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Whole genome survey of big cats (Genus: Panthera) identifies novel microsatellites of utility in conservation genetic study. Sci Rep 2021; 11:14164. [PMID: 34238947 PMCID: PMC8266911 DOI: 10.1038/s41598-021-92781-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 06/14/2021] [Indexed: 02/06/2023] Open
Abstract
Big cats (Genus: Panthera) are among the most threatened mammal groups of the world, owing to hunting, habitat loss, and illegal transnational trade. Conservation genetic studies and effective curbs on poaching are important for the conservation of these charismatic apex predators. A limited number of microsatellite markers exists for Panthera species and researchers often cross-amplify domestic cat microsatellites to study these species. We conducted data mining of seven Panthera genome sequences to discover microsatellites for conservation genetic studies of four threatened big cat species. A total of 32 polymorphic microsatellite loci were identified in silico and tested with 152 big cats, and were found polymorphic in most of the tested species. We propose a set of 12 novel microsatellite markers for use in conservation genetics and wildlife forensic investigations of big cat species. Cumulatively, these markers have a high discriminatory power of one in a million for unrelated individuals and one in a thousand for siblings. Similar PCR conditions of these markers increase the prospects of achieving efficient multiplex PCR assays. This study is a pioneering attempt to synthesise genome wide microsatellite markers for big cats.
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2
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Avoiding common numts to provide reliable species identification for tiger parts. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2021. [DOI: 10.1016/j.fsir.2020.100166] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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3
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Smart U, Cihlar JC, Budowle B. International Wildlife Trafficking: A perspective on the challenges and potential forensic genetics solutions. Forensic Sci Int Genet 2021; 54:102551. [PMID: 34134047 DOI: 10.1016/j.fsigen.2021.102551] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/29/2022]
Abstract
International wildlife trafficking (IWT) is a thriving and pervasive illegal enterprise that adversely affects modern societies. Yet, despite being globally recognized as a threat to biodiversity, national security, economy, and biosecurity, IWT remains largely unabated and is proliferating at an alarming rate. The increase in IWT is generally attributed to a lack of prioritization to curb wildlife crime through legal and scientific infrastructure. This review: (1) lays out the damaging scope and influence of IWT; (2) discusses the potential of DNA marker systems, barcodes, and emerging molecular technologies, such as long-read portable sequencing, to facilitate rapid, in situ identification of species and individuals; and (3) encourages initiatives that promote quality and innovation. Interdisciplinary collaboration promises to be one of the most effective ways forward to surmounting the complex scientific and legal challenges posed by IWT.
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Affiliation(s)
- Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA.
| | - Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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Sinha K, Sharma P, Som Chaudhury S, Das Mukhopadhyay C, Ruidas B. Species detection using probe technology. FOOD TOXICOLOGY AND FORENSICS 2021:313-346. [DOI: 10.1016/b978-0-12-822360-4.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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5
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Using blood and non-invasive shed skin samples to identify sex of caenophidian snakes based on multiplex PCR assay. ZOOL ANZ 2017. [DOI: 10.1016/j.jcz.2017.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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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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Lindberg MR, Schmedes SE, Hewitt FC, Haas JL, Ternus KL, Kadavy DR, Budowle B. A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes. PLoS One 2016; 11:e0167600. [PMID: 27936026 PMCID: PMC5147911 DOI: 10.1371/journal.pone.0167600] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/16/2016] [Indexed: 12/17/2022] Open
Abstract
Single source and multiple donor (mixed) samples of human mitochondrial DNA were analyzed and compared using the MinION and the MiSeq platforms. A generalized variant detection strategy was employed to provide a cursory framework for evaluating the reliability and accuracy of mitochondrial sequences produced by the MinION. The feasibility of long-read phasing was investigated to establish its efficacy in quantitatively distinguishing and deconvolving individuals in a mixture. Finally, a proof-of-concept was demonstrated by integrating both platforms in a hybrid assembly that leverages solely mixture data to accurately reconstruct full mitochondrial genomes.
