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Thanakiatkrai P, Chenphun C, Kitpipit T. African and Asian elephant ivory discrimination using a portable strip test. Forensic Sci Int Genet 2024; 70:103027. [PMID: 38422900 DOI: 10.1016/j.fsigen.2024.103027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/17/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
Currently, the global elephant population has significantly declined due to the poaching of elephants for their ivory, and this is the reason why elephants are listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). However, Thailand allows the legal trade of ivory from registered, domesticated Asian elephants, leading to the smuggling of African elephant ivory, and passing them off as Asian elephant ivory. Therefore, this research aims to develop and validate a portable strip test to discriminate between Asian and African elephants DNA, using Recombinase Polymerase Amplification (RPA) and Lateral Flow Dipstick assay (LFD) according to international standards. The results showed that the strip test can be successfully developed with 100% accuracy (n = 105). This kit is specific to elephants, has a detection limit of 0.125 ng of DNA, and can effectively discriminate a variety of elephant ivory, including raw ivory, ivory products, and aged ivory over 25 years old, which had been damaged by fire, all with 100% accuracy (n = 117). Additionally, the developed strip test is designed to be portable and cost-effective. It does not require expensive laboratory equipment and provides a faster analysis process compared with conventional PCR-based methods. This will expedite the legal process and enforcement of laws related to elephant conservation, reducing the opportunities for illegal activities, and enabling timely prosecution under relevant wildlife conservation laws in Thailand and internationally.
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Affiliation(s)
- Phuvadol Thanakiatkrai
- Forensic Science Program, Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Thailand; Forensic Science Innovation and Service Center, Prince of Songkla University, Thailand
| | - Chanokkarn Chenphun
- Forensic Science Program, Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Thailand
| | - Thitika Kitpipit
- Forensic Science Program, Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Thailand; Forensic Science Innovation and Service Center, Prince of Songkla University, Thailand.
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2
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Gilbert C, Krupicka V, Galluzzi F, Popowich A, Bathany K, Claverol S, Arslanoglu J, Tokarski C. Species identification of ivory and bone museum objects using minimally invasive proteomics. SCIENCE ADVANCES 2024; 10:eadi9028. [PMID: 38277452 PMCID: PMC10816696 DOI: 10.1126/sciadv.adi9028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 12/27/2023] [Indexed: 01/28/2024]
Abstract
Ivory is a highly prized material in many cultures since it can be carved into intricate designs and have a highly polished surface. Due to its popularity, the animals from which ivory can be sourced are under threat of extinction. Identification of ivory species is not only important for CITES compliance, it can also provide information about the context in which a work was created. Here, we have developed a minimally invasive workflow to remove minimal amounts of material from precious objects and, using high-resolution mass spectrometry-based proteomics, identified the taxonomy of ivory and bone objects from The Metropolitan Museum of Art collection dating from as early as 4000 B.C. We built a proteomic database of underrepresented species based on exemplars from the American Museum of Natural History, and proposed alternative data analysis workflows for samples containing inconsistently preserved organic material. This application demonstrates extensive ivory species identification using proteomics to unlock sequence uncertainties, e.g., Leu/Ile discrimination.
