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Harper CK. Poaching Forensics: Animal Victims in the Courtroom. Annu Rev Anim Biosci 2023; 11:269-286. [PMID: 36790886 DOI: 10.1146/annurev-animal-070722-084803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Poaching and the international trade in wildlife are escalating problems driven by poverty and greed and coordinated by increasingly sophisticated criminal networks. Biodiversity loss, caused by habitat change, is exacerbated by poaching, and species globally are facing extinction. Forensic evidence underpins human and animal criminal investigations and is critical in criminal prosecution and conviction. The application of forensic tools, particularly forensic genetics, to animal case work continues to advance, providing the systems to confront the challenges of wildlife investigations. This article discusses some of these tools, their development, and implementations, as well as recent advances. Examples of cases are provided in which forensic evidence played a key role in obtaining convictions, thus laying the foundation for the future application of techniques to disrupt the criminal networks and safeguard biodiversity through species protection.
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Affiliation(s)
- Cindy K Harper
- Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa;
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2
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Stanbridge D, O’Riain MJ, Dreyer C, le Roex N. Genetic restoration of black rhinoceroses in South Africa: conservation implications. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01486-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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3
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Chanyandura A, Muposhi VK, Gandiwa E, Muboko N. An analysis of threats, strategies, and opportunities for African rhinoceros conservation. Ecol Evol 2021; 11:5892-5910. [PMID: 34141191 PMCID: PMC8207337 DOI: 10.1002/ece3.7536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 03/14/2021] [Accepted: 03/19/2021] [Indexed: 12/11/2022] Open
Abstract
The complexity and magnitude of threats to black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros conservation in Africa have triggered global concerns and actions. In this study, we analyzed (i) threats to rhinoceros conservation including external shocks, (ii) historical rhinoceros conservation strategies in Zimbabwe and Africa, more broadly, and (iii) opportunities for enhanced rhinoceros conservation in Zimbabwe and Africa. A literature search from 1975 to 2020 was carried out using a predefined search protocol, involving a number of filters based on a set of keywords to balance search sensitivity with specificity. A total of 193 articles, which were most relevant to key themes on rhinoceros conservation, were used in this study. The common threats to rhinoceros conservation identified in this paper include poaching, habitat fragmentation and loss, international trade in illegal rhino products, and external shocks such as global financial recessions and pandemics. Cascading effects emanating from these threats include small and isolated populations, which are prone to genetic, demographic, and environmental uncertainties. Rhinoceros conservation strategies being implemented include education and awareness campaigns, better equipped and more antipoaching efforts, use of innovative systems and technologies, dehorning, and enhancing safety nets, and livelihoods of local communities. Opportunities for rhinoceros conservation vary across the spatial scale, and these include (a) a well-coordinated stakeholder and community involvement, (b) strategic meta-population management, (c) enhancing law enforcement initiatives through incorporating real-time surveillance technologies and intruder detection sensor networks for crime detection, (d) scaling up demand reduction awareness campaigns, and (e) developing more certified wildlife crime and forensic laboratories, and information repository for international corporation.
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Affiliation(s)
- Admire Chanyandura
- School of Wildlife, Ecology and ConservationChinhoyi University of TechnologyChinhoyiZimbabwe
| | - Victor K. Muposhi
- School of Wildlife, Ecology and ConservationChinhoyi University of TechnologyChinhoyiZimbabwe
| | - Edson Gandiwa
- Scientific ServicesZimbabwe Parks and Wildlife Management AuthorityHarareZimbabwe
| | - Never Muboko
- School of Wildlife, Ecology and ConservationChinhoyi University of TechnologyChinhoyiZimbabwe
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4
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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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5
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Abstract
Wildlife crime is on a massive scale by whatever metric is used. The illegal trade in wildlife and related products is leading to the decline and extinction of many iconic species from rhino to tigers. Almost all countries are signatures to CITES and therefore should enforce national legislation if alleged infringements of trade of wildlife occur. No country is immune from this illegal trade although countries like Australia have their own specific wildlife crimes. Australia is home to many reptilian, amphibian and avian species that are highly prized, predominantly as pets. Collection of protected species from the wild is illegal in all jurisdictions yet policing remote areas of the outback, where so much of the native endemic fauna and flora lives, is nearly impossible. The illegal international trade in these species is highlighted by two case studies provided in this review. A further case highlights the issues of each of the six states of Australia having separate legislation, which is compounded when wildlife crime can be inter-state crime. Australia is one of the few countries having an institute, based at the Australian Museum, with an accredited wildlife forensic science laboratory and therefore the capability to undertake forensic testing of seized samples. One way to reduce wildlife crime may be by educating those who buy illegally seized products that there is a direct connection between the dead animal from which it came and the devasting effect this purchase has on the environment.