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Affiliation(s)
| | - Sarah E. Schmedes
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | | | - Jamie L. Haas
- Signature Science, LLC, Austin, Texas, United States of America
| | | | - Dana R. Kadavy
- Signature Science, LLC, Austin, Texas, United States of America
| | - Bruce Budowle
- Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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CIORPAC M, DRUICĂ RC, GHIORGHIȚĂ G, COJOCARU D, GORGAN DL. CHD genes: a reliable marker for bird populations and phylogenetic analysis?Case study of the superfamily Sylvioidea (Aves: Passeriformes). TURK J ZOOL 2016. [DOI: 10.3906/zoo-1510-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Molecular identification of python species: development and validation of a novel assay for forensic investigations. Forensic Sci Int Genet 2014; 16:64-70. [PMID: 25541013 DOI: 10.1016/j.fsigen.2014.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 11/28/2014] [Accepted: 12/09/2014] [Indexed: 11/20/2022]
Abstract
Python snake species are often encountered in illegal activities and the question of species identity can be pertinent to such criminal investigations. Morphological identification of species of pythons can be confounded by many issues and molecular examination by DNA analysis can provide an alternative and objective means of identification. Our paper reports on the development and validation of a PCR primer pair that amplifies a segment of the mitochondrial cytochrome b gene that has been suggested previously as a good candidate locus for differentiating python species. We used this DNA region to perform species identification of pythons, even when the template DNA was of poor quality, as might be the case with forensic evidentiary items. Validation tests are presented to demonstrate the characteristics of the assay. Tests involved the cross-species amplification of this marker in non-target species, minimum amount of DNA template required, effects of degradation on product amplification and a blind trial to simulate a casework scenario that provided 100% correct identity. Our results demonstrate that this assay performs reliably and robustly on pythons and can be applied directly to forensic investigations where the presence of a species of python is in question.
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Yang Y, Xie B, Yan J. Application of next-generation sequencing technology in forensic science. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:190-7. [PMID: 25462152 PMCID: PMC4411420 DOI: 10.1016/j.gpb.2014.09.001] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/28/2014] [Accepted: 09/09/2014] [Indexed: 12/03/2022]
Abstract
Next-generation sequencing (NGS) technology, with its high-throughput capacity and low cost, has developed rapidly in recent years and become an important analytical tool for many genomics researchers. New opportunities in the research domain of the forensic studies emerge by harnessing the power of NGS technology, which can be applied to simultaneously analyzing multiple loci of forensic interest in different genetic contexts, such as autosomes, mitochondrial and sex chromosomes. Furthermore, NGS technology can also have potential applications in many other aspects of research. These include DNA database construction, ancestry and phenotypic inference, monozygotic twin studies, body fluid and species identification, and forensic animal, plant and microbiological analyses. Here we review the application of NGS technology in the field of forensic science with the aim of providing a reference for future forensics studies and practice.
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Affiliation(s)
- Yaran Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bingbing Xie
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiangwei Yan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
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11
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Pilli E, Casamassima R, Vai S, Virgili A, Barni F, D’Errico G, Berti A, Lago G, Caramelli D. Pet fur or fake fur? A forensic approach. INVESTIGATIVE GENETICS 2014; 5:7. [PMID: 24991403 PMCID: PMC4079164 DOI: 10.1186/2041-2223-5-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/29/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND In forensic science there are many types of crime that involve animals. Therefore, the identification of the species has become an essential investigative tool. The exhibits obtained from such offences are very often a challenge for forensic experts. Indeed, most biological materials are traces, hair or tanned fur. With hair samples, a common forensic approach should proceed from morphological and structural microscopic examination to DNA analysis. However, the microscopy of hair requires a lot of experience and a suitable comparative database to be able to recognize with a high degree of accuracy that a sample comes from a particular species and then to determine whether it is a protected one. DNA analysis offers the best opportunity to answer the question, 'What species is this?' In our work, we analyzed different samples of fur coming from China used to make hats and collars. Initially, the samples were examined under a microscope, then the mitochondrial DNA was tested for species identification. For this purpose, the genetic markers used were the 12S and 16S ribosomal RNA, while the hypervariable segment I of the control region was analyzed afterwards, to determine whether samples belonged to the same individual. RESULTS Microscopic examination showed that the fibres were of animal origin, although it was difficult to determine with a high degree of confidence which species they belonged to and if they came from a protected species. Therefore, DNA analysis was essential to try to clarify the species of these fur samples. CONCLUSIONS Macroscopic and microscopic analysis confirmed the hypothesis regarding the analyzed hair belonging to real animals, although it failed to prove with any kind of certainty which actual family it came from, therefore, the species remains unknown. Sequence data analysis and comparisons with the samples available in GenBank showed that the hair, in most cases, belonged to the Canidae family, and in one case only to Felidae.