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Affiliation(s)
- Catherine Gilbert
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
- Bordeaux Proteome Platform, University of Bordeaux, F-33000 Bordeaux, France
| | - Vaclav Krupicka
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
- Bordeaux Proteome Platform, University of Bordeaux, F-33000 Bordeaux, France
| | - Francesca Galluzzi
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
- Bordeaux Proteome Platform, University of Bordeaux, F-33000 Bordeaux, France
| | - Aleksandra Popowich
- Department of Scientific Research, The Metropolitan Museum of Art, New York, NY, USA
| | - Katell Bathany
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
- Bordeaux Proteome Platform, University of Bordeaux, F-33000 Bordeaux, France
| | - Stéphane Claverol
- Bordeaux Proteome Platform, University of Bordeaux, F-33000 Bordeaux, France
| | - Julie Arslanoglu
- Department of Scientific Research, The Metropolitan Museum of Art, New York, NY, USA
| | - Caroline Tokarski
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
- Bordeaux Proteome Platform, University of Bordeaux, F-33000 Bordeaux, France
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3
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Schweizer TM, DeSaix MG. Cost-effective library preparation for whole genome sequencing with feather DNA. CONSERV GENET RESOUR 2023. [DOI: 10.1007/s12686-023-01299-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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4
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Wasser SK, Wolock CJ, Kuhner MK, Brown JE, Morris C, Horwitz RJ, Wong A, Fernandez CJ, Otiende MY, Hoareau Y, Kaliszewska ZA, Jeon E, Han KL, Weir BS. Elephant genotypes reveal the size and connectivity of transnational ivory traffickers. Nat Hum Behav 2022; 6:371-382. [PMID: 35165434 PMCID: PMC10693927 DOI: 10.1038/s41562-021-01267-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/01/2021] [Indexed: 11/08/2022]
Abstract
Transnational ivory traffickers continue to smuggle large shipments of elephant ivory out of Africa, yet prosecutions and convictions remain few. We identify trafficking networks on the basis of genetic matching of tusks from the same individual or close relatives in separate shipments. Analyses are drawn from 4,320 savannah (Loxodonta africana) and forest (L. cyclotis) elephant tusks, sampled from 49 large ivory seizures totalling 111 t, shipped out of Africa between 2002 and 2019. Network analyses reveal a repeating pattern wherein tusks from the same individual or close relatives are found in separate seizures that were containerized in, and transited through, common African ports. Results suggest that individual traffickers are exporting dozens of shipments, with considerable connectivity between traffickers operating in different ports. These tools provide a framework to combine evidence from multiple investigations, strengthen prosecutions and support indictment and prosecution of transnational ivory traffickers for the totality of their crimes.
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Affiliation(s)
- Samuel K Wasser
- Center for Environmental Forensic Science, University of Washington, Seattle, WA, USA.
| | - Charles J Wolock
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Mary K Kuhner
- Center for Environmental Forensic Science, University of Washington, Seattle, WA, USA
| | - John E Brown
- US Department of Homeland Security, Homeland Security Investigations, Washington, DC, USA
| | | | - Ryan J Horwitz
- Geospatial Data Sciences, University of Michigan School for Environment and Sustainability, Ann Arbor, MI, USA
| | - Anna Wong
- Center for Wildlife Forensics, National Parks Board, Singapore, Singapore
| | | | - Moses Y Otiende
- Forensic and Genetics Laboratory, Kenya Wildlife Service, Nairobi, Kenya
| | - Yves Hoareau
- Center for Environmental Forensic Science, University of Washington, Seattle, WA, USA
| | - Zofia A Kaliszewska
- Center for Environmental Forensic Science, University of Washington, Seattle, WA, USA
| | - Eunjin Jeon
- Center for Environmental Forensic Science, University of Washington, Seattle, WA, USA
| | - Kin-Lan Han
- Center for Environmental Forensic Science, University of Washington, Seattle, WA, USA
| | - Bruce S Weir
- Department of Biostatistics, University of Washington, Seattle, WA, USA
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5
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Lendvay B, Cartier LE, Gysi M, Meyer JB, Krzemnicki MS, Kratzer A, Morf NV. DNA fingerprinting: an effective tool for taxonomic identification of precious corals in jewelry. Sci Rep 2020; 10:8287. [PMID: 32427854 PMCID: PMC7237452 DOI: 10.1038/s41598-020-64582-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 04/17/2020] [Indexed: 11/09/2022] Open
Abstract
Precious coral species have been used to produce jewelry and ornaments since antiquity. Due to the high value and demand for corals, some coral beds have been heavily fished over past centuries. Fishing and international trade regulations were put in place to regulate fishing practices in recent decades. To this date, the control of precious coral exploitation and enforcement of trade rules have been somewhat impaired by the fact that different species of worked coral samples can be extremely difficult to distinguish, even for trained experts. Here, we developed methods to use DNA recovered from precious coral samples worked for jewelry to identify their species. We evaluated purity and quantity of DNA extracted using five different techniques. Then, a minimally invasive sampling protocol was tested, which allowed genetic analysis without compromising the value of the worked coral objects.The best performing DNA extraction technique applies decalcification of the skeletal material with EDTA in the presence of laurylsarcosyl and proteinase, and purification of the DNA with a commercial silica membrane. This method yielded pure DNA in all cases using 100 mg coral material and in over half of the cases when using "quasi non-destructive" sampling with sampled material amounts as low as 2.3 mg. Sequence data of the recovered DNA gave an indication that the range of precious coral species present in the trade is broader than previously anticipated.
