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Baxter JR, Kotze A, de Bruyn M, Matlou K, Labuschagne K, Mwale M. DNA barcoding of southern African mammal species and construction of a reference library for forensic application. Genome 2024; 67:378-391. [PMID: 38996389 DOI: 10.1139/gen-2023-0050] [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] [Indexed: 07/14/2024]
Abstract
Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of cytochrome c oxidase subunit 1 and cytochrome b sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94%-95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera.
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Affiliation(s)
- J R Baxter
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - A Kotze
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
- Department of Genetics, Faculty of Natural and Agricultural Sciences, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa
| | - M de Bruyn
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - K Matlou
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - K Labuschagne
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
| | - M Mwale
- South African National Biodiversity Institute, PO BOX 754, Pretoria 0001, South Africa
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Tian X, Wang P, Tian Y, Zhang R, Jiang Z, Gao J. Classification method based on Siamese-like neural network for inter-species blood Raman spectra similarity measure. JOURNAL OF BIOPHOTONICS 2023; 16:e202200377. [PMID: 36906736 DOI: 10.1002/jbio.202200377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 06/07/2023]
Abstract
Analysis of blood species is an extremely important part in customs inspection, forensic investigation, wildlife protection and other fields. In this study, a classification method based on Siamese-like neural network (SNN) for interspecies blood (22 species) was proposed to measure Raman Spectra similarity. The average accuracy was above 99.20% in the test set of spectra (known species) that did not appear in the training set. This model could detect species not represented in the dataset underlying the model. After adding new species to the training set, we can update the training based on the original model without retraining the model from scratch. For species with lower accuracy, SNN model can be trained intensively in the form of enriched training data for that species. A single model can achieve both multiple-classification and binary classification functions. Moreover, SNN showed higher accuracy rates when trained with smaller datasets compared to other methods.
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Affiliation(s)
- Xianli Tian
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, China
| | - Peng Wang
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, China
| | - Yubing Tian
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, China
| | - Rui Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, China
| | - Zhehan Jiang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, China
| | - Jing Gao
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, 215163, China
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Siriwut W, Jeratthitikul E, Panha S, Chanabun R, Ngor PB, Sutcharit C. Evidence of cryptic diversity in freshwater Macrobrachium prawns from Indochinese riverine systems revealed by DNA barcode, species delimitation and phylogenetic approaches. PLoS One 2021; 16:e0252546. [PMID: 34077477 PMCID: PMC8171930 DOI: 10.1371/journal.pone.0252546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/18/2021] [Indexed: 12/04/2022] Open
Abstract
The diversity of Indochinese prawns in genus Macrobrachium is enormous due to the habitat diversification and broad tributary networks of two river basins: the Chao Phraya and the Mekong. Despite long-standing interest in SE-Asian decapod diversity, the subregional Macrobrachium fauna is still not yet comprehensively clarified in terms of taxonomic identification or genetic diversification. In this study, integrative taxonomic approaches including morphological examination, DNA barcoding, and molecular species delimitation were used to emphasize the broad scale systematics of Macrobrachium prawns in Indochina. Twenty-seven nominal species were successfully re-verified by traditional and molecular taxonomy. Barcode gap analysis supported broad overlapping of species boundaries. Taxonomic ambiguity of several deposited samples in the public database is related to inter- and intraspecific genetic divergence as indicated by BOLD discordance. Diagnostic nucleotide positions were found in six Macrobrachium species. Eighteen additional putative lineages are herein assigned using the consensus of species delimitation methods. Genetic divergence indicates the possible existence of cryptic species in four morphologically complex and wide-ranging species: M. lanchesteri, M. niphanae, M. sintangense, and some members of the M. pilimanus group. The geographical distribution of some species supports the connections and barriers attributed to paleo-historical events of SE-Asian rivers and land masses. Results of this study show explicitly the importance of freshwater ecosystems in Indochinese subregions, especially for the Mekong River Basin due to its high genetic diversity and species composition found throughout its tributaries.
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Affiliation(s)
- Warut Siriwut
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Ekgachai Jeratthitikul
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Somsak Panha
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Academy of Science, The Royal Society of Thailand, Dusit, Bangkok, Thailand
| | - Ratmanee Chanabun
- Program in Animal Science, Faculty of Agricultural Technology, Sakon Nakhon Rajabhat University, Sakon Nakhon, Thailand
| | - Peng Bun Ngor
- Inland Fisheries Research and Development Institute (IFReDI), Fisheries Administration, Phnom Penh, Cambodia
- Wonders of the Mekong Project, Phnom Penh, Cambodia
| | - Chirasak Sutcharit
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Gaillard D, Yeh FC, Lin L, Chen HQ, Zhang T, Luo SJ, Shi HT. Lost at sea: determining geographic origins of illegally traded green sea turtles (Chelonia mydas) rescued on Hainan Island, China. WILDLIFE RESEARCH 2021. [DOI: 10.1071/wr19127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
ContextGreen sea turtles are threatened by exploitation for food and medicine markets, with Asian populations facing the heaviest pressures. Sea turtle confiscations that happen out at sea can give a general area that poachers are targeting, but it can be difficult to determine the impact on specific nesting rookeries. Previous studies circumvented this difficulty by using genetic markers to identify nesting rookery origins of confiscated green turtles.