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Affiliation(s)
- Elena Pilli
- Dipartimento di Biologia, Università di Firenze, via del Proconsolo 12, 50122 Florence, Italy
| | - Rosario Casamassima
- Reparto Carabinieri Investigazioni Scientifiche di Roma, Sezione di Chimica, viale Tor di Quinto 119, Rome, Italy
| | - Stefania Vai
- Dipartimento di Biologia, Università di Firenze, via del Proconsolo 12, 50122 Florence, Italy
| | - Antonino Virgili
- Istituto Superiore di Tecniche Investigative dei Carabinieri, viale Salvo D’Acquisto 2, 00049 Velletri (Roma), Italy
| | - Filippo Barni
- Reparto Carabinieri Investigazioni Scientifiche di Roma, Sezione di Biologia, viale Tor di Quinto 119, Rome, Italy
| | - Giancarlo D’Errico
- Reparto Carabinieri Investigazioni Scientifiche di Roma, Sezione di Biologia, viale Tor di Quinto 119, Rome, Italy
| | - Andrea Berti
- Reparto Carabinieri Investigazioni Scientifiche di Roma, Sezione di Biologia, viale Tor di Quinto 119, Rome, Italy
| | - Giampietro Lago
- Reparto Carabinieri Investigazioni Scientifiche di Parma, Parco Ducale 3, Parma, Italy
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, via del Proconsolo 12, 50122 Florence, Italy
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12
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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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13
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A universal method for species identification of mammals utilizing next generation sequencing for the analysis of DNA mixtures. PLoS One 2013; 8:e83761. [PMID: 24358309 PMCID: PMC3865308 DOI: 10.1371/journal.pone.0083761] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 11/07/2013] [Indexed: 11/19/2022] Open
Abstract
Species identification can be interesting in a wide range of areas, for example, in forensic applications, food monitoring and in archeology. The vast majority of existing DNA typing methods developed for species determination, mainly focuses on a single species source. There are, however, many instances where all species from mixed sources need to be determined, even when the species in minority constitutes less than 1 % of the sample. The introduction of next generation sequencing opens new possibilities for such challenging samples. In this study we present a universal deep sequencing method using 454 GS Junior sequencing of a target on the mitochondrial gene 16S rRNA. The method was designed through phylogenetic analyses of DNA reference sequences from more than 300 mammal species. Experiments were performed on artificial species-species mixture samples in order to verify the method's robustness and its ability to detect all species within a mixture. The method was also tested on samples from authentic forensic casework. The results showed to be promising, discriminating over 99.9 % of mammal species and the ability to detect multiple donors within a mixture and also to detect minor components as low as 1 % of a mixed sample.
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Mitochondrial 16S ribosomal RNA gene for forensic identification of crocodile species. J Forensic Leg Med 2013; 20:334-8. [DOI: 10.1016/j.jflm.2012.09.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 07/15/2012] [Accepted: 09/07/2012] [Indexed: 02/07/2023]
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15
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Recovery of human DNA profiles from poached deer remains part 2: improved recovery protocol without the need for LCN analysis. Sci Justice 2013; 53:23-7. [PMID: 23380058 DOI: 10.1016/j.scijus.2012.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 02/24/2012] [Accepted: 03/06/2012] [Indexed: 11/22/2022]
Abstract
Although poaching is a common wildlife crime, the high and prohibitive cost of specialised animal testing means that many cases are left un-investigated. We previously described a novel approach to wildlife crime investigation that looked at the identification of human DNA on poached animal remains (Tobe, Govan and Welch, 2011). Human DNA was successfully isolated and amplified from simulated poaching incidents, however a low template protocol was required which made this method unsuitable for use in many laboratories. We now report on an optimised recovery and amplification protocol which removes the need for low template analysis. Samples from 10 deer (40 samples total - one from each leg) analysed in the original study were re-analysed in the current study with an additional 11 deer samples. Four samples analysed using Chelex did not show any results and a new method was devised whereby the available DNA was concentrated. By combining the DNA extracts from all tapings of the same deer remains followed by concentration, the recovered quantity of human DNA was found to be 29.5pg±43.2pg, 31× greater than the previous study. The use of the Investigator Decaplex SE (QIAGEN) STR kit provided better results in the form of more complete profiles than did the AmpFℓSTR® SGM Plus® kit at 30cycles (Applied Biosystems). Re-analysis of the samples from the initial study using the new, optimised protocol resulted in an average increase of 18% of recovered alleles. Over 17 samples, 71% of the samples analysed using the optimised protocol showed sufficient amplification for comparison to a reference profile and gave match probabilities ranging from 7.7690×10(-05) to 2.2706×10(-14). The removal of low template analysis means this optimised method provides evidence of high probative value and is suitable for immediate use in forensic laboratories. All methods and techniques used are standard and are compatible with current SOPs. As no high cost non-human DNA analysis is required the overall process is no more expensive than the investigation of other volume crime samples. The technique is suitable for immediate use in poaching incidents.