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Affiliation(s)
- Bertalan Lendvay
- Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, CH-8057, Zurich, Switzerland. .,Swiss Gemmological Institute SSEF, Aeschengraben 26, CH-4051, Basel, Switzerland.
| | - Laurent E Cartier
- Swiss Gemmological Institute SSEF, Aeschengraben 26, CH-4051, Basel, Switzerland.,Institute of Earth Sciences, University of Lausanne, Géopolis, CH-1015, Lausanne, Switzerland
| | - Mario Gysi
- Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, CH-8057, Zurich, Switzerland
| | - Joana B Meyer
- Federal Office for the Environment FOEN, Worblentalstrasse 68, CH-3063, Ittigen, Switzerland
| | - Michael S Krzemnicki
- Swiss Gemmological Institute SSEF, Aeschengraben 26, CH-4051, Basel, Switzerland
| | - Adelgunde Kratzer
- Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, CH-8057, Zurich, Switzerland
| | - Nadja V Morf
- Zurich Institute of Forensic Medicine, University of Zurich, Winterthurerstrasse 190/52, CH-8057, Zurich, Switzerland
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Ngatia JN, Lan TM, Ma Y, Dinh TD, Wang Z, Dahmer TD, Chun Xu Y. Distinguishing extant elephants ivory from mammoth ivory using a short sequence of cytochrome b gene. Sci Rep 2019; 9:18863. [PMID: 31827140 PMCID: PMC6906310 DOI: 10.1038/s41598-019-55094-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/14/2019] [Indexed: 11/08/2022] Open
Abstract
Trade in ivory from extant elephant species namely Asian elephant (Elephas maximus), African savanna elephant (Loxodonta africana) and African forest elephant (Loxodonta cyclotis) is regulated internationally, while the trade in ivory from extinct species of Elephantidae, including woolly mammoth, is unregulated. This distinction creates opportunity for laundering and trading elephant ivory as mammoth ivory. The existing morphological and molecular genetics methods do not reliably distinguish the source of ivory items that lack clear identification characteristics or for which the quality of extracted DNA cannot support amplification of large gene fragments. We present a PCR-sequencing method based on 116 bp target sequence of the cytochrome b gene to specifically amplify elephantid DNA while simultaneously excluding non-elephantid species and ivory substitutes, and while avoiding contamination by human DNA. The partial Cytochrome b gene sequence enabled accurate association of ivory samples with their species of origin for all three extant elephants and from mammoth. The detection limit of the PCR system was as low as 10 copy numbers of target DNA. The amplification and sequencing success reached 96.7% for woolly mammoth ivory and 100% for African savanna elephant and African forest elephant ivory. This is the first validated method for distinguishing elephant from mammoth ivory and it provides forensic support for investigation of ivory laundering cases.
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Affiliation(s)
- Jacob Njaramba Ngatia
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China
| | - Tian Ming Lan
- BGI - Shenzhen, Shenzhen, 518083, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, DK-2100, Denmark
- China National GeneBank, BGI - Shenzhen, Shenzhen, 518083, China
| | - Yue Ma
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China
- State Forestry and Grassland Administration Detecting Center of Wildlife, Harbin, 150040, China
| | - Thi Dao Dinh
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China
| | - Zhen Wang
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China
- State Forestry and Grassland Administration Detecting Center of Wildlife, Harbin, 150040, China
| | - Thomas D Dahmer
- Ecosystems Ltd, No. 40 Shek Pai Wan Road, Aberdeen, Hong Kong, China
| | - Yan Chun Xu
- College of Wildlife and Protected Areas, Northeast Forestry University, Harbin, 150040, China.
- State Forestry and Grassland Administration Detecting Center of Wildlife, Harbin, 150040, China.
- State Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization of China, Harbin, 150040, China.
