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Kanthaswamy S. Review: Wildlife forensic genetics-Biological evidence, DNA markers, analytical approaches, and challenges. Anim Genet 2024; 55:177-192. [PMID: 38123142 DOI: 10.1111/age.13390] [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: 12/02/2023] [Revised: 12/02/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023]
Abstract
Wildlife-related crimes are the second most prevalent lawbreaking offense globally. This illicit trade encompasses hunting, breeding and trafficking. Besides diminishing many species and their habitats and ecosystems, hindering the economic development of local communities that depend on them, undermining the rule of law and financing terrorism, various cross-species transmissions (zoonoses) of pathogens, including COVID-19, can be attributed to wildlife crimes. Wildlife forensics applies interdisciplinary scientific analyses to support law enforcement in investigating wildlife crimes. Its main objectives are to identify the taxonomic species in question, determine if a crime has been committed, link a suspect to the crime and support the conviction and prosecution of the perpetrator. This article reviews wildlife crime and its implications, wildlife forensic science investigation, common forms of wildlife biological evidence, including DNA, wildlife DNA techniques and challenges in wildlife forensic genetics. The article also reviews the contributions of genetic markers such as short tandem repeat (STR) and mitochondrial DNA (mtDNA) markers, which provide the probative genetic data representing the bulk of DNA evidence for solving wildlife crime. This review provides an overview of wildlife DNA databases, which are critical for searching and matching forensic DNA profiles and sequences and establishing how frequent forensic DNA profiles and sequences are in a particular population or geographic region. As such, this review will contain an in-depth analysis of the current status of wildlife forensic genetics, and it will be of general interest to wildlife and conservation biologists, law enforcement officers, and academics interested in combating crimes against wildlife using animal forensic DNA methods.
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Affiliation(s)
- Sree Kanthaswamy
- School of Interdisciplinary Forensics, Arizona State University, Tempe, Arizona, USA
- California National Primate Research Center, University of California, Davis, California, USA
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Ng CH, Ng KKS, Lee SL, Zakaria NF, Lee CT, Tnah LH. DNA databases of an important tropical timber tree species Shorea leprosula (Dipterocarpaceae) for forensic timber identification. Sci Rep 2022; 12:9546. [PMID: 35680966 PMCID: PMC9184630 DOI: 10.1038/s41598-022-13697-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
International timber trade communities are increasingly demanding that timber in the wood supply chain be sourced from sustainably harvested forests and certified plantations. This is to combat illegal logging activities to prevent further depletion of our precious forests worldwide. Hence, timber tracking tools are important to support law enforcement officials in ensuring only sustainably harvested timbers are traded in the market. In this study, we developed chloroplast DNA (cpDNA) and simple sequence repeat (SSR) databases as tracking tools for an important tropical timber tree species, Shorealeprosula from Peninsular Malaysia. A total of 1410 individual trees were sampled from 44 natural populations throughout Peninsular Malaysia. Four cpDNA regions were used to generate a cpDNA haplotype database, resulting in a haplotype map comprising 22 unique haplotypes derived from 28 informative intraspecific variable sites. This cpDNA database can be used to trace the origin of an unknown log at the regional level. Ten SSR loci were used to develop the SSR allele frequency database. Bayesian cluster analysis divided the 44 populations into two genetic clusters corresponding to Region A and Region B. Based on conservativeness evaluation of the SSR databases for individual identification, the coancestry coefficients (θ) were adjusted to 0.1900 and 0.1500 for Region A and B, respectively. These databases are useful tools to complement existing timber tracking systems in ensuring only legally sourced timbers are allowed to enter the wood supply chain.
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Affiliation(s)
- Chin Hong Ng
- Genetics Laboratory, Forest Research Institute Malaysia, 52109, Kepong, Selangor, Malaysia.
| | - Kevin Kit Siong Ng
- Genetics Laboratory, Forest Research Institute Malaysia, 52109, Kepong, Selangor, Malaysia
| | - Soon Leong Lee
- Genetics Laboratory, Forest Research Institute Malaysia, 52109, Kepong, Selangor, Malaysia
| | - Nurul-Farhanah Zakaria
- Genetics Laboratory, Forest Research Institute Malaysia, 52109, Kepong, Selangor, Malaysia
| | - Chai Ting Lee
- Genetics Laboratory, Forest Research Institute Malaysia, 52109, Kepong, Selangor, Malaysia
| | - Lee Hong Tnah
- Genetics Laboratory, Forest Research Institute Malaysia, 52109, Kepong, Selangor, Malaysia
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Lee SL, Zakaria NF, Tnah LH, Ng CH, Ng KKS, Lee CT, Lau KH, Chua LSL. DNA databases of a CITES listed species Aquilaria malaccensis (Thymelaeaceae) as the tracking tools for forensic identification and chain of custody certification. Forensic Sci Int Genet 2021; 57:102658. [PMID: 34998185 DOI: 10.1016/j.fsigen.2021.102658] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 11/04/2022]
Abstract
Aquilaria malaccensis (Thymelaeaceae) is the main source of high-grade agarwood in Southeast Asia. Aggressive collections and trade activities over the past decades have put great pressure on the natural stands and raised concerns over the long-term survival potential of A. malaccensis. Tracking and authentication of agarwood require method with a high degree of accuracy. Therefore, this study aimed to develop DNA databases of A. malaccensis as the tracking tools at species, population and individual levels for forensic identification and chain of custody certification. Using two cpDNA (rbcL and matK) and an rDNA (ITS2) markers, species identification database of Aquilaria was developed to distinguish A. malaccensis from A. hirta, A. microcarpa, A. beccariana, A. crassna, A. sinensis and A. rostrata. In addition, based on 35 populations of A. malaccensis throughout Peninsular Malaysia, cpDNA haplotype and STR allele frequency databases were developed for population and individual identification. A haplotype distribution map based on 29 haplotypes derived from seven cpDNA showed that the A. malaccensis in Peninsular Malaysia can be associated to Kedah-Perak and Kelantan-Johor regions. Similarly, genetic relatedness and Bayesian clustering analyses based on 10 STR markers also divided the 35 populations into two main genetic clusters, corresponding to Kedah-Perak and Kelantan-Johor regions. The STR allele frequency databases were established and characterized according to these two regions. To determine the performance of the STR allele frequency databases for population identification, independent self-assignment tests showed that the percentage of individuals correctly assigned into the origin population was 93.88% in Kedah-Perak and 90.29% in Kelantan-Johor. For the STR allele frequency databases to be used for individual identification, conservativeness tests showed that the θ should be adjusted to 0.250 and 0.200 in the Kedah-Perak and Kelantan-Johor databases, respectively. To ensure consistency in allele calling for the dinucleotide repeat loci across different electrophoretic platforms or laboratories, allelic ladders have been developed for the 10 STR loci. Two case studies are presented of how these databases were used to track A. malaccensis to the origin population and stump. These databases are ready to be used to provide admissible forensic evidence for legal proceedings against the illegal harvesters of agarwood and for agarwood certification to meet the consumer country regulations.