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Ghorpade PB, Gupta PK, Prakash V, Cuthbert RJ, Kulkarni M, Prakash N, Das A, Sharma AK, Saini M. Molecular sexing of threatened Gyps vultures: an important strategy for conservation breeding and ecological studies. SPRINGERPLUS 2012; 1:62. [PMID: 23316450 PMCID: PMC3540358 DOI: 10.1186/2193-1801-1-62] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Accepted: 12/07/2012] [Indexed: 11/10/2022]
Abstract
During the last two decades populations of three resident species of Gyps vulture have declined dramatically and are now threatened with extinction in South Asia. Sex identification of vultures is of key importance for the purpose of conservation breeding as it is desirable to have an equal sex ratio in these monogamous species which are housed together in large colony aviaries. Because vultures are monomorphic, with no differences in external morphology or plumage colour between the sexes, other methods are required for sex identification. Molecular methods for sex identification in birds rely on allelic length or nucleotide sequence discrimination of the chromohelicase-DNA binding (CHD) gene located on male and female chromosomes ZZ and ZW, respectively. We characterized the partial sequences of CHD alleles from Gyps indicus, Gyps bengalensis, Gyps himalayensis and Aegypius monachus and analysed the applicability of five molecular methods of sex identification of 46 individual vultures including 26 known-sex G. bengalensis and G. indicus. The results revealed that W-specific PCR in combination with ZW-common PCR is a quick, accurate and simple method, and is ideal for sex identification of vultures. The method is also suitable to augment ecological studies for identifying sex of these endangered birds during necropsy examinations especially when gonads are not apparent, possibly due to regression during non-breeding seasons.
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Affiliation(s)
- Prabhakar B Ghorpade
- Centre for Wildlife Conservation, Management & Disease Surveillance, Indian Veterinary Research Institute, Izatnagar, 243 122 India
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Morinha F, Cabral J, Bastos E. Molecular sexing of birds: A comparative review of polymerase chain reaction (PCR)-based methods. Theriogenology 2012; 78:703-14. [DOI: 10.1016/j.theriogenology.2012.04.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 04/18/2012] [Accepted: 04/26/2012] [Indexed: 02/08/2023]
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18
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Wozney KM, Wilson PJ. Real-time PCR detection and quantification of elephantid DNA: Species identification for highly processed samples associated with the ivory trade. Forensic Sci Int 2012; 219:106-12. [DOI: 10.1016/j.forsciint.2011.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 12/12/2011] [Accepted: 12/18/2011] [Indexed: 10/14/2022]
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Morinha F, Magalhães P, Ferro A, Guedes-Pinto H, Rodrigues R, Bastos E. Advances in Molecular Sexing of Birds: A High-Resolution Melting-Curve Analysis Based onCHD1Gene Applied toCoturnixspp. ANN ZOOL FENN 2011. [DOI: 10.5735/086.048.0605] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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MORINHA FRANCISCO, CARVALHO MÁRCIA, FERRO ANABELA, GUEDES-PINTO HENRIQUE, RODRIGUES ROGÉRIO, BASTOS ESTELA. Molecular sexing and analysis of CHD1-Z and CHD1-W sequence variations in wild common quail (Coturnix c. coturnix) and domesticated Japanese quail (Coturnix c. japonica). J Genet 2011. [DOI: 10.1007/s12041-011-0053-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Recovery of human DNA profiles from poached deer remains: a feasibility study. Sci Justice 2011; 51:190-5. [PMID: 22137052 DOI: 10.1016/j.scijus.2011.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 06/27/2011] [Accepted: 06/29/2011] [Indexed: 11/23/2022]
Abstract
