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Vasiljevic N, Morf NV, Senn J, Pérez‐Espona S, Mattucci F, Mucci N, Moore‐Jones G, Pisano SRR, Kratzer A, Ogden R. Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization. Ecol Evol 2022; 12:e8626. [PMID: 35222977 PMCID: PMC8858214 DOI: 10.1002/ece3.8626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/03/2022] [Accepted: 01/26/2022] [Indexed: 11/12/2022] Open
Abstract
In the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad‐scale geographic origin assignment using nuclear markers to support law enforcement.
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Affiliation(s)
- Nina Vasiljevic
- Zurich Institute of Forensic Medicine University of Zurich Switzerland
| | - Nadja V. Morf
- Zurich Institute of Forensic Medicine University of Zurich Switzerland
| | - Josef Senn
- Swiss Federal Research Institute WSL Birmensdorf Switzerland
| | - Sílvia Pérez‐Espona
- Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Midlothian UK
| | - Federica Mattucci
- ISPRA‐Istituto Superiore per la Protezione e la Ricerca Ambientale Area per la Genetica della Conservazione BIO‐CGE Bologna Italy
| | - Nadia Mucci
- ISPRA‐Istituto Superiore per la Protezione e la Ricerca Ambientale Area per la Genetica della Conservazione BIO‐CGE Bologna Italy
| | - Gaia Moore‐Jones
- Institute for Fish and Wildlife Health (FIWI), Department of Infectious Diseases and Pathobiology, Vetsuisse‐Faculty University of Bern Bern Switzerland
| | - Simone Roberto Rolando Pisano
- Institute for Fish and Wildlife Health (FIWI), Department of Infectious Diseases and Pathobiology, Vetsuisse‐Faculty University of Bern Bern Switzerland
| | - Adelgunde Kratzer
- Zurich Institute of Forensic Medicine University of Zurich Switzerland
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Midlothian UK
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Lendvay B, Cartier LE, Costantini F, Iwasaki N, Everett MV, Krzemnicki MS, Kratzer A, Morf NV. Coral-ID: A forensically validated genetic test to identify precious coral material and its application to objects seized from illegal traffic. Forensic Sci Int Genet 2022; 58:102663. [DOI: 10.1016/j.fsigen.2022.102663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 12/01/2022]
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Vasiljevic N, Lim M, Humble E, Seah A, Kratzer A, Morf NV, Prost S, Ogden R. Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification. Forensic Sci Int Genet 2021; 53:102493. [PMID: 33770699 DOI: 10.1016/j.fsigen.2021.102493] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/09/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022]
Abstract
Species identification of non-human biological evidence through DNA nucleotide sequencing is routinely used for forensic genetic analysis to support law enforcement. The gold standard for forensic genetics is conventional Sanger sequencing; however, this is gradually being replaced by high-throughput sequencing (HTS) approaches which can generate millions of individual reads in a single experiment. HTS sequencing, which now dominates molecular biology research, has already been demonstrated for use in a number of forensic genetic analysis applications, including species identification. However, the generation of HTS data to date requires expensive equipment and is cost-effective only when large numbers of samples are analysed simultaneously. The Oxford Nanopore Technologies (ONT) MinION™ is an affordable and small footprint DNA sequencing device with the potential to quickly deliver reliable and cost effective data. However, there has been no formal validation of forensic species identification using high-throughput (deep read) sequence data from the MinION making it currently impractical for many wildlife forensic end-users. Here, we present a MinION deep read sequence data validation study for species identification. First, we tested whether the clustering-based bioinformatics pipeline NGSpeciesID can be used to generate an accurate consensus sequence for species identification. Second, we systematically evaluated the read variation distribution around the generated consensus sequences to understand what confidence we have in the accuracy of the resulting consensus sequence and to determine how to interpret individual sample results. Finally, we investigated the impact of differences between the MinION consensus and Sanger control sequences on correct species identification to understand the ability and accuracy of the MinION consensus sequence to differentiate the true species from the next most similar species. This validation study establishes that ONT MinION sequence data used in conjunction with the NGSpeciesID pipeline can produce consensus DNA sequences of sufficient accuracy for forensic genetic species identification.
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Affiliation(s)
- Nina Vasiljevic
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland.
| | - Marisa Lim
- Wildlife Conservation Society, Zoological Health Program, Bronx, NY, USA
| | - Emily Humble
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, UK
| | - Adeline Seah
- Wildlife Conservation Society, Zoological Health Program, Bronx, NY, USA
| | - Adelgunde Kratzer
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Nadja V Morf
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg, Frankfurt, Germany; South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, UK; TRACE Wildlife Forensics Network, Edinburgh, UK
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Gascho D, Morf NV, Thali MJ, Schaerli S. The use of immunochromatographic rapid test for soft tissue remains identification in order to distinguish between human and non-human origin. Sci Justice 2017; 57:165-168. [DOI: 10.1016/j.scijus.2017.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 02/23/2017] [Accepted: 02/25/2017] [Indexed: 10/20/2022]
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Morf NV, Sulzer A, Kratzer A, Bär W. Internal validation of Tecan robots (Freedom EVO® 150 and 75) for PCR and capillary electrophoresis setup. Forensic Science International: Genetics Supplement Series 2011. [DOI: 10.1016/j.fsigss.2011.08.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Morrogh-Bernard HC, Morf NV, Chivers DJ, Krützen M. Dispersal Patterns of Orang-utans (Pongo spp.) in a Bornean Peat-swamp Forest. INT J PRIMATOL 2010. [DOI: 10.1007/s10764-010-9474-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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