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Affiliation(s)
- Soon Leong Lee
- Genetics Laboratory, Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia.
| | - Nurul-Farhanah Zakaria
- Genetics Laboratory, Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia.
| | - Lee Hong Tnah
- Genetics Laboratory, Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia.
| | - Chin Hong Ng
- Genetics Laboratory, Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia.
| | - Kevin Kit Siong Ng
- Genetics Laboratory, Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia.
| | - Chai Ting Lee
- Genetics Laboratory, Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia.
| | - Kah Hoo Lau
- Forest Health and Conservation Programme, Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia.
| | - Lillian Swee Lian Chua
- Forest Health and Conservation Programme, Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia.
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Hamlin BC, Meredith EP, Rodzen J, Strand JM. OdoPlex: An STR multiplex panel optimized and validated for forensic identification and sex determination of North American mule deer (Odocoileus hemionus) and white-tailed deer (Odocoileus virginianus). FORENSIC SCIENCE INTERNATIONAL: ANIMALS AND ENVIRONMENTS 2021. [DOI: 10.1016/j.fsiae.2021.100026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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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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Gaillard D, Yeh FC, Lin L, Chen HQ, Zhang T, Luo SJ, Shi HT. Lost at sea: determining geographic origins of illegally traded green sea turtles (Chelonia mydas) rescued on Hainan Island, China. WILDLIFE RESEARCH 2021. [DOI: 10.1071/wr19127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
ContextGreen sea turtles are threatened by exploitation for food and medicine markets, with Asian populations facing the heaviest pressures. Sea turtle confiscations that happen out at sea can give a general area that poachers are targeting, but it can be difficult to determine the impact on specific nesting rookeries. Previous studies circumvented this difficulty by using genetic markers to identify nesting rookery origins of confiscated green turtles.
AimsTo determine the impact on nesting rookeries from the illegal harvesting of green sea turtles by Hainan fishermen and describe the genetic diversity of the Paracel Islands’ green sea turtle population.
MethodsIn the present study, we sequenced 384bp of mitochondrial DNA control region from 85 illegally traded green sea turtles rescued on Hainan Island, China, to investigate their population of origin. For reference-source data, we used previously published mtDNA haplotype data from rookeries from Australasian waters and mtDNA haplotype data from 16 newly collected samples from the Paracel Islands in the South China Sea, a previously unsampled area.
Key resultsTen and four mtDNA haplotypes, all being reported before, were detected from the Hainan confiscation and Paracel Islands rookery respectively. However, CmP19, an infrequent haplotype that has been found only in 10 green sea turtles previously, made up ~45% of our rescued samples and ~62% of the Paracel Islands sample, suggesting a potential association between CmP19 and the Paracel Island rookery. Haplotype diversity of the rescued green sea turtles was relatively high (h=0.7143±0.04), whereas nucleotide diversity was relatively low (π=0.0031±0.00), compared with other rookeries. Mixed-stock analysis suggested that the rookeries in the Paracel Islands (~57%) and the Sulu Sea (~29%) are experiencing the greatest impact from illegal harvesting by fishermen from Hainan and neighbouring countries.
ConclusionsThe Paracel Islands population contains a unique genetic makeup compared with other studied rookeries, particularly the high frequency of the previously rare CmP19 haplotype. The current harvesting of green sea turtles by Hainan fishermen affects not only protected local populations (Paracel Islands), but also distant populations (Sulu Sea) in protected international waters.
ImplicationsEstablishment of a large-scale Sea Turtle Nature Reserve in the South China Sea, including a special law enforcement team to monitor this National Marine Park, needs to be top priority to help curb illegal harvesting. The Paracel Islands represents a newly defined population, and conservation measures need to be taken immediately to preserve this distinct population.
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Development and technical application of SSR-based individual identification system for Chamaecyparis taiwanensis against illegal logging convictions. Sci Rep 2020; 10:22095. [PMID: 33328522 PMCID: PMC7744516 DOI: 10.1038/s41598-020-79061-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 11/24/2020] [Indexed: 11/23/2022] Open
Abstract
Chamaecyparis taiwanensis is an endemic plant suffering illegal logging in Taiwan for its high economic value. Lack of direct evidence to correlate stump and timber remains a hurdle for law enforcement. In this report, 23 polymorphic Genomic Simple Sequence Repeat (gSSR) and 12 Expressed Sequence Tag (EST)-SSR markers were developed and their transferability was assessed. The individual identification system built from selected non-linkage 30 SSR markers has a combined probability of identity as 5.596 × 10–12 equivalents to identifying an individual in a population of up to 18 million C. taiwanensis with 99.99% confidence level. We also applied the system in an actual criminal case by selecting 19 of these markers to correlate illegally felled timbers and victim trees. Our data demonstrate that molecular signals from three timbers hit with three victim trees with confidence level more than 99.99%. This is the first example of successfully applying SSR in C. taiwanensis as a court evidence for law enforcement. The identification system adapted advanced molecular technology and exhibits its great potential for natural resource management on C. taiwanensis.