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Ghosh T, Sharma A, Mondol S. Optimisation and application of a forensic microsatellite panel to combat Greater-one horned rhinoceros (Rhinoceros unicornis) poaching in India. Forensic Sci Int Genet 2021; 52:102472. [PMID: 33548856 DOI: 10.1016/j.fsigen.2021.102472] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 11/28/2022]
Abstract
The Greater one-horned (GoH) rhinoceros is one of the most charismatic endemic megaherbivores of the Indian subcontinent. Threatened by poaching, habitat loss and disease, the species is found only in small areas of its historical distribution. Increasing demands for rhino horns in chinese traditional medicine has put the existing population under continuing threat, and large profits and low conviction rates make poaching difficult to contain. DNA forensics such as the RhoDIS-Africa program has helped in combating illegal rhino horn trade, but the approach is yet to be optimised for Indian GoH rhinoceros. Here we followed the International Society for Forensic Genetics (ISFG) guidelines to establish a 14 dinucleotide microsatellite panel for Indian GoH rhinoceros DNA profiling. Selected from a large initial pool (n = 34), the microsatellite markers showed high polymorphism, stable peak characteristics, consistent allele calls and produced precise, reproducible genotypes from different types of rhino samples. The panel also showed low genotyping error and produced high statistical power during individual identification (PIDsibs value of 1.2*10-4). As part of the official RhoDIS-India program, we used this panel to match poached rhino carcass with seized contraband as scientific evidence in court procedure. This program now moves to generate detailed allele-frequency maps of all GoH rhinoceros populations in India and Nepal for development of a genetic database and identification of poaching hotspots and trade routes across the subcontinent and beyond.
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Affiliation(s)
- Tista Ghosh
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand, 248001, India
| | - Amit Sharma
- World Wide Fund for Nature-India, 172B Lodhi Estate, New Delhi, 110003, India
| | - Samrat Mondol
- Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand, 248001, India.
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7
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O'Brien SJ. A Beautiful Life: High Risk-High Payoff in Genetic Science. Annu Rev Anim Biosci 2020; 8:1-24. [PMID: 31743063 DOI: 10.1146/annurev-animal-021419-083944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This narrative is a personal view of adventures in genetic science and society that have blessed my life and career across five decades. The advances I enjoyed and the lessons I learned derive from educational training, substantial collaboration, and growing up in the genomics age. I parse the stories into six research disciplines my students, fellows, and colleagues have entered and, in some cases, made an important difference. The first is comparative genetics, where evolutionary inference is applied to genome organization, from building gene maps in the 1970s to building whole genome sequences today. The second area tracks the progression of molecular evolutionary advances and applications to resolve the hierarchical relationship among living species in the silence of prehistory. The third endeavor outlines the birth and maturation of genetic studies and application to species conservation. The fourth theme discusses how emerging viruses studied in a genomic sense opened our eyes to host-pathogen interaction and interdependence. The fifth research emphasis outlines the population genetic-based search and discovery of human restriction genes that influence the epidemiological outcome of abrupt outbreaks, notably HIV-AIDS and several cancers. Finally, the last arena explored illustrates how genetic individualization in human and animals has improved forensic evidence in capital crimes. Each discipline has intuitive and technological overlaps, and each has benefitted from the contribution of genetic and genomic principles I learned so long ago from Drosophila. The journey continues.
