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Linacre A. Animal Forensic Genetics. Genes (Basel) 2021; 12:genes12040515. [PMID: 33916063 PMCID: PMC8066154 DOI: 10.3390/genes12040515] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 12/27/2022] Open
Abstract
Animal forensic genetics, where the focus is on non-human species, is broadly divided in two: domestic species and wildlife. When traces of a domestic species are relevant to a forensic investigation the question of species identification is less important, as the material comes from either a dog or a cat for instance, but more relevant may be the identification of the actual pet. Identification of a specific animal draws on similar methods to those used in human identification by using microsatellite markers. The use of cat short tandem repeats to link a cat hair to a particular cat paved the way for similar identification of dogs. Wildlife forensic science is becoming accepted as a recognised discipline. There is growing acceptance that the illegal trade in wildlife is having devasting effects on the numbers of iconic species. Loci on the mitochondrial genome are used to identify the most likely species present. Sequencing the whole locus may not be needed if specific bases can be targeted. There can be benefits of increased sensitivity using mitochondrial loci for species testing, but occasionally there is an issue if hybrids are present. The use of massively parallel DNA sequencing has a role in the identification of the ingredients of traditional medicines where studies found protected species to be present, and a potential role in future species assignments. Non-human animal forensic testing can play a key role in investigations provided that it is performed to the same standards as all other DNA profiling processes.
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Affiliation(s)
- Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide, SA 5042, Australia
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2
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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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Roccaro M, Bini C, Fais P, Merialdi G, Pelotti S, Peli A. Who killed my dog? Use of forensic genetics to investigate an enigmatic case. Int J Legal Med 2020; 135:387-392. [PMID: 32783156 PMCID: PMC7870635 DOI: 10.1007/s00414-020-02388-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/03/2020] [Indexed: 11/09/2022]
Abstract
Genetic testing of animal biological material has become a valuable tool in forensic investigations, and it is successfully used to identify unknown crime perpetrators, to unmask food frauds, or to clarify cases of animal attacks on humans or other animals. When DNA profiling is not possible due to inadequate amounts of nuclear DNA, mitochondrial DNA (mtDNA) testing is the only viable alternative, as in the case of shed hair samples. In this case, a dog was allegedly killed by wild animals while being hosted in a boarding house. Extraneous hair fragments recovered from the dog’s mouth and paws were subjected to genetic analysis: the cytochrome b gene located on mtDNA was amplified and sequenced in order to determine the species responsible for the killing. The mtDNA analysis provided evidence that the dog was killed by other dogs, thus unmasking a false wild animal attack and putting the case in an entirely different perspective.
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Affiliation(s)
- Mariana Roccaro
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy.
| | - Carla Bini
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, Bologna, Italy
| | - Paolo Fais
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, Bologna, Italy
| | - Giuseppe Merialdi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "Bruno Ubertini", Bologna Unit, Bologna, Italy
| | - Susi Pelotti
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, Bologna, Italy
| | - Angelo Peli
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy
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Bhaskar R, Mohindra V. Phylogenetic relationships among Indian freshwater turtles (family Trionychidae and Geoemydidae) with special reference to Lissemys punctata, inferred from mitochondrial cytochrome b gene sequences. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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5
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Lalitha R, Chandavar VR. Analysis of genetic diversity in CYTB and control region sequences of Melanochelys trijuga (Schweigger, 1812) from Karnataka. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2018. [DOI: 10.1016/j.japb.2018.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Chang CH, Dai WY, Chen TY, Lee AH, Hou HY, Liu SH, Jang-Liaw NH. DNA barcoding reveals CITES-listed species among Taiwanese government-seized chelonian specimens. Genome 2018; 61:615-624. [PMID: 29916730 DOI: 10.1139/gen-2017-0264] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Compared to traditional morphological identification, DNA barcoding-molecular identification based on sequencing of a segment of mitochondrial cytochrome c oxidase subunit I (COI)-provides a shortcut to authenticating chelonian identifications. Here, we selected 63 government-seized chelonian specimens deposited at Taipei Zoo for DNA barcoding analysis. DNA barcoding and subsequent phylogenetic analysis successfully authenticated 36 chelonian species, including five that are listed in CITES Appendix I. Approximately 90% (57/63) of the specimens were successfully authenticated by our molecular approach, but lack or error of BOLD reference sequences, biological processes such as hybridization, and uncertain species delimitation all reduced the accuracy of DNA barcoding. To increase the accuracy of DNA barcoding, Taipei Zoo will continue to enrich the BOLD database and also establish a genetic database, to include additional genetic markers, by using government-seized chelonian specimens. A fast and accurate method to authenticate seized samples could assist law enforcement agencies to prosecute criminals and restrict illegal exploitation of wild chelonian resources.