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Cui W, Jin X, Guo Y, Chen C, Zhang W, Wang Y, Lan J, Zhu B. Development and Validation of a Novel Five-Dye Short Tandem Repeat Panel for Forensic Identification of 11 Species. Front Genet 2020; 11:1005. [PMID: 33193588 PMCID: PMC7541953 DOI: 10.3389/fgene.2020.01005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/06/2020] [Indexed: 01/16/2023] Open
Abstract
Species identification of unknown biological samples is of fundamental importance for forensic applications, especially in crime detection, poaching, and illegal trade of endangered animals as well as meat fraud. In this study, a novel panel was developed to simultaneously identify 10 different animal species (Gallus domesticus, Anas platyrhynchos domesticus, Ovis aries, Sus scrofa domesticus, Bos taurus, Equus caballus, Columba livia domestica, Rattus norvegicus, Mus musculus, and Canis lupus familiaris) and human beings by amplifying 22 short tandem repeat (STR) loci in a multiplex PCR using a set of five fluorescently labeled dyes. This novel 22-STR panel was validated by optimization of PCR conditions as well as species specificity, sensitivity, reproducibility, precision, DNA mixture, and tissue/organ consistency. The results of developmental validation showed that the 22-STR loci achieved high species specificity among 10 animal species and human beings, and the sensitivity of this panel was 0.09 ng. This 22-STR panel identified different meats in mixed samples, and the minimum detected mixture ratio in the current test was 10% (0.1 ng/1 ng). This sensitive, accurate, and specific 22-STR panel can be used for forensic species identification and the detection of meat fraud and adulteration.
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Affiliation(s)
- Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Wenqing Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Yijie Wang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Jiangwei Lan
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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Bourret V, Albert V, April J, Côté G, Morissette O. Past, present and future contributions of evolutionary biology to wildlife forensics, management and conservation. Evol Appl 2020; 13:1420-1434. [PMID: 32684967 PMCID: PMC7359848 DOI: 10.1111/eva.12977] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022] Open
Abstract
Successfully implementing fundamental concepts into concrete applications is challenging in any given field. It requires communication, collaboration and shared will between researchers and practitioners. We argue that evolutionary biology, through research work linked to conservation, management and forensics, had a significant impact on wildlife agencies and department practices, where new frameworks and applications have been implemented over the last decades. The Quebec government's Wildlife Department (MFFP: Ministère des Forêts, de la Faune et des Parcs) has been proactive in reducing the “research–implementation” gap, thanks to prolific collaborations with many academic researchers. Among these associations, our department's outstanding partnership with Dr. Louis Bernatchez yielded significant contributions to harvest management, stocking programmes, definition of conservation units, recovery of threatened species, management of invasive species and forensic applications. We discuss key evolutionary biology concepts and resulting concrete examples of their successful implementation that derives directly or indirectly from this successful partnership. While old and new threats to wildlife are bringing new challenges, we expect recent developments in eDNA and genomics to provide innovative solutions as long as the research–implementation bridge remains open.
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Affiliation(s)
- Vincent Bourret
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Vicky Albert
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Julien April
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Guillaume Côté
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Olivier Morissette
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
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A geographical traceability system for Merbau (Intsia palembanica Miq.), an important timber species from peninsular Malaysia. Forensic Sci Int Genet 2019; 44:102188. [PMID: 31648150 DOI: 10.1016/j.fsigen.2019.102188] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/22/2019] [Accepted: 10/12/2019] [Indexed: 11/21/2022]
Abstract
To inform product users about the origin of timber, the implementation of a traceability system is necessary for the forestry industry. In this study, we developed a comprehensive genetic database for the important tropical timber species Merbau, Intsia palembanica, to trace its geographic origin within peninsular Malaysia. A total of 1373 individual trees representing 39 geographically distinct populations of I. palembanica were sampled throughout peninsular Malaysia. We analyzed the samples using a combination of four chloroplast DNA (cpDNA) markers and 14 short tandem repeat (STR) markers to establish both cpDNA haplotype and STR allele frequency databases. A haplotype map was generated through cpDNA sequencing for population identification, resulting in six unique haplotypes based on 10 informative intraspecifically variable sites. Subsequently, an STR allele frequency database was developed from 14 STRs allowing individual identification. Bayesian cluster analysis divided the individuals into two genetic clusters corresponding to the northern and southern regions of peninsular Malaysia. Tests of conservativeness showed that the databases were conservative after the adjustment of the θ values to 0.2000 and 0.2900 for the northern (f = 0.0163) and southern (f = 0.0285) regions, respectively. Using self-assignment tests, we observed that individuals were correctly assigned to populations at rates of 40.54-94.12% and to the identified regions at rates of 79.80-80.62%. Both the cpDNA and STR markers appear to be useful for tracking Merbau timber originating from peninsular Malaysia. The use of these forensic tools in addition to the existing paper-based timber tracking system will help to verify the legality of the origin of I. palembanica and to combat illegal logging issues associated with the species.
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George K, Masters A, Dawnay N. Development of HyBeacon® probes for the forensic detection of Panthera, rhinoceros, and pangolin species. Mol Cell Probes 2019; 48:101450. [PMID: 31563668 DOI: 10.1016/j.mcp.2019.101450] [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: 07/15/2019] [Revised: 08/14/2019] [Accepted: 09/16/2019] [Indexed: 10/25/2022]
Abstract
The Illegal Wildlife Trade (IWT) represents a multi-billion dollar black-market industry whereby wild species are illegally taken from their natural environment and sold. A common question asked by wildlife forensic scientists pertains to species and/or genus identity, which currently requires multi-step processing. Our work details the development of three HyBeacon® probes, used for the presumptive detection of rhinoceros, pangolin and key target species in the Panthera genus. The approach can be performed in a single tube using melt curve analysis and provide rapid assessment of sample identity. Using synthetic DNA of representative species, early data suggest the approach is sensitive enough to achieve species identification with <10 cells. Future development and assay validation can allow the rapid screening of multiple seized items before confirmatory DNA sequencing.