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Affiliation(s)
- Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004; .,Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, Florida 33004, USA
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8
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Power A, Ingleby S, Chapman J, Cozzolino D. Lighting the Ivory Track: Are Near-Infrared and Chemometrics Up to the Job? A Proof of Concept. APPLIED SPECTROSCOPY 2019; 73:816-822. [PMID: 30990063 DOI: 10.1177/0003702819837297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A rapid tool to discriminate rhino horn and ivory samples from different mammalian species based on the combination of near-infrared reflection (NIR) spectroscopy and chemometrics was evaluated. In this study, samples from the Australian Museum mammalogy collection were scanned between 950 nm and 1650 nm using a handheld spectrophotometer and analyzed using principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA). An overall correct classification rate of 73.5% was obtained for the classification of all samples. This study demonstrates the potential of NIR spectroscopy coupled with chemometrics as a means of a rapid, nondestructive classification technique of horn and ivory samples sourced from a museum. Near-infrared spectroscopy can be used as an alternative or complementary method in the detection of horn and ivory assisting in the combat of illegal trade and aiding the preservation of at-risk species.
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Affiliation(s)
- Aoife Power
- 1 Agri-Chemistry Group, School of Medical and Applied Sciences, Central Queensland University (CQU), North Rockhampton, QLD, Australia
| | - Sandy Ingleby
- 2 Mammalogy Collection, Australian Museum, Sydney, NSW, Australia
| | - James Chapman
- 3 School of Science, RMIT University, Melbourne, VIC, Australia
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Harper C, Ludwig A, Clarke A, Makgopela K, Yurchenko A, Guthrie A, Dobrynin P, Tamazian G, Emslie R, van Heerden M, Hofmeyr M, Potter R, Roets J, Beytell P, Otiende M, Kariuki L, du Toit R, Anderson N, Okori J, Antonik A, Koepfli KP, Thompson P, O'Brien SJ. Robust forensic matching of confiscated horns to individual poached African rhinoceros. Curr Biol 2019; 28:R13-R14. [PMID: 29316411 DOI: 10.1016/j.cub.2017.11.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Black and white rhinoceros (Diceros bicornis and Ceratotherium simum) are iconic African species that are classified by the International Union for the Conservation of Nature (IUCN) as Critically Endangered and Near Threatened (http://www.iucnredlist.org/), respectively [1]. At the end of the 19th century, Southern white rhinoceros (Ceratotherium simum simum) numbers had declined to fewer than 50 animals in the Hluhluwe-iMfolozi region of the KwaZulu-Natal (KZN) province of South Africa, mainly due to uncontrolled hunting [2,3]. Efforts by the Natal Parks Board facilitated an increase in population to over 20,000 in 2015 through aggressive conservation management [2]. Black rhinoceros (Diceros bicornis) populations declined from several hundred thousand in the early 19th century to ∼65,000 in 1970 and to ∼2,400 by 1995 [1] with subsequent genetic reduction, also due to hunting, land clearances and later poaching [4]. In South Africa, rhinoceros poaching incidents have increased from 13 in 2007 to 1,215 in 2014 [1]. This has occurred despite strict trade bans on rhinoceros products and strict enforcement in recent years.
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Affiliation(s)
- Cindy Harper
- Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa; Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004.
| | - Anette Ludwig
- Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
| | - Amy Clarke
- Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
| | - Kagiso Makgopela
- Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
| | - Andrey Yurchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004
| | - Alan Guthrie
- Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
| | - Pavel Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004
| | - Gaik Tamazian
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004
| | - Richard Emslie
- IUCN SSC African Rhino Specialist Group, Hilton 3245, South Africa
| | | | - Markus Hofmeyr
- Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa; Veterinary Wildlife Services, South African National Parks, Skukuza, South Africa