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Affiliation(s)
- Chia-Hao Chang
- a Department of Animal Biology, University of Illinois, 202 Shelford Vivarium, 606 East Healey St., Champaign, IL 61820, USA
| | - Wei-Yu Dai
- b Taipei Zoo, No. 30, Section 2, Xinguang Rd., Wenshan District, Taipei City 11656, Taiwan
| | - Ting-Yu Chen
- b Taipei Zoo, No. 30, Section 2, Xinguang Rd., Wenshan District, Taipei City 11656, Taiwan
| | - An-Hsin Lee
- b Taipei Zoo, No. 30, Section 2, Xinguang Rd., Wenshan District, Taipei City 11656, Taiwan
| | - Hsuan-Yi Hou
- b Taipei Zoo, No. 30, Section 2, Xinguang Rd., Wenshan District, Taipei City 11656, Taiwan
| | - Shih-Hui Liu
- c Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei City 11529, Taiwan
| | - Nian-Hong Jang-Liaw
- b Taipei Zoo, No. 30, Section 2, Xinguang Rd., Wenshan District, Taipei City 11656, Taiwan
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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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8
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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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Arenas M, Pereira F, Oliveira M, Pinto N, Lopes AM, Gomes V, Carracedo A, Amorim A. Forensic genetics and genomics: Much more than just a human affair. PLoS Genet 2017; 13:e1006960. [PMID: 28934201 PMCID: PMC5608170 DOI: 10.1371/journal.pgen.1006960] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material-including other animal species, plants, or microorganisms-is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Filipe Pereira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal
| | - Manuela Oliveira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Nadia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Centre of Mathematics of the University of Porto, Porto, Portugal
| | - Alexandra M. Lopes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Veronica Gomes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Angel Carracedo
- Institute of Forensic Sciences Luis Concheiro, University of Santiago de Compostela, Santiago de Compostela, Spain
- Genomics Medicine Group, CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
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Mitochondrial haplotype distribution and phylogenetic relationship of an endangered species Reeve's turtle (Mauremys reevesii) in East Asia. JOURNAL OF ASIA-PACIFIC BIODIVERSITY 2017. [DOI: 10.1016/j.japb.2016.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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11
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Foran DR, Ray RL. Mitochondrial DNA Profiling of Illegal Tortoiseshell Products Derived from Hawksbill Sea Turtles. J Forensic Sci 2016; 61:1062-6. [PMID: 27364288 DOI: 10.1111/1556-4029.13062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/11/2015] [Accepted: 08/22/2015] [Indexed: 11/30/2022]
Abstract
The hawksbill sea turtle (Eretmochelys imbricata) is a highly endangered species, commonly poached for its ornate shell. "Tortoiseshell" products made from the shell are widely, although illegally, available in many countries. Hawksbills have a circumglobal distribution; thus, determining their origin is difficult, although genetic differences exist geographically. In the research presented, a procedure was developed to extract and amplify mitochondrial DNA from tortoiseshell items, in an effort to better understand where the species is being poached. Confiscated tortoiseshell items were obtained from the U.S. Fish and Wildlife Service, and DNA from 56 of them was analyzed. Multiple mitochondrial haplotypes were identified, including five not previously reported. Only one tortoiseshell item proved to be of Atlantic origin, while all others corresponded to genetic stocks in the Indo-Pacific region. The developed methodology allows for unique, and previously unattainable, genetic information on the illegal poaching of sea turtles for the decorative tortoiseshell trade.