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Affiliation(s)
- Kimberley George
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Alice Masters
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Nick Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK.
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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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13
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Campbell CD, Pecon-Slattery J, Pollak R, Joseph L, Holleley CE. The origin of exotic pet sugar gliders ( Petaurus breviceps) kept in the United States of America. PeerJ 2019; 7:e6180. [PMID: 30643698 PMCID: PMC6329365 DOI: 10.7717/peerj.6180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/29/2018] [Indexed: 11/25/2022] Open
Abstract
The demand for exotic non-domesticated animals kept as pets in the United States of America (USA) is increasing the exportation rates of these species from their native ranges. Often, illegal harvesting of these species is used to boost captive-bred numbers and meet this demand. One such species, the sugar glider (Petaurus breviceps), endemic to Australia and New Guinea is a popular domestic pet due to its small size and "cute" demeanour. Despite a legal avenue for trade existing in Indonesia, concerns have been raised that sugar gliders may be entering the USA from other parts of their native range where exportation is prohibited such as Australia, Papua New Guinea and the surrounding Indonesian islands. We compared previously published DNA sequences from across the native range of sugar gliders with samples collected from domestically kept sugar gliders within the USA to determine provenance and gene flow between source and introduced populations. Here we show that as predicted, the USA sugar glider population originates from West Papua, Indonesia with no illegal harvesting from other native areas such as Papua New Guinea or Australia evident in the samples tested within this study.
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Affiliation(s)
- Catriona D. Campbell
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australian Capital Territory, Australia
| | - Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute—National Institutes of Health, Frederick, MD, United States of America
- Smithsonian Conservation Biology Institute—National Zoological Park, Front Royal, VA, United States of America
| | - Rebecca Pollak
- Laboratory of Genomic Diversity, National Cancer Institute—National Institutes of Health, Frederick, MD, United States of America
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australian Capital Territory, Australia
| | - Clare E. Holleley
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australian Capital Territory, Australia
- Laboratory of Genomic Diversity, National Cancer Institute—National Institutes of Health, Frederick, MD, United States of America
- Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory, Australia
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Kundu S, Kumar V, Tyagi K, Rath S, Pakrashi A, Saren PC, Kosygin L, Chandra K. Mitochondrial DNA detects Arctonyx collaris from burnt body parts: a wildlife forensic case study in Indo-Burma biodiversity hotspot. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1591175] [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)
- Shantanu Kundu
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
| | - Vikas Kumar
- 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
| | - Shibananda Rath
- Freshwater Fish Section, Zoological Survey of India, Kolkata, India
| | - Avas Pakrashi
- 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
- Freshwater Fish Section, Zoological Survey of India, Kolkata, India
- Wildlife Section, Zoological Survey of India, Kolkata, India
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15
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Shang S, Zhang M, Zhao Y, Dang W, Hua P, Zhang S, Wang Z. Development and validation of a novel 13‐plex
PCR
system for commonly used short tandem repeats in horses (
Equus caballus
). Equine Vet J 2018; 51:688-695. [DOI: 10.1111/evj.13047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 11/13/2018] [Indexed: 11/30/2022]
Affiliation(s)
- S. Shang
- Institute of Equine Sciences College of Animal Science and Veterinary Medicine Shenyang Agricultural University Shenyang PR China
- College of Food Science Shenyang Agricultural University Shenyang PR China
| | - M. Zhang
- College of Economics and Management Shenyang Agricultural University Shenyang PR China
| | - Y. Zhao
- Institute of Equine Sciences College of Animal Science and Veterinary Medicine Shenyang Agricultural University Shenyang PR China
| | - W. Dang
- Institute of Equine Sciences College of Animal Science and Veterinary Medicine Shenyang Agricultural University Shenyang PR China
| | - P. Hua
- School of Ecological and Environmental Sciences East China Normal University Shanghai PR China
| | - S. Zhang
- Institute of Equine Sciences College of Animal Science and Veterinary Medicine Shenyang Agricultural University Shenyang PR China
| | - Z. Wang
- Institute of Equine Sciences College of Animal Science and Veterinary Medicine Shenyang Agricultural University Shenyang PR China
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16
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Ciavaglia S, Linacre A. OzPythonPlex: An optimised forensic STR multiplex assay set for the Australasian carpet python (Morelia spilota). Forensic Sci Int Genet 2018; 34:231-248. [PMID: 29571024 DOI: 10.1016/j.fsigen.2018.03.002] [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: 11/05/2017] [Revised: 01/24/2018] [Accepted: 03/01/2018] [Indexed: 12/12/2022]
Abstract
Reptile species, and in particular snakes, are protected by national and international agreements yet are commonly handled illegally. To aid in the enforcement of such legislation, we report on the development of three 11-plex assays from the genome of the carpet python to type 24 loci of tetra-nucleotide and penta-nucleotide repeat motifs (pure, compound and complex included). The loci range in size between 70 and 550 bp. Seventeen of the loci are newly characterised with the inclusion of seven previously developed loci to facilitate cross-comparison with previous carpet python genotyping studies. Assays were optimised in accordance with human forensic profiling kits using one nanogram template DNA. Three loci are included in all three of the multiplex reactions as quality assurance markers, to ensure sample identity and genotyping accuracy is maintained across the three profiling assays. Allelic ladders have been developed for the three assays to ensure consistent and precise allele designation. A DNA reference database of allele frequencies is presented based on 249 samples collected from throughout the species native range. A small number of validation tests are conducted to demonstrate the utility of these multiplex assays. We suggest further appropriate validation tests that should be conducted prior to the application of the multiplex assays in criminal investigations involving carpet pythons.