| | - Roderick Potter
- Ezemvelo KZN Wildlife, Queen Elizabeth Park, Pietermaritzburg 3201, South Africa
| | - Johannes Roets
- South African Police Service, Stock Theft and Endangered Species Unit, Pretoria 0001, South Africa
| | - Piet Beytell
- Ministry of Environment and Tourism, Windhoek, Namibia
| | | | | | | | | | - Joseph Okori
- WWF: African Rhino Programme, Cape Town, South Africa
| | - Alexey Antonik
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004
| | - Klaus-Peter Koepfli
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004; Smithsonian Conservation Biology Institute, 3001 Connecticut Ave NW, Washington, DC 20008, USA
| | - Peter Thompson
- Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004; Guy Harvey Oceanographic Center, Nova Southeastern University, 8000 North Ocean Drive, Ft Lauderdale, FL 33004, USA
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Purisotayo T, Jonsson NN, Mable BK, Verreynne FJ. Combining molecular and incomplete observational data to inform management of southern white rhinoceros (Ceratotherium simum simum). CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01166-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Price ER, McClure PJ, Jacobs RL, Espinoza EO. Identification of rhinoceros keratin using direct analysis in real time time-of-flight mass spectrometry and multivariate statistical analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:2106-2112. [PMID: 30230063 DOI: 10.1002/rcm.8285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Trade in rhinoceros horn is regulated or banned internationally in recognition of its impact on wild populations worldwide. Enforcement of the laws and regulations depends on successfully identifying when violations occur, which is complicated by the presence of alternative/imitation rhinoceros horn keratin (e.g., bovid horn keratin). In this study, we assess the potential for Direct Analysis in Real Time (DART) ionization paired with Time-Of-Flight Mass Spectrometry (DART-TOFMS) to classify different keratin types from four taxonomic groups: rhinoceros, bovid, domestic horse, and pangolin. METHODS The spectra of 156 keratin samples from all five rhinoceros species (horn keratin), eight genera of bovids (horn keratin), domestic horses (hoof keratin), and all extant species of pangolins (scale keratin) were collected. Fisher ratio analysis identified the most important ions that characterized each class and these ions were used for the training model, which consisted of 143 spectra. Kernel Discriminant Analysis (KDA) was used to classify the different groups. RESULTS The spectra collected for each taxonomic group are distinctive. The chemotypes demonstrate that the spectra of rhinoceros, bovids, and domestic horse are similar to each other, whereas the chemotypes of pangolins show a different chemical profile. The model built by KDA resolved each taxonomic group: 95% of samples were correctly assigned using leave-one-out cross validation. The 13 blind samples not used in model development were all correctly classified to taxonomic source. CONCLUSIONS DART-TOFMS appears to be a reliable approach for taxonomic identification of keratin. This analysis can be carried out with a small sliver of keratin, with minimal sample preparation, inexpensively and quickly, making it a potential valuable tool for identification of rhinoceros horn and other keratin types.
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Affiliation(s)
- Erin R Price
- National Fish & Wildlife Forensics Laboratory, 1490 East Main Street, Ashland, OR, 97520-131, USA
| | - Pamela J McClure
- National Fish & Wildlife Forensics Laboratory, 1490 East Main Street, Ashland, OR, 97520-131, USA
| | - Rachel L Jacobs
- National Fish & Wildlife Forensics Laboratory, 1490 East Main Street, Ashland, OR, 97520-131, USA
| | - Edgard O Espinoza
- National Fish & Wildlife Forensics Laboratory, 1490 East Main Street, Ashland, OR, 97520-131, USA
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12
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Carroll EL, Bruford MW, DeWoody JA, Leroy G, Strand A, Waits L, Wang J. Genetic and genomic monitoring with minimally invasive sampling methods. Evol Appl 2018; 11:1094-1119. [PMID: 30026800 PMCID: PMC6050181 DOI: 10.1111/eva.12600] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/02/2018] [Indexed: 12/12/2022] Open
Abstract
The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.