Poaching is a crime that occurs worldwide and can be extremely difficult to investigate and prosecute due to the nature of the evidence available. If a species is protected by international legislation such as the Convention on International Trade in Endangered Species of Wild Fauna and Flora then simply possessing any part of that species is illegal. Previous studies have focused on the identification of endangered species in cases of potential poaching. Difficulties arise if the poached animal is not endangered. Species such as deer have hunting seasons whereby they can legally be hunted however poaching is the illegal take of deer, irrespective of season. Therefore, identification of deer alone has little probative value as samples could have originated from legal hunting activities in season. After a deer is hunted it is usual to remove the innards, head and lower limbs. The limbs are removed through manual force and represent a potential source of human touch DNA. We investigate the potential to recover and profile human autosomal DNA from poached deer remains. Samples from the legs of ten culled deer were obtained (40 in total) using minitapes. DNA from samples was extracted, quantified and amplified to determine if it would be possible to recover human STR profiles. Low quantification data led to the use of an extended PCR cycling protocol of 34 cycles. Samples from seven deer amplified, however some samples were excluded from further analysis due to 'drop in' alleles or the low level of successfully amplified loci. Samples from five deer could be further analysed and gave match probabilities ranging from 6.37×10(-3) to 9.53×10(-11). This study demonstrates the potential of recovering human touch DNA from poached animal remains. There is the potential for this test to be used in relation to other species of poached remains or other types of wildlife crimes. This is the first time, to our knowledge, that human STR profiling has been successfully applied to touch DNA in regards to simulated wildlife crime.
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22
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Arif IA, Khan HA, Bahkali AH, Al Homaidan AA, Al Farhan AH, Al Sadoon M, Shobrak M. DNA marker technology for wildlife conservation. Saudi J Biol Sci 2011; 18:219-25. [PMID: 23961128 PMCID: PMC3730548 DOI: 10.1016/j.sjbs.2011.03.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Revised: 03/22/2011] [Accepted: 03/28/2011] [Indexed: 02/05/2023] Open
Abstract
Use of molecular markers for identification of protected species offers a greater promise in the field of conservation biology. The information on genetic diversity of wildlife is necessary to ascertain the genetically deteriorated populations so that better management plans can be established for their conservation. Accurate classification of these threatened species allows understanding of the species biology and identification of distinct populations that should be managed with utmost care. Molecular markers are versatile tools for identification of populations with genetic crisis by comparing genetic diversities that in turn helps to resolve taxonomic uncertainties and to establish management units within species. The genetic marker analysis also provides sensitive and useful tools for prevention of illegal hunting and poaching and for more effective implementation of the laws for protection of the endangered species. This review summarizes various tools of DNA markers technology for application in molecular diversity analysis with special emphasis on wildlife conservation.
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Affiliation(s)
- Ibrahim A. Arif
- Molecular Fingerprinting and Biodiversity Unit, Prince Sultan Research Chair for Environment and Wildlife, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Haseeb A. Khan
- Molecular Fingerprinting and Biodiversity Unit, Prince Sultan Research Chair for Environment and Wildlife, College of Sciences, King Saud University, Riyadh, Saudi Arabia
- Corresponding author. Address: College of Science, Bld 5, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia. Tel.: +966 1 4674712.