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Affiliation(s)
- Sherryn Ciavaglia
- Science and Advice for Scottish Agriculture, Edinburgh, United Kingdom; College of Science & Engineering, Flinders University, Adelaide, Australia.
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide, Australia
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17
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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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18
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Hogg CJ, Dennison S, Frankham GJ, Hinds M, Johnson RN. Stopping the spin cycle: genetics and bio-banking as a tool for addressing the laundering of illegally caught wildlife as ‘captive-bred’. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0784-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Ng CH, Lee SL, Tnah LH, Ng KKS, Lee CT, Diway B, Khoo E. Geographic origin and individual assignment of Shorea platyclados (Dipterocarpaceae) for forensic identification. PLoS One 2017; 12:e0176158. [PMID: 28430826 PMCID: PMC5400268 DOI: 10.1371/journal.pone.0176158] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/06/2017] [Indexed: 11/18/2022] Open
Abstract
The development of timber tracking methods based on genetic markers can provide scientific evidence to verify the origin of timber products and fulfill the growing requirement for sustainable forestry practices. In this study, the origin of an important Dark Red Meranti wood, Shorea platyclados, was studied by using the combination of seven chloroplast DNA and 15 short tandem repeats (STRs) markers. A total of 27 natural populations of S. platyclados were sampled throughout Malaysia to establish population level and individual level identification databases. A haplotype map was generated from chloroplast DNA sequencing for population identification, resulting in 29 multilocus haplotypes, based on 39 informative intraspecific variable sites. Subsequently, a DNA profiling database was developed from 15 STRs allowing for individual identification in Malaysia. Cluster analysis divided the 27 populations into two genetic clusters, corresponding to the region of Eastern and Western Malaysia. The conservativeness tests showed that the Malaysia database is conservative after removal of bias from population subdivision and sampling effects. Independent self-assignment tests correctly assigned individuals to the database in an overall 60.60−94.95% of cases for identified populations, and in 98.99−99.23% of cases for identified regions. Both the chloroplast DNA database and the STRs appear to be useful for tracking timber originating in Malaysia. Hence, this DNA-based method could serve as an effective addition tool to the existing forensic timber identification system for ensuring the sustainably management of this species into the future.
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Affiliation(s)
- Chin Hong Ng
- Division of Forestry Biotechnology, Forest Research Institute Malaysia, Kepong, Selangor, Malaysia
- * E-mail:
| | - Soon Leong Lee
- Division of Forestry Biotechnology, Forest Research Institute Malaysia, Kepong, Selangor, Malaysia
| | - Lee Hong Tnah
- Division of Forestry Biotechnology, Forest Research Institute Malaysia, Kepong, Selangor, Malaysia
| | - Kevin Kit Siong Ng
- Division of Forestry Biotechnology, Forest Research Institute Malaysia, Kepong, Selangor, Malaysia
| | - Chai Ting Lee
- Division of Forestry Biotechnology, Forest Research Institute Malaysia, Kepong, Selangor, Malaysia
| | - Bibian Diway
- Sarawak Forestry Corporation, Kuching, Sarawak, Malaysia
| | - Eyen Khoo
- Forest Research Centre, Sandakan, Sabah, Malaysia
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20
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Ng KKS, Lee SL, Tnah LH, Nurul-Farhanah Z, Ng CH, Lee CT, Tani N, Diway B, Lai PS, Khoo E. Forensic timber identification: a case study of a CITES listed species, Gonystylus bancanus (Thymelaeaceae). Forensic Sci Int Genet 2016; 23:197-209. [PMID: 27213560 DOI: 10.1016/j.fsigen.2016.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 05/06/2016] [Accepted: 05/07/2016] [Indexed: 11/26/2022]
Abstract
Illegal logging and smuggling of Gonystylus bancanus (Thymelaeaceae) poses a serious threat to this fragile valuable peat swamp timber species. Using G. bancanus as a case study, DNA markers were used to develop identification databases at the species, population and individual level. The species level database for Gonystylus comprised of an rDNA (ITS2) and two cpDNA (trnH-psbA and trnL) markers based on a 20 Gonystylus species database. When concatenated, taxonomic species recognition was achieved with a resolution of 90% (18 out of the 20 species). In addition, based on 17 natural populations of G. bancanus throughout West (Peninsular Malaysia) and East (Sabah and Sarawak) Malaysia, population and individual identification databases were developed using cpDNA and STR markers respectively. A haplotype distribution map for Malaysia was generated using six cpDNA markers, resulting in 12 unique multilocus haplotypes, from 24 informative intraspecific variable sites. These unique haplotypes suggest a clear genetic structuring of West and East regions. A simulation procedure based on the composition of the samples was used to test whether a suspected sample conformed to a given regional origin. Overall, the observed type I and II errors of the databases showed good concordance with the predicted 5% threshold which indicates that the databases were useful in revealing provenance and establishing conformity of samples from West and East Malaysia. Sixteen STRs were used to develop the DNA profiling databases for individual identification. Bayesian clustering analyses divided the 17 populations into two main genetic clusters, corresponding to the regions of West and East Malaysia. Population substructuring (K=2) was observed within each region. After removal of bias resulting from sampling effects and population subdivision, conservativeness tests showed that the West and East Malaysia databases were conservative. This suggests that both databases can be used independently for random match probability estimation within respective regions. The reliability of the databases was further determined by independent self-assignment tests based on the likelihood of each individual's multilocus genotype occurring in each identified population, genetic cluster and region with an average percentage of correctly assigned individuals of 54.80%, 99.60% and 100% respectively. Thus, after appropriate validation, the genetic identification databases developed for G. bancanus in this study could support forensic applications and help safeguard this valuable species into the future.