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Affiliation(s)
- Emma L. Carroll
- Scottish Oceans Institute and Sea Mammal Research UnitUniversity of St AndrewsSt AndrewsUK
| | - Mike W. Bruford
- Cardiff School of Biosciences and Sustainable Places Research InstituteCardiff UniversityCardiff, WalesUK
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Gregoire Leroy
- Animal Production and Health DivisionFood and Agriculture Organization of the United NationsRomeItaly
| | - Alan Strand
- Grice Marine LaboratoryDepartment of BiologyCollege of CharlestonCharlestonSCUSA
| | - Lisette Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
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Ewart KM, Frankham GJ, McEwing R, The DT, Hogg CJ, Wade C, Lo N, Johnson RN. A rapid multiplex PCR assay for presumptive species identification of rhinoceros horns and its implementation in Vietnam. PLoS One 2018; 13:e0198565. [PMID: 29902212 PMCID: PMC6002117 DOI: 10.1371/journal.pone.0198565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/21/2018] [Indexed: 12/04/2022] Open
Abstract
Rhinoceros (rhinos) have suffered a dramatic increase in poaching over the past decade due to the growing demand for rhino horn products in Asia. One way to reverse this trend is to enhance enforcement and intelligence gathering tools used for species identification of horns, in particular making them fast, inexpensive and accurate. Traditionally, species identification tests are based on DNA sequence data, which, depending on laboratory resources, can be either time or cost prohibitive. This study presents a rapid rhino species identification test, utilizing species-specific primers within the cytochrome b gene multiplexed in a single reaction, with a presumptive species identification based on the length of the resultant amplicon. This multiplex PCR assay can provide a presumptive species identification result in less than 24 hours. Sequence-based definitive testing can be conducted if/when required (e.g. court purposes). This work also presents an actual casework scenario in which the presumptive test was successfully utlitised, in concert with sequence-based definitive testing. The test was carried out on seized suspected rhino horns tested at the Institute of Ecology and Biological Resources, the CITES mandated laboratory in Vietnam, a country that is known to be a major source of demand for rhino horns. This test represents the basis for which future 'rapid species identification tests' can be trialed.
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Affiliation(s)
- Kyle M. Ewart
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, New South Wales, Australia
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Greta J. Frankham
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, New South Wales, Australia
| | - Ross McEwing
- TRACE Wildlife Forensics Network, Edinburgh, Scotland
| | - Dang Tat The
- Institute of Ecology and Biological Resources, Hanoi, Vietnam
| | - Carolyn J. Hogg
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, New South Wales, Australia
- Zoo and Aquarium Association Australasia, Mosman, New South Wales, Australia
| | - Claire Wade
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Nathan Lo
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Rebecca N. Johnson
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, New South Wales, Australia
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14
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Moodley Y, Russo IRM, Dalton DL, Kotzé A, Muya S, Haubensak P, Bálint B, Munimanda GK, Deimel C, Setzer A, Dicks K, Herzig-Straschil B, Kalthoff DC, Siegismund HR, Robovský J, O’Donoghue P, Bruford MW. Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis). Sci Rep 2017; 7:41417. [PMID: 28176810 PMCID: PMC5296875 DOI: 10.1038/srep41417] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/09/2016] [Indexed: 11/09/2022] Open
Abstract
The black rhinoceros is again on the verge of extinction due to unsustainable poaching in its native range. Despite a wide historic distribution, the black rhinoceros was traditionally thought of as depauperate in genetic variation, and with very little known about its evolutionary history. This knowledge gap has hampered conservation efforts because hunting has dramatically reduced the species' once continuous distribution, leaving five surviving gene pools of unknown genetic affinity. Here we examined the range-wide genetic structure of historic and modern populations using the largest and most geographically representative sample of black rhinoceroses ever assembled. Using both mitochondrial and nuclear datasets, we described a staggering loss of 69% of the species' mitochondrial genetic variation, including the most ancestral lineages that are now absent from modern populations. Genetically unique populations in countries such as Nigeria, Cameroon, Chad, Eritrea, Ethiopia, Somalia, Mozambique, Malawi and Angola no longer exist. We found that the historic range of the West African subspecies (D. b. longipes), declared extinct in 2011, extends into southern Kenya, where a handful of individuals survive in the Masai Mara. We also identify conservation units that will help maintain evolutionary potential. Our results suggest a complete re-evaluation of current conservation management paradigms for the black rhinoceros.
