/19/2022] Open
Abstract
The cheap and easy identification of species is necessary within multiple fields of molecular biology. The use of high-resolution melting (HRM) of DNA provides a fast closed-tube method for analysis of the sequence composition of the mitochondrial genes 12S rRNA and cytochrome b. We investigated the potential use of HRM for species identification within eleven different animal groups commonly found in Europe by animal-group-specific DNA amplification followed by DNA melting. Influence factors as DNA amount, additional single base alterations, and the existence of mixed samples were taken into consideration. Visual inspection combined with mathematical evaluation of the curve shapes did resolve nearly all species within an animal group. The assay can therefore not only be used for identification of animal groups and mixture analysis but also for species identification within the respective groups. The use of a universal 12S rRNA system additionally revealed a possible approach for species discrimination, mostly by exclusion. The use of the HRM assay showed to be a reliable, fast, and cheap method for species discrimination within a broad range of different animal species and can be used in a flexible "modular" manner depending on the question to be solved.
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Molecular identification of python species: development and validation of a novel assay for forensic investigations. Forensic Sci Int Genet 2014; 16:64-70. [PMID: 25541013 DOI: 10.1016/j.fsigen.2014.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 11/28/2014] [Accepted: 12/09/2014] [Indexed: 11/20/2022]
Abstract
Python snake species are often encountered in illegal activities and the question of species identity can be pertinent to such criminal investigations. Morphological identification of species of pythons can be confounded by many issues and molecular examination by DNA analysis can provide an alternative and objective means of identification. Our paper reports on the development and validation of a PCR primer pair that amplifies a segment of the mitochondrial cytochrome b gene that has been suggested previously as a good candidate locus for differentiating python species. We used this DNA region to perform species identification of pythons, even when the template DNA was of poor quality, as might be the case with forensic evidentiary items. Validation tests are presented to demonstrate the characteristics of the assay. Tests involved the cross-species amplification of this marker in non-target species, minimum amount of DNA template required, effects of degradation on product amplification and a blind trial to simulate a casework scenario that provided 100% correct identity. Our results demonstrate that this assay performs reliably and robustly on pythons and can be applied directly to forensic investigations where the presence of a species of python is in question.
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Ferri G, Corradini B, Ferrari F, Santunione AL, Palazzoli F, Alu' M. Forensic botany II, DNA barcode for land plants: Which markers after the international agreement? Forensic Sci Int Genet 2014; 15:131-6. [PMID: 25457632 DOI: 10.1016/j.fsigen.2014.10.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/23/2014] [Accepted: 10/03/2014] [Indexed: 11/17/2022]
Abstract
The ambitious idea of using a short piece of DNA for large-scale species identification (DNA barcoding) is already a powerful tool for scientists and the application of this standard technique seems promising in a range of fields including forensic genetics. While DNA barcoding enjoyed a remarkable success for animal identification through cytochrome c oxidase I (COI) analysis, the attempts to identify a single barcode for plants remained a vain hope for a longtime. From the beginning, the Consortium for the Barcode of Life (CBOL) showed a lack of agreement on a core plant barcode, reflecting the diversity of viewpoints. Different research groups advocated various markers with divergent set of criteria until the recent publication by the CBOL-Plant Working Group. After a four-year effort, in 2009 the International Team concluded to agree on standard markers promoting a multilocus solution (rbcL and matK), with 70-75% of discrimination to the species level. In 2009 our group firstly proposed the broad application of DNA barcoding principles as a tool for identification of trace botanical evidence through the analysis of two chloroplast loci (trnH-psbA and trnL-trnF) in plant species belonging to local flora. Difficulties and drawbacks that were encountered included a poor coverage of species in specific databases and the lack of authenticated reference sequences for the selected markers. Successful preliminary results were obtained providing an approach to progressively identify unknown plant specimens to a given taxonomic rank, usable by any non-specialist botanist or in case of a shortage of taxonomic expertise. Now we considered mandatory to update and to compare our previous findings with the new selected plastid markers (matK+rbcL), taking into account forensic requirements. Features of all the four loci (the two previously analyzed trnH-psbA+trnL-trnF and matK+rbcL) were compared singly and in multilocus solutions to assess the most suitable combination for forensic botany. Based on obtained results, we recommend the adoption of a two-locus combination with rbcL+trnH-psbA plastid markers, which currently best satisfies forensic needs for botanical species identification.
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Affiliation(s)
- G Ferri
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy.
| | - B Corradini
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - F Ferrari
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - A L Santunione
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - F Palazzoli
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - M Alu'
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
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48
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Xu J, Zhao W, Zhu M, Wen Y, Xie T, He X, Zhang Y, Cao S, Niu L, Zhang H, Zhong T. Molecular identification of adulteration in mutton based on mitochondrial16S rRNAgene. ACTA ACUST UNITED AC 2014; 27:628-32. [DOI: 10.3109/19401736.2014.908377] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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49
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Xie J, Zhu W, Zhou Y, Liu Z, Chen Y, Zhao Z. Identification of mammalian species using the short and highly variable regions of mitochondrial DNA. ACTA ACUST UNITED AC 2014; 26:550-4. [PMID: 24438314 DOI: 10.3109/19401736.2013.873892] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The mitochondrial DNA (mtDNA) typing is useful for the species determination of degraded samples and the nucleotide diversity of target fragments across species is crucial for the discrimination. In this study, the short and highly polymorphic regions flanked by two conserved termini were sought by the sequence alignment of mtDNA across species and two target regions located at 12S rRNA gene were characterized. Two universal primer sets were developed that appear to be effective for a wide variety of mammalian species, even for domestic birds. The two target regions could be efficiently amplified using their universal primer sets on degraded samples and provide sufficient information for species determination. Therefore, the two short and highly variable target regions might provide a high discriminative capacity and should be suitable for the species determination of degraded samples.
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Affiliation(s)
- Jianhui Xie
- Department of Forensic Medicine, Shanghai Medical College, Fudan University , Shanghai , China
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50
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Iyengar A, Hadi S. Use of non-human DNA analysis in forensic science: a mini review. MEDICINE, SCIENCE, AND THE LAW 2014; 54:41-50. [PMID: 23929675 DOI: 10.1177/0025802413487522] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Analysis of non-human DNA in forensic science, first reported about two decades ago, is now commonplace. Results have been used as evidence in court in a variety of cases ranging from abduction and murder to patent infringement and dog attack. DNA from diverse species, including commonly encountered pets such as dogs and cats, to plants, viruses and bacteria has been used and the sheer potential offered by such analyses has been proven. In this review, using case examples throughout, we detail the considerable literature in this field.
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Affiliation(s)
- Arati Iyengar
- School of Forensic & Investigative Sciences, University of Central Lancashire, Preston, UK
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