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7
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Zhao K, Ishida Y, Green CE, Davidson AG, Sitam FAT, Donnelly CL, De Flamingh A, Perrin-Stowe TIN, Bourgeois S, Brandt AL, Mundis SJ, Van Aarde RJ, Greenberg JA, Malhi RS, Georgiadis NJ, Mcewing R, Roca AL. Loxodonta Localizer: A Software Tool for Inferring the Provenance of African Elephants and Their Ivory Using Mitochondrial DNA. J Hered 2019; 110:761-768. [DOI: 10.1093/jhered/esz058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Illegal hunting is a major threat to the elephants of Africa, with more elephants killed by poachers than die from natural causes. DNA from tusks has been used to infer the source populations for confiscated ivory, relying on nuclear genetic markers. However, mitochondrial DNA (mtDNA) sequences can also provide information on the geographic origins of elephants due to female elephant philopatry. Here, we introduce the Loxodonta Localizer (LL; www.loxodontalocalizer.org), an interactive software tool that uses a database of mtDNA sequences compiled from previously published studies to provide information on the potential provenance of confiscated ivory. A 316 bp control region sequence, which can be readily generated from DNA extracted from ivory, is used as a query. The software generates a listing of haplotypes reported among 1917 African elephants in 24 range countries, sorted in order of similarity to the query sequence. The African locations from which haplotype sequences have been previously reported are shown on a map. We demonstrate examples of haplotypes reported from only a single locality or country, examine the utility of the program in identifying elephants from countries with varying degrees of sampling, and analyze batches of confiscated ivory. The LL allows for the source of confiscated ivory to be assessed within days, using widely available molecular methods that do not depend on a particular platform or laboratory. The program enables identification of potential regions or localities from which elephants are being poached, with capacity for rapid identification of populations newly or consistently targeted by poachers.
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Affiliation(s)
- Kai Zhao
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Cory E Green
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Alexis G Davidson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Frankie A T Sitam
- National Wildlife Forensic Laboratory, Ex-Situ Conservation Division, Department of Wildlife and National Parks, Jalan Cheras, Kuala Lumpur, Malaysia
| | - Cassidy L Donnelly
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Alida De Flamingh
- Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana IL
| | - Tolulope I N Perrin-Stowe
- Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana IL
| | | | - Adam L Brandt
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL
- Division of Natural Sciences, St. Norbert College, De Pere, WI
| | | | - Rudi J Van Aarde
- Conservation Ecology Research Unit, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Jonathan A Greenberg
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV
| | - Ripan S Malhi
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL
| | | | | | - Alfred L Roca
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL
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8
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Ewart KM, Lightson AL, Sitam FT, Rovie-Ryan JJ, Mather N, McEwing R. Expediting the sampling, decalcification, and forensic DNA analysis of large elephant ivory seizures to aid investigations and prosecutions. Forensic Sci Int Genet 2019; 44:102187. [PMID: 31670244 DOI: 10.1016/j.fsigen.2019.102187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/27/2019] [Accepted: 10/12/2019] [Indexed: 02/02/2023]
Abstract
The illegal ivory trade continues to drive elephant poaching. Large ivory seizures in Africa and Asia are still commonplace. Wildlife forensics is recognised as a key enforcement tool to combat this trade. However, the time and resources required to effectively test large ivory seizures is often prohibitive. This limits or delays testing, which may impede investigations and/or prosecutions. Typically, DNA analysis of an ivory seizure involves pairing and sorting the tusks, sampling the tusks, powdering the sample, decalcification, then DNA extraction. Here, we optimize the most time-consuming components of this process: sampling and decalcification. Firstly, using simulations, we demonstrate that tusks do not need to be paired to ensure an adequate number of unique elephants are sampled in a large seizure. Secondly, we determined that directly powdering the ivory using a Dremel drill with a high-speed cutter bit, instead of cutting the ivory with a circular saw and subsequently powdering the sample in liquid nitrogen with a freezer mill, produces comparable results. Finally, we optimized a rapid 2 -h decalcification protocol that produces comparable results to a standard 3-day protocol. We tested/optimised the protocols on 33 raw and worked ivory samples, and demonstrated their utility on a case study, successfully identifying 94% of samples taken from 123 tusks. Using these new rapid protocols, the entire sampling and DNA extraction process takes less than one day and requires less-expensive equipment. We expect that the implementation of these rapid protocols will promote more consistent and timely testing of ivory seizures suitable for enforcement action.
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Affiliation(s)
- Kyle M Ewart
- TRACE Wildlife Forensics Network, Edinburgh, Scotland, United Kingdom.
| | - Amanda L Lightson
- TRACE Wildlife Forensics Network, Edinburgh, Scotland, United Kingdom
| | - Frankie T Sitam
- National Wildlife Forensic Laboratory, Department of Wildlife and National Parks (PERHILITAN), Kuala Lumpur, Malaysia
| | - Jeffrine J Rovie-Ryan
- National Wildlife Forensic Laboratory, Department of Wildlife and National Parks (PERHILITAN), Kuala Lumpur, Malaysia
| | | | - Ross McEwing
- TRACE Wildlife Forensics Network, Edinburgh, Scotland, United Kingdom
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