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Affiliation(s)
- Yoshan Moodley
- Department of Zoology, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, Austria, Savoyenstr. 1A, 1160 Austria
| | - Isa-Rita M. Russo
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
| | - Desiré L. Dalton
- National Zoological Gardens of South Africa, 232 Boom Street, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, 205 Nelson Mandela Drive, West Park, Bloemfontein, 9300 South Africa
| | - Antoinette Kotzé
- National Zoological Gardens of South Africa, 232 Boom Street, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, 205 Nelson Mandela Drive, West Park, Bloemfontein, 9300 South Africa
| | - Shadrack Muya
- Department of Zoology, Jomo Kenyatta University of Agriculture and Technology, Kenyatta Avenue, Nairobi, 00200, Kenya
| | - Patricia Haubensak
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, Austria, Savoyenstr. 1A, 1160 Austria
| | - Boglárka Bálint
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, Austria, Savoyenstr. 1A, 1160 Austria
| | - Gopi K. Munimanda
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, Austria, Savoyenstr. 1A, 1160 Austria
| | - Caroline Deimel
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, Austria, Savoyenstr. 1A, 1160 Austria
| | - Andrea Setzer
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, Austria, Savoyenstr. 1A, 1160 Austria
| | - Kara Dicks
- Department of Biological Sciences, Thomas Building, University of Chester, Chester, CH1 4BJ, United Kingdom
| | | | - Daniela C. Kalthoff
- Swedish Museum of Natural History, Frescativägen 40, Stockholm, 10405, Sweden
| | - Hans R. Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, DK-2200, Denmark
| | - Jan Robovský
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic
| | - Paul O’Donoghue
- Department of Biological Sciences, Thomas Building, University of Chester, Chester, CH1 4BJ, United Kingdom
| | - Michael W. Bruford
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
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15
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Labuschagne C, Dalton DL, Grobler JP, Kotzé A. SNP discovery and characterisation in White Rhino (Ceratotherium simum) with application to parentage assignment. Genet Mol Biol 2017; 40:84-92. [PMID: 28170027 PMCID: PMC5409770 DOI: 10.1590/1678-4685-gmb-2016-0058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/17/2016] [Indexed: 11/24/2022] Open
Abstract
The white rhino is one of the great success stories of modern wildlife conservation,
growing from as few as 50-100 animals in the 1880s, to approximately 20,000 white
rhinoceros remaining today. However, illegal trade in conservational rhinoceros horns
is adding constant pressure on remaining populations. Captive management of
ex situ populations of endangered species using molecular methods
can contribute to improving the management of the species. Here we compare for the
first time the utility of 33 Single Nucleotide Polymorphisms (SNPs) and nine
microsatellites (MS) in isolation and in combination for assigning parentage in
captive White Rhinoceros. We found that a combined dataset of SNPs and
microsatellites was most informative with the highest confidence level. This study
thus provided us with a useful set of SNP and MS markers for parentage and
relatedness testing. Further assessment of the utility of these markers over multiple
(> three) generations and the incorporation of a larger variety of relationships
among individuals (e.g. half-siblings or cousins) is strongly suggested.
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Affiliation(s)
- Christiaan Labuschagne
- Department of Genetics, University of the Free State, Bloemfontein, Free State, South Africa.,Inqaba Biotechnical Industries (Pty) Ltd, Pretoria, Gauteng, South Africa
| | - Desiré L Dalton
- Department of Genetics, University of the Free State, Bloemfontein, Free State, South Africa.,National Zoological Gardens of South Africa, Pretoria, Gauteng, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, Free State, South Africa
| | - Antoinette Kotzé
- Department of Genetics, University of the Free State, Bloemfontein, Free State, South Africa.,National Zoological Gardens of South Africa, Pretoria, Gauteng, South Africa
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16
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Validation studies on dinucleotide STRs for forensic identification of black rhinoceros Diceros bicornis. Forensic Sci Int Genet 2017; 26:e25-e27. [DOI: 10.1016/j.fsigen.2016.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/19/2016] [Accepted: 10/23/2016] [Indexed: 11/21/2022]
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17
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Hadas L, Hermon D, Bar-Gal GK. Before they are gone - improving gazelle protection using wildlife forensic genetics. Forensic Sci Int Genet 2016; 24:51-54. [PMID: 27294679 DOI: 10.1016/j.fsigen.2016.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 05/04/2016] [Accepted: 05/29/2016] [Indexed: 11/25/2022]
Abstract
Throughout their habitats gazelles (genus Gazella) face immediate threats due to anthropogenic effects and natural environmental changes. Excessive poaching plays a major role in their populations decline. Three unique populations of gazelles currently live in Israel: mountain gazelle (Gazella gazella), Dorcas gazelle (Gazella Dorcas) and acacia gazelle (Gazella arabica acacia). Ongoing habitat degradation and constant pressure from illegal hunting has caused a continuous decrease in the last 10 years, stressing the need for drastic measures to prevent species extinction. Wildlife forensic science assists enforcement agencies in the escalating arms race against poachers. Wildlife forensic genetic tests being implemented in our laboratory offer both species and individual identification, which rely on two mitochondrial genes (12S rRNA and 16S rRNA) and nine nuclear Short Tandem Repeats (STR), respectively. The current study, presents a poaching case in which mitochondrial DNA-based species identification revealed the presence of mountain gazelle DNA on the seized items. Subsequently, STR markers linked the suspect to more than one gazelle, increasing the severity of the criminal charges.