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Affiliation(s)
- Kevin Kit Siong Ng
- Genetics Laboratory, Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia.
| | - Soon Leong Lee
- Genetics Laboratory, Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia.
| | - Lee Hong Tnah
- Genetics Laboratory, Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia.
| | - Zakaria Nurul-Farhanah
- Genetics Laboratory, Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia.
| | - Chin Hong Ng
- Genetics Laboratory, Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia.
| | - Chai Ting Lee
- Genetics Laboratory, Forest Research Institute Malaysia, 52109 Kepong, Selangor Darul Ehsan, Malaysia.
| | - Naoki Tani
- Forestry Division, Japan International Research Center for Agricultural Sciences, Ohwashi, Ibaraki 305-8686, Japan.
| | - Bibian Diway
- Sarawak Forestry Corporation, Botanical Research Centre Semenggoh, KM20, Jalan Puncak Borneo, 93250 Kuching, Sarawak, Malaysia.
| | - Pei Sing Lai
- Malaysia Pepper Board, Lot 1115, Jalan Utama, Tanah Putih, 93916 Kuching, Sarawak, Malaysia.
| | - Eyen Khoo
- Forest Research Centre, KM 23, Labuk Road, Sepilok, 90715 Sandakan, Sabah, Malaysia.
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21
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Antognazza CM, Andreou D, Zaccara S, Britton RJ. Loss of genetic integrity and biological invasions result from stocking and introductions of Barbus barbus: insights from rivers in England. Ecol Evol 2016; 6:1280-92. [PMID: 26843923 PMCID: PMC4729780 DOI: 10.1002/ece3.1906] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/02/2015] [Accepted: 12/03/2015] [Indexed: 11/18/2022] Open
Abstract
Anthropogenic activities, including the intentional releases of fish for enhancing populations (stocking), are recognized as adversely impacting the adaptive potential of wild populations. Here, the genetic characteristics of European barbel Barbus barbus were investigated using 18 populations in England, where it is indigenous to eastern‐flowing rivers and where stocking has been used to enhance these populations. Invasive populations are also present in western‐flowing rivers following introductions of translocated fish. Two genetic clusters were evident in the indigenous range, centered on catchments in northeast and southeast England. However, stocking activities, including the release of hatchery‐reared fish, have significantly reduced the genetic differentiation across the majority of this range. In addition, in smaller indigenous rivers, populations appeared to mainly comprise fish of hatchery origin. In the nonindigenous range, genetic data largely aligned to historical stocking records, corroborating information that one particular river (Kennet) in southeast England was the original source of most invasive B. barbus in England. It is recommended that these genetic outputs inform management measures to either restore or maintain the original genetic diversity of the indigenous rivers, as this should help ensure populations can maintain their ability to adapt to changing environmental conditions. Where stocking is considered necessary, it is recommended that only broodstock from within the catchment is used.
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Affiliation(s)
- Caterina Maria Antognazza
- Department of Life and Environmental Sciences Bournemouth University BH12 5BB Poole Dorset UK; Dipartimento di Scienze Teoriche e Applicate Università degli Studi de ll'Insubria 21100 Varese Italy
| | - Demetra Andreou
- Department of Life and Environmental Sciences Bournemouth University BH12 5BB Poole Dorset UK
| | - Serena Zaccara
- Dipartimento di Scienze Teoriche e Applicate Università degli Studi dell'Insubria 21100 Varese Italy
| | - Robert J Britton
- Department of Life and Environmental Sciences Bournemouth University BH12 5BB Poole Dorset UK
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22
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The illegal exploitation of hog badgers (Arctonyx collaris) in China: genetic evidence exposes regional population impacts. CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-015-0467-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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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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24
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Szabolcsi Z, Egyed B, Zenke P, Padar Z, Borsy A, Steger V, Pasztor E, Csanyi S, Buzas Z, Orosz L. Constructing STR multiplexes for individual identification of Hungarian red deer. J Forensic Sci 2014; 59:1090-9. [PMID: 24512288 DOI: 10.1111/1556-4029.12403] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 04/02/2013] [Accepted: 04/06/2013] [Indexed: 11/28/2022]
Abstract
Red deer is the most valuable game of the fauna in Hungary, and there is a strong need for genetic identification of individuals. For this purpose, 10 tetranucleotide STR markers were developed and amplified in two 5-plex systems. The study presented here includes the flanking region sequence analysis and the allele nomenclature of the 10 loci as well as the PCR optimization of the DeerPlex I and II. LD pairwise tests and cross-species similarity analyses showed the 10 loci to be independently inherited. Considerable levels of genetic differences between two subpopulations were recorded, and F(ST) was 0.034 using AMOVA. The average probability of identity (PI(ave)) was at the value of 2.6736 × 10(-15). This low value for PI(ave) nearly eliminates false identification. An illegal hunting case solved by DeerPlex is described herein. The calculated likelihood ratio (LR) illustrates the potential of the 10 red deer microsatellite markers for forensic investigations.
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Affiliation(s)
- Zoltan Szabolcsi
- Department of Genetics, Eötvös Loránd University, Pázmány Péter s. 1/c, 1117, Budapest, Hungary; Institute of Molecular Genetics, Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100, Gödöllő, Hungary; Department of Genetics, Institute for Forensic Sciences, Mosonyi u. 9, 1087, Budapest, Hungary
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25
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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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26
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Validation of two canine STR multiplex-assays following the ISFG recommendations for non-human DNA analysis. Forensic Sci Int Genet 2013; 8:90-100. [PMID: 24315595 DOI: 10.1016/j.fsigen.2013.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 06/07/2013] [Accepted: 07/01/2013] [Indexed: 11/22/2022]
Abstract
To gain general acceptance forensic DNA testing in animals needs to improve standardization of analysis methods and data interpretation. Recently, the International Society of Forensic Genetics (ISFG) took particular care of this topic by publishing recommendations for forensic non-human DNA analysis following the successful example of human DNA analysis in order to provide a basis for harmonization of the still existing inter-laboratory variability. By following these recommendations we demonstrate the performance of two short tandem repeat (STR) multiplexes for forensic identity testing of canine biological material. Thirteen STRs and two sex-specific markers were selected and validated according to the ISFG guidelines. Population genetic parameters were calculated based on 295 dog samples collected in Austria (124) and Germany (171). A repeat-based nomenclature of the mainly tetrameric STRs and corresponding allelic ladders are presented. All 146 different alleles included in the ladders were sequenced for correct allele calling. Additionally, a canine cell line (DH82-D3167) was evaluated as standard reference material.