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Affiliation(s)
- David R Foran
- Forensic Science Program, School of Criminal Justice and Department of Integrative Biology, Michigan State University, 655 Auditorium Road, 560 Baker Hall, East Lansing, MI, 48824
| | - Rebecca L Ray
- Forensic Science Program, School of Criminal Justice, Michigan State University, 655 Auditorium Road, 560 Baker Hall, East Lansing, MI, 48824
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Abstract
The illegal trade in ivory and rhino horn has led to a catastrophic decline in elephant and rhino populations worldwide. These iconic high profile species are one part of the illegal trade in wildlife products that threatens these species and the ecological balance in the habitats in which they live. Identification of the species present is required to determine that the trade is illegal and contrary to national legislation. This chapter details a robust DNA technique using part of the cytochrome b gene on the mitochondrial genome that will work on poor quality samples such as powdered horn or ivory products including statues and carvings. An appropriate DNA extraction technique is required to obtain at least 1 ng of DNA from which the amplification of part of the cytochrome b gene using universal primers is performed. This produces a fragment of 486 bp in size which can be sequenced using standard technologies. The resulting sequences are then aligned to voucher specimens or sequences on reliable databases. Analyses of the data should lead to confident species identification.
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Affiliation(s)
- Adrian Linacre
- Department of Biological Sciences, Flinders University, Box 2100, Adelaide, 5001, SA, Australia.
| | - James Chun-I Lee
- Department of Forensic Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan ROC
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Ciavaglia S, Donnellan S, Henry J, Linacre A. Species identification of protected carpet pythons suitable for degraded forensic samples. Forensic Sci Med Pathol 2014; 10:295-305. [DOI: 10.1007/s12024-014-9573-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2014] [Indexed: 10/25/2022]
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Iyengar A. Forensic DNA analysis for animal protection and biodiversity conservation: A review. J Nat Conserv 2014. [DOI: 10.1016/j.jnc.2013.12.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Johnson RN, Wilson-Wilde L, Linacre A. Current and future directions of DNA in wildlife forensic science. Forensic Sci Int Genet 2013; 10:1-11. [PMID: 24680123 DOI: 10.1016/j.fsigen.2013.12.007] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 12/13/2013] [Accepted: 12/18/2013] [Indexed: 12/22/2022]
Abstract
Wildlife forensic science may not have attained the profile of human identification, yet the scale of criminal activity related to wildlife is extensive by any measure. Service delivery in the arena of wildlife forensic science is often ad hoc, unco-ordinated and unregulated, yet many of those currently dedicated to wildlife conservation and the protection of endangered species are striving to ensure that the highest standards are met. The genetic markers and software used to evaluate data in wildlife forensic science are more varied than those in human forensic identification and are rarely standardised between species. The time and resources required to characterise and validate each genetic maker is considerable and in some cases prohibitive. Further, issues are regularly encountered in the construction of allelic databases and allelic ladders; essential in human identification studies, but also applicable to wildlife criminal investigations. Accreditation and certification are essential in human identification and are currently being strived for in the forensic wildlife community. Examples are provided as to how best practice can be demonstrated in all areas of wildlife crime analysis and ensure that this field of forensic science gains and maintains the respect it deserves. This review is aimed at those conducting human identification to illustrate how research concepts in wildlife forensic science can be used in the criminal justice system, as well as describing the real importance of this type of forensic analysis.
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Affiliation(s)
- Rebecca N Johnson
- Australian Museum Research Institute, Australian Centre for Wildlife Genomics, Science and Learning Division, Australian Museum, Sydney, Australia.