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Affiliation(s)
- Lia Hadas
- The Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Dalia Hermon
- DNA and Forensic Biology Laboratory, Division of Identification and Forensic Science (DIFS), Israel Police, National H.Q., Jerusalem, Israel
| | - Gila Kahila Bar-Gal
- The Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel.
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18
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Miller SM, Clarke AB, Bloomer P, Guthrie AJ, Harper CK. Evaluation of microsatellites for common ungulates in the South African wildlife industry. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0554-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Miller SM, Harper CK, Bloomer P, Hofmeyr J, Funston PJ. Evaluation of microsatellite markers for populations studies and forensic identification of African lions (Panthera leo). J Hered 2014; 105:762-72. [PMID: 25151647 DOI: 10.1093/jhered/esu054] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The South African lion (Panthera leo) population is highly fragmented. One-third of its wild lions occur in small (<1000 km(2)) reserves. These lions were reintroduced from other areas of the species' historical range. Management practices on these reserves have not prioritized genetic provenance or heterozygosity. These trends potentially constrain the conservation value of these lions. To ensure the best management and long-term survival of these subpopulations as a viable collective population, the provenance and current genetic diversity must be described. Concurrently, poaching of lions to supply a growing market for lion bones in Asia may become a serious conservation challenge in the future. Having a standardized, validated method for matching confiscated lion parts with carcasses will be a key tool in investigating these crimes. We evaluated 28 microsatellites in the African lion using samples from 18 small reserves and 1 captive facility in South Africa, two conservancies in Zimbabwe, and Kruger National and Kgalagadi Transfrontier Parks to determine the loci most suited for population management and forensic genetic applications. Twelve microsatellite loci with a match probability of 1.1×10(-5) between siblings were identified for forensics. A further 10 could be added for population genetics studies.
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Affiliation(s)
- Susan M Miller
- From the Department of Nature Conservation, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa (Miller); the Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa (Miller and Harper); the Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa (Bloomer); the Veterinary Wildlife Services, South African National Parks, Private Bag X402, Skukuza 1350, South Africa (Hofmeyr); the Department of Nature Conservation, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa (Funston); and the Lion Program, Panthera, New York, NY (Funston).
| | - Cindy K Harper
- From the Department of Nature Conservation, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa (Miller); the Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa (Miller and Harper); the Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa (Bloomer); the Veterinary Wildlife Services, South African National Parks, Private Bag X402, Skukuza 1350, South Africa (Hofmeyr); the Department of Nature Conservation, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa (Funston); and the Lion Program, Panthera, New York, NY (Funston)
| | - Paulette Bloomer
- From the Department of Nature Conservation, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa (Miller); the Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa (Miller and Harper); the Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa (Bloomer); the Veterinary Wildlife Services, South African National Parks, Private Bag X402, Skukuza 1350, South Africa (Hofmeyr); the Department of Nature Conservation, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa (Funston); and the Lion Program, Panthera, New York, NY (Funston)
| | - Jennifer Hofmeyr
- From the Department of Nature Conservation, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa (Miller); the Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa (Miller and Harper); the Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa (Bloomer); the Veterinary Wildlife Services, South African National Parks, Private Bag X402, Skukuza 1350, South Africa (Hofmeyr); the Department of Nature Conservation, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa (Funston); and the Lion Program, Panthera, New York, NY (Funston)
| | - Paul J Funston
- From the Department of Nature Conservation, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa (Miller); the Veterinary Genetics Laboratory, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa (Miller and Harper); the Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa (Bloomer); the Veterinary Wildlife Services, South African National Parks, Private Bag X402, Skukuza 1350, South Africa (Hofmeyr); the Department of Nature Conservation, Tshwane University of Technology, Private Bag X680, Pretoria 0001, South Africa (Funston); and the Lion Program, Panthera, New York, NY (Funston)
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20
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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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