| | - Ali H. Bahkali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ali A. Al Homaidan
- Molecular Fingerprinting and Biodiversity Unit, Prince Sultan Research Chair for Environment and Wildlife, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ahmad H. Al Farhan
- Molecular Fingerprinting and Biodiversity Unit, Prince Sultan Research Chair for Environment and Wildlife, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Al Sadoon
- Molecular Fingerprinting and Biodiversity Unit, Prince Sultan Research Chair for Environment and Wildlife, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Shobrak
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
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23
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Lee SJ, Jung G, Min MS, Kim CK, Lee H, Kim CB, Lee MY. Genetic origin identification of Siberian chipmunks (Tamias sibiricus) in pet shops of South Korea. Anim Cells Syst (Seoul) 2011. [DOI: 10.1080/19768354.2011.577586] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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24
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Linacre A, Tobe SS. An overview to the investigative approach to species testing in wildlife forensic science. INVESTIGATIVE GENETICS 2011; 2:2. [PMID: 21232099 PMCID: PMC3032691 DOI: 10.1186/2041-2223-2-2] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 01/13/2011] [Indexed: 11/28/2022]
Abstract
The extent of wildlife crime is unknown but it is on the increase and has observable effects with the dramatic decline in many species of flora and fauna. The growing awareness of this area of criminal activity is reflected in the increase in research papers on animal DNA testing, either for the identification of species or for the genetic linkage of a sample to a particular organism. This review focuses on the use of species testing in wildlife crime investigations. Species identification relies primarily on genetic loci within the mitochondrial genome; focusing on the cytochrome b and cytochrome oxidase 1 genes. The use of cytochrome b gained early prominence in species identification through its use in taxonomic and phylogenetic studies, while the gene sequence for cytochrome oxidase was adopted by the Barcode for Life research group. This review compares how these two loci are used in species identification with respect to wildlife crime investigations. As more forensic science laboratories undertake work in the wildlife area, it is important that the quality of work is of the highest standard and that the conclusions reached are based on scientific principles. A key issue in reporting on the identification of a particular species is a knowledge of both the intraspecies variation and the possible overlap of sequence variation from one species to that of a closely related species. Recent data showing this degree of genetic separation in mammalian species will allow greater confidence when preparing a report on an alleged event where the identification of the species is of prime importance. The aim of this review is to illustrate aspects of species testing in wildlife forensic science and to explain how a knowledge of genetic variation at the genus and species level can aid in the reporting of results.
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Affiliation(s)
- Adrian Linacre
- South Australia Justice Chair in Forensic Science, School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
| | - Shanan S Tobe
- Centre for Forensic Science, WestChem, University of Strathclyde, Glasgow, UK
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25
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Russell TC, Neaves LE, Herbert CA. Allocating sex in road-killed possums using PCR. AUSTRALIAN MAMMALOGY 2011. [DOI: 10.1071/am09028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Road-killed animals are a readily available but often overlooked source of specimens and data. Determining the sex of road-killed possums is often difficult due to the severe damage carcasses sustain on impact with vehicles. Consequently, valuable information is lost. To assess the potential application of genetic techniques to address this problem, tissue biopsies (n = 47) taken from road-killed possums were sexed via PCR, through the simultaneous use of W- (G6PD) and Y-linked (SRY) primers. Comparisons with animals of known sex were used to validate the accuracy of this method, with 100% (n = 19) of samples correctly identified in a blind test. This methodology can provide researchers with valuable, additional data for road-kill studies where assigning sex in the field is not possible.
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26
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Steiner CC, Houck ML, Ryder OA. Species identification and chromosome variation of captive two-toed sloths. Zoo Biol 2010; 30:623-35. [PMID: 22147591 DOI: 10.1002/zoo.20360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 09/22/2010] [Accepted: 09/30/2010] [Indexed: 11/06/2022]
Abstract
Two-toed sloth species, Linnaeus's and Hoffmman's, are frequent residents of zoo collections in North America. However, species identification has always been problematic because of their large overlap in external morphology, which represents an obstacle to the captive breeding program. We describe here a PCR-based technique that allows species identification of two-toed sloths without requiring sequencing, by using a mitochondrial marker (COI gene) and restriction enzyme assay. We also report intra- and inter-specific patterns of chromosome variation in captive two-toed sloths. Molecularly, we identified 22 samples of Linnaeus's and Hoffmman's two-toed sloths corresponding to 14 and 8 individuals, respectively. One animal was identified as a hybrid using the nuclear gene Enam having alleles derived from both species. The chromosome number in Hoffman's two-toed sloths showed low variation ranging only between 50 and 51. In contrast, Linnaeus's two-toed sloths appeared to vary widely, with diploid numbers ranging from 53 to 67, suggesting distinct geographic groups. The species identification method presented here represents a low-cost easy-to-use tool that will help to improve management of the captive population of two-toed sloths.
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Affiliation(s)
- Cynthia C Steiner
- San Diego Zoo Institute for Conservation Research, Escondido, California 92027, USA.