| | - Linzi Wilson-Wilde
- Australia New Zealand Policing Advisory Agency - National Institute of Forensic Science, Melbourne, Australia
| | - Adrian Linacre
- School of Biological Sciences, Flinders University, Bedford Park, Adelaide, Australia
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Suzuki D, Ota H, Oh HS, Hikida T. Origin of Japanese Populations of Reeves' Pond Turtle, Mauremys reevesii (Reptilia: Geoemydidae), as Inferred by a Molecular Approach. CHELONIAN CONSERVATION AND BIOLOGY 2011. [DOI: 10.2744/ccb-0885.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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17
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Coghlan ML, White NE, Parkinson L, Haile J, Spencer PBS, Bunce M. Egg forensics: an appraisal of DNA sequencing to assist in species identification of illegally smuggled eggs. Forensic Sci Int Genet 2011; 6:268-73. [PMID: 21741338 PMCID: PMC7102845 DOI: 10.1016/j.fsigen.2011.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 05/12/2011] [Accepted: 06/13/2011] [Indexed: 10/29/2022]
Abstract
Psittaciformes (parrots and cockatoos) are charismatic birds, their plumage and capacity for learning make them highly sought after pets. The illegal trade in parrots and cockatoos poses a serious threat to the viability of native populations; in addition, species transported to non-endemic areas may potentially vector disease and genetically 'pollute' local native avifauna. To reduce the logistical difficulties associated with trafficking live birds, smugglers often transport eggs. This creates a problem for authorities in elucidating accurate species identification without the laborious task of incubation and hand rearing until a morphological identification can be made. Here, we use 99 avian eggs seized from carriers coming into and within Australia, as a result of suspected illegal trade. We investigate and evaluate the use of mitochondrial DNA (mtDNA) to accurately identify eggs to family, genus or species level. However, Identification of a species based on percentage mtDNA similarities is difficult without good representations of the inter- and intra-levels of species variation. Based on the available reference database, we were able to identify 52% of the eggs to species level. Of those, 10 species from eight genera were detected, all of which belong to the parrot (Psittacidae) and cockatoo (Cacatuidae) families. Of the remaining 48%, a further 36% of eggs were identified to genus level, and 12% identified to family level using our assignment criteria. Clearly the lack of validated DNA reference sequences is hindering our ability to accurately assign a species identity, and accordingly, we advocate that more attention needs to be paid to establishing validated, multi locus mtDNA reference databases for exotic birds that can both assist in genetic identifications and withstand legal scrutiny.
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Affiliation(s)
- Megan L Coghlan
- Australian Wildlife Forensic Services and Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, South St, Murdoch, WA 6150, Australia
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Dalvin S, Glover KA, Sørvik AGE, Seliussen BB, Taggart JB. Forensic identification of severely degraded Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) tissues. INVESTIGATIVE GENETICS 2010; 1:12. [PMID: 21092346 PMCID: PMC2990734 DOI: 10.1186/2041-2223-1-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 11/03/2010] [Indexed: 11/25/2022]
Abstract
BACKGROUND Aquaculture is a globally important and rapidly growing industry. It contributes positively to the economy and sustainability of coastal communities, but it is not without regulatory challenges. These challenges are diverse, and may include identification of fish discarded in an illegal manner, biological discharge from fish ensilage tanks, and partially destroyed or processed tissues. Robust genetic tools are required by management authorities to address these challenges. In this paper, we describe nine species-specific primer sets amplifying very short DNA fragments within the mitochondrial DNA cytochrome c oxidase (COI) gene, which were designed to permit diagnostic identification of degraded DNA from two of the most commonly farmed salmonids in Europe and North America. RESULTS Of the nine designed primer sets, six were found to be species-specific (four Atlantic salmon, two rainbow trout), whereas the remaining three sets (two Atlantic salmon, one rainbow trout) also amplified a product from other, closely related, salmonid DNA templates. Screening of DNA templates from 11 other non-salmonid native fish species did not produce PCR products with any of the primer sets. Specific tests confirmed the ability of these markers to identify Atlantic salmon and rainbow trout tissues in treated food products, chemically treated ensilage waste and fillets left to degrade in saltwater for up to 31 days at 15°C. Importantly, these markers provided diagnostic identification in cases where other genetic methods failed because of degraded DNA quality. CONCLUSIONS Results from this study demonstrate that amplification of very short DNA fragments using species-specific primers represents a robust and versatile method to create cheap and efficient genetic tests that can be implemented in a range of forensic applications. These markers will provide fishery, aquaculture and food regulatory authorities with a method to investigate and enforce regulations within these industries.
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Affiliation(s)
- Sussie Dalvin
- Institute of Marine Research. P.O. Box 1870, Nordnes. N- 5817 Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research. P.O. Box 1870, Nordnes. N- 5817 Bergen, Norway
| | - Anne GE Sørvik
- Institute of Marine Research. P.O. Box 1870, Nordnes. N- 5817 Bergen, Norway
| | | | - John B Taggart
- Institute of Aquaculture, University of Stirling, Scotland, FK9 4LA, UK
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Johnson RN. The use of DNA identification in prosecuting wildlife-traffickers in Australia: do the penalties fit the crimes? Forensic Sci Med Pathol 2010; 6:211-6. [DOI: 10.1007/s12024-010-9174-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2010] [Indexed: 11/24/2022]
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