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27
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Barbanera F, Guerrini M, Beccani C, Forcina G, Anayiotos P, Panayides P. Conservation of endemic and threatened wildlife: Molecular forensic DNA against poaching of the Cypriot mouflon (Ovis orientalis ophion, Bovidae). Forensic Sci Int Genet 2012; 6:671-5. [DOI: 10.1016/j.fsigen.2011.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 11/28/2011] [Accepted: 12/05/2011] [Indexed: 11/16/2022]
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28
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Andreassen R, Schregel J, Kopatz A, Tobiassen C, Knappskog PM, Hagen SB, Kleven O, Schneider M, Kojola I, Aspi J, Rykov A, Tirronen KF, Danilov PI, Eiken HG. A forensic DNA profiling system for Northern European brown bears (Ursus arctos). Forensic Sci Int Genet 2012; 6:798-809. [PMID: 22483764 DOI: 10.1016/j.fsigen.2012.03.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 02/10/2012] [Accepted: 03/11/2012] [Indexed: 11/29/2022]
Abstract
A set of 13 dinucleotide STR loci (G1A, G10B, G1D, G10L, MU05, MU09, MU10, MU15, MU23, MU26, MU50, MU51, MU59) were selected as candidate markers for a DNA forensic profiling system for Northern European brown bear (Ursus arctos). We present results from validation of the markers with respect to their sensitivity, species specificity and performance (precision, heterozygote balance and stutter ratios). All STRs were amplified with 0.6ng template input, and there were no false bear genotypes in the cross-species amplification tests. The validation experiments showed that stutter ratios and heterozygote balance was more pronounced than in the tetranucleotide loci used in human forensics. The elevated ratios of stutter and heterozygote balance at the loci validated indicate that these dinucleotide STRs are not well suited for interpretation of individual genotypes in mixtures. Based on the results from the experimental validations we discuss the challenges related to genotyping dinucleotide STRs in single source samples. Sequence studies of common alleles showed that, in general, the size variation of alleles corresponded with the variation in number of repeats. The samples characterized by sequence analysis may serve as standard DNA samples for inter laboratory calibration. A total of 479 individuals from eight Northern European brown bear populations were analyzed in the 13 candidate STRs. Locus MU26 was excluded as a putative forensic marker after revealing large deviations from expected heterozygosity likely to be caused by null-alleles at this locus. The remaining STRs did not reveal significant deviations from Hardy-Weinberg equilibrium expectations except for loci G10B and MU10 that showed significant deviations in one population each, respectively. There were 9 pairwise locus comparisons that showed significant deviation from linkage equilibrium in one or two out of the eight populations. Substantial genetic differentiation was detected in some of the pairwise population comparisons and the average estimate of population substructure (F(ST)) was 0.09. The average estimate of inbreeding (F(IS)) was 0.005. Accounting for population substructure and inbreeding the total average probability of identity in each of the eight populations was lower than 1.1×10(-9) and the total average probability of sibling identity was lower than 1.3×10(-4). The magnitude of these measurements indicates that if applying these twelve STRs in a DNA profiling system this would provide individual specific evidence.
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Affiliation(s)
- R Andreassen
- Faculty of Health Sciences, Oslo and Akershus University College, Oslo, Norway.
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29
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Genetic data from 15 STR loci for forensic individual identification and parentage analyses in UK domestic dogs (Canis lupus familiaris). Forensic Sci Int Genet 2012; 6:e63-5. [DOI: 10.1016/j.fsigen.2011.04.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 04/06/2011] [Accepted: 04/20/2011] [Indexed: 11/22/2022]
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30
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Lorenzini R, Cabras P, Fanelli R, Carboni GL. Wildlife molecular forensics: identification of the Sardinian mouflon using STR profiling and the Bayesian assignment test. Forensic Sci Int Genet 2011; 5:345-9. [PMID: 21371958 DOI: 10.1016/j.fsigen.2011.01.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 01/24/2011] [Accepted: 01/31/2011] [Indexed: 11/20/2022]
Abstract
A forensic short tandem repeat (STR) typing test using a population database was developed to investigate an instance of poaching on the protected Sardinian mouflon. The case study involves a suspected poacher found in possession of a carcass, which he claimed was that of a sheep from his flock and had died accidentally. His claim was refuted by the molecular forensic analyses as DNA typing and the Bayesian assignment test revealed the carcass to be mouflon-derived; the genetic profile of the carcass matched also that of additional trace evidence collected by forestry officers at the scene of the kill. The matching evidence led to the poacher being charged with the illegal harvest of protected wildlife. Molecular techniques, in combination with a reference population database, and the appropriate statistical evaluation of genetic information, are fundamental to wildlife forensics. This approach allows DNA testing to be accepted in court as submissible evidence in the fight against poaching and other crimes involving wildlife.
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Affiliation(s)
- Rita Lorenzini
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana, Via Tancia 21, 02100 Rieti, Italy.