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27
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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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28
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Alacs EA, Georges A, FitzSimmons NN, Robertson J. DNA detective: a review of molecular approaches to wildlife forensics. Forensic Sci Med Pathol 2009; 6:180-94. [PMID: 20013321 DOI: 10.1007/s12024-009-9131-7] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2009] [Indexed: 11/26/2022]
Abstract
Illegal trade of wildlife is growing internationally and is worth more than USD$20 billion per year. DNA technologies are well suited to detect and provide evidence for cases of illicit wildlife trade yet many of the methods have not been verified for forensic applications and the diverse range of methods employed can be confusing for forensic practitioners. In this review, we describe the various genetic techniques used to provide evidence for wildlife cases and thereby exhibit the diversity of forensic questions that can be addressed using currently available genetic technologies. We emphasise that the genetic technologies to provide evidence for wildlife cases are already available, but that the research underpinning their use in forensics is lacking. Finally we advocate and encourage greater collaboration of forensic scientists with conservation geneticists to develop research programs for phylogenetic, phylogeography and population genetics studies to jointly benefit conservation and management of traded species and to provide a scientific basis for the development of forensic methods for the regulation and policing of wildlife trade.
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Affiliation(s)
- E A Alacs
- Institute for Applied Ecology and National Centre for Forensic Studies, University of Canberra, Canberra, ACT, Australia.
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29
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Oliveira R, Castro D, Godinho R, Luikart G, Alves PC. Species identification using a small nuclear gene fragment: application to sympatric wild carnivores from South-western Europe. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9947-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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30
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Marín JC, Saucedo CE, Corti P, González BA. Application of DNA forensic techniques for identifying poached guanacos (Lama guanicoe) in Chilean Patagonia*. J Forensic Sci 2009; 54:1073-6. [PMID: 19549029 DOI: 10.1111/j.1556-4029.2009.01087.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Guanaco (Lama guanicoe) is a protected and widely distributed ungulate in South America. A poacher, after killing guanacos in Valle Chacabuco, Chilean Patagonia, transported and stored the meat. Samples were retrieved by local police but the suspect argued that the meat was from a horse. Mitochondrial cytochrome b gene (774 pb), 15 loci microsatellites, and SRY gene were used to identify the species, number of animals and their population origin, and the sex of the animals, respectively. Analysis revealed that the samples came from a female (absence of SRY gene) Patagonian guanaco (assignment probability between 0.0075 and 0.0282), and clearly distinguishing it from sympatric ungulates (E-value = 0). Based on the evidence obtained in the field in addition to forensic data, the suspect was convicted of poaching and illegally carrying fire arms. This is the first report of molecular tools being used in forensic investigations of Chilean wildlife indicating its promising future application in guanaco management and conservation.
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Affiliation(s)
- Juan C Marín
- Departamento de Ciencias Básicas, Facultad de Ciencias, Laboratorio de Genómica y Biodiversidad, Universidad del Bío-Bío, Casilla 447, Chillán, Chile.
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31
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Polymerase chain reaction-single strand conformation polymorphism applied to sex identification of Accipiter cooperii. Mol Cell Probes 2009; 23:115-8. [DOI: 10.1016/j.mcp.2008.12.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 11/07/2008] [Accepted: 12/11/2008] [Indexed: 11/23/2022]
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32
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Forensic species identification based on size variation of mitochondrial DNA hypervariable regions. Int J Legal Med 2008; 123:177-84. [PMID: 19052767 DOI: 10.1007/s00414-008-0306-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Accepted: 11/17/2008] [Indexed: 10/21/2022]
Abstract
In this study, two new systems for species identification were developed based on size variation of mitochondrial DNA hypervariable regions among animals: one was a conventional method using non-fluorescent primer sets and agarose gel electrophoresis and the other was an automatic method using fluorescent primer sets and capillary electrophoresis. DNA samples from 18 mammal, four birds, and 19 fish species were amplified using three primer sets specific for mammals, birds, and fishes, respectively. The differences in the sizes of the polymerase chain reaction (PCR) products, ranging from about 350 to 900 bp, permitted us to identify species. These systems were successfully applied to various specimens from several criminal cases. In unknown samples, which were different in size from reference DNA markers, sequencing of the PCR products and subsequent BLAST analysis helped to identify species. Furthermore, the sequence data provided us with information on individuals. Because these species identification methods are very simple, easy, rapid, and exact, they are useful in the field of forensic science.
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34
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Ong AH, Vellayan S. An evaluation of CHD-Specific primer sets for sex typing of birds from feathers. Zoo Biol 2008; 27:62-9. [DOI: 10.1002/zoo.20163] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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