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OGDEN ROB. Unlocking the potential of genomic technologies for wildlife forensics. Mol Ecol Resour 2011; 11 Suppl 1:109-16. [DOI: 10.1111/j.1755-0998.2010.02954.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Linacre A, Gusmão L, Hecht W, Hellmann AP, Mayr WR, Parson W, Prinz M, Schneider PM, Morling N. ISFG: recommendations regarding the use of non-human (animal) DNA in forensic genetic investigations. Forensic Sci Int Genet 2010; 5:501-5. [PMID: 21106449 DOI: 10.1016/j.fsigen.2010.10.017] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 10/30/2010] [Indexed: 10/18/2022]
Abstract
The use of non-human DNA typing in forensic science investigations, and specifically that from animal DNA, is ever increasing. The term animal DNA in this document refers to animal species encountered in a forensic science examination but does not include human DNA. Non-human DNA may either be: the trade and possession of a species, or products derived from a species, which is contrary to legislation; as evidence where the crime is against a person or property; instances of animal cruelty; or where the animal is the offender. The first instance is addressed by determining the species present, and the other scenarios can often be addressed by assigning a DNA sample to a particular individual organism. Currently there is little standardization of methodologies used in the forensic analysis of animal DNA or in reporting styles. The recommendations in this document relate specifically to animal DNA that is integral to a forensic science investigation and are not relevant to the breeding of animals for commercial purposes. This DNA commission was formed out of discussions at the International Society for Forensic Genetics 23rd Congress in Buenos Aires to outline recommendations on the use of non-human DNA in a forensic science investigation. Due to the scope of non-human DNA typing that is possible, the remit of this commission is confined to animal DNA typing only.
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Affiliation(s)
- A Linacre
- School of Biology, Flinders University, Adelaide, Australia.
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Analysis of 11 tetrameric STRs in wild boars for forensic purposes. Forensic Sci Int Genet 2010; 4:339-42. [DOI: 10.1016/j.fsigen.2010.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 06/22/2010] [Accepted: 07/06/2010] [Indexed: 11/22/2022]
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Ogden R. Forensic science, genetics and wildlife biology: getting the right mix for a wildlife DNA forensics lab. Forensic Sci Med Pathol 2010; 6:172-9. [DOI: 10.1007/s12024-010-9178-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2010] [Indexed: 10/19/2022]
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Tobe SS, Linacre A. DNA typing in wildlife crime: recent developments in species identification. Forensic Sci Med Pathol 2010; 6:195-206. [PMID: 20526699 DOI: 10.1007/s12024-010-9168-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2010] [Indexed: 11/27/2022]
Abstract
Species identification has become a tool in the investigation of acts of alleged wildlife crimes. This review details the steps required in DNA testing in wildlife crime investigations and highlights recent developments where not only can individual species be identified within a mixture of species but multiple species can be identified simultaneously. 'What species is this?' is a question asked frequently in wildlife crime investigations. Depending on the material being examined, DNA analysis may offer the best opportunity to answer this question. Species testing requires the comparison of the DNA type from the unknown sample to DNA types on a database. The areas of DNA tested are on the mitochondria and include predominantly the cytochrome b gene and the cytochrome oxidase I gene. Standard analysis requires the sequencing of part of one of these genes and comparing the sequence to that held on a repository of DNA sequences such as the GenBank database. Much of the DNA sequence of either of these two genes is conserved with only parts being variable. A recent development is to target areas of those sequences that are specific to a species; this can increase the sensitivity of the test with no loss of specificity. The benefit of targeting species specific sequences is that within a mixture of two of more species, the individual species within the mixture can be identified. This identification would not be possible using standard sequencing. These new developments can lead to a greater number of samples being tested in alleged wildlife crimes.
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Affiliation(s)
- Shanan S Tobe
- Centre for Forensic Science, Strathclyde University, WestCHEM, Glasgow, UK
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Chen JW, Uboh CE, Soma LR, Li X, Guan F, You Y, Liu Y. Identification of racehorse and sample contamination by novel 24-plex STR system. Forensic Sci Int Genet 2010; 4:158-67. [DOI: 10.1016/j.fsigen.2009.08.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 08/04/2009] [Accepted: 08/04/2009] [Indexed: 10/20/2022]
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van Asch B, Pinheiro R, Pereira R, Alves C, Pereira V, Pereira F, Gusmão L, Amorim A. A framework for the development of STR genotyping in domestic animal species: Characterization and population study of 12 canine X-chromosome loci. Electrophoresis 2010; 31:303-8. [DOI: 10.1002/elps.200900389] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Affiliation(s)
- T. A. Brettell
- Department of Chemical and Physical Sciences, Cedar Crest College, 100 College Drive, Allentown, Pennsylvania 18104-6196
| | - J. M. Butler
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8312
| | - J. R. Almirall
- Department of Chemistry and Biochemistry and International Forensic Research Institute, Florida International University, University Park, Miami, Florida 33199
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Dawnay N, Ogden R, Wetton JH, Thorpe RS, McEwing R. Genetic data from 28 STR loci for forensic individual identification and parentage analyses in 6 bird of prey species. Forensic Sci Int Genet 2008; 3:e63-9. [PMID: 19215871 DOI: 10.1016/j.fsigen.2008.07.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Revised: 06/06/2008] [Accepted: 07/01/2008] [Indexed: 11/28/2022]
Abstract
Twenty-eight STR loci were screened in wild populations of six bird of prey species providing allele frequencies and population genetic parameters necessary for the application of STRs in wildlife forensic genetic casework. Individual STR loci were validated according to forensic recommendations in specimens of golden eagle (Aquila chrysaetos), goshawk (Accipiter gentilis), merlin (Falco columbarius), peregrine falcon (Falco peregrinus), gyr falcon (Falco rusticolus) and saker falcon (Falco cherrug). Deviations from Hardy-Weinberg expectations and linkage disequilibrium between locus pairs were examined. The average probability of identity (PI(ave)) and power of exclusion (PE) suggest the profiling systems of golden eagle, goshawk, merlin and peregrine falcons are capable of providing robust and highly discriminatory forensic evidence for legal proceedings. Due to low sample numbers the allele frequency data for gyr and saker falcons is not currently capable of providing an effective probability of identity. Further work should focus on increasing the size of these data sets.
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Affiliation(s)
- Nick Dawnay
- School of Biological Sciences, Bangor University, Deiniol Road, Bangor LL57 2UW, United Kingdom.
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