AimsTo determine the impact on nesting rookeries from the illegal harvesting of green sea turtles by Hainan fishermen and describe the genetic diversity of the Paracel Islands’ green sea turtle population.
MethodsIn the present study, we sequenced 384bp of mitochondrial DNA control region from 85 illegally traded green sea turtles rescued on Hainan Island, China, to investigate their population of origin. For reference-source data, we used previously published mtDNA haplotype data from rookeries from Australasian waters and mtDNA haplotype data from 16 newly collected samples from the Paracel Islands in the South China Sea, a previously unsampled area.
Key resultsTen and four mtDNA haplotypes, all being reported before, were detected from the Hainan confiscation and Paracel Islands rookery respectively. However, CmP19, an infrequent haplotype that has been found only in 10 green sea turtles previously, made up ~45% of our rescued samples and ~62% of the Paracel Islands sample, suggesting a potential association between CmP19 and the Paracel Island rookery. Haplotype diversity of the rescued green sea turtles was relatively high (h=0.7143±0.04), whereas nucleotide diversity was relatively low (π=0.0031±0.00), compared with other rookeries. Mixed-stock analysis suggested that the rookeries in the Paracel Islands (~57%) and the Sulu Sea (~29%) are experiencing the greatest impact from illegal harvesting by fishermen from Hainan and neighbouring countries.
ConclusionsThe Paracel Islands population contains a unique genetic makeup compared with other studied rookeries, particularly the high frequency of the previously rare CmP19 haplotype. The current harvesting of green sea turtles by Hainan fishermen affects not only protected local populations (Paracel Islands), but also distant populations (Sulu Sea) in protected international waters.
ImplicationsEstablishment of a large-scale Sea Turtle Nature Reserve in the South China Sea, including a special law enforcement team to monitor this National Marine Park, needs to be top priority to help curb illegal harvesting. The Paracel Islands represents a newly defined population, and conservation measures need to be taken immediately to preserve this distinct population.
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Khedkar G, Khedkar C, Prakash B, Khedkar A, Haymer D. DNA barcode based identification of a suspected tiger skin: A case to resolve mimicry. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2019. [DOI: 10.1016/j.fsir.2019.100027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Tizard J, Patel S, Waugh J, Tavares E, Bergmann T, Gill B, Norman J, Christidis L, Scofield P, Haddrath O, Baker A, Lambert D, Millar C. DNA barcoding a unique avifauna: an important tool for evolution, systematics and conservation. BMC Evol Biol 2019; 19:52. [PMID: 30744573 PMCID: PMC6369544 DOI: 10.1186/s12862-019-1346-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 01/02/2019] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND DNA barcoding utilises a standardised region of the cytochrome c oxidase I (COI) gene to identify specimens to the species level. It has proven to be an effective tool for identification of avian samples. The unique island avifauna of New Zealand is taxonomically and evolutionarily distinct. We analysed COI sequence data in order to determine if DNA barcoding could accurately identify New Zealand birds. RESULTS We sequenced 928 specimens from 180 species. Additional Genbank sequences expanded the dataset to 1416 sequences from 211 of the estimated 236 New Zealand species. Furthermore, to improve the assessment of genetic variation in non-endemic species, and to assess the overall accuracy of our approach, sequences from 404 specimens collected outside of New Zealand were also included in our analyses. Of the 191 species represented by multiple sequences, 88.5% could be successfully identified by their DNA barcodes. This is likely a conservative estimate of the power of DNA barcoding in New Zealand, given our extensive geographic sampling. The majority of the 13 groups that could not be distinguished contain recently diverged taxa, indicating incomplete lineage sorting and in some cases hybridisation. In contrast, 16 species showed evidence of distinct intra-species lineages, some of these corresponding to recognised subspecies. For species identification purposes a character-based method was more successful than distance and phylogenetic tree-based methods. CONCLUSIONS DNA barcodes accurately identify most New Zealand bird species. However, low levels of COI sequence divergence in some recently diverged taxa limit the identification power of DNA barcoding. A small number of currently recognised species would benefit from further systematic investigations. The reference database and analysis presented will provide valuable insights into the evolution, systematics and conservation of New Zealand birds.
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Affiliation(s)
- Jacqueline Tizard
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Selina Patel
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - John Waugh
- Unitec Institute of Technology, Auckland, New Zealand
| | - Erika Tavares
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, M5S 2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario, M5S 3B2, Canada
- Present address: Laboratory Research Project Manager, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tjard Bergmann
- Institute for Animal Ecology and Cell Biology, University of Veterinary Medicine Hannover Foundation, Bünteweg 17d, D-30559, Hannover, Germany
| | - Brian Gill
- Associate Emeritus, Auckland War Memorial Museum, Private Bag 92018, Auckland, 1142, New Zealand
| | - Janette Norman
- Molecular Biology Sciences Department, Museum Victoria, GPO Box 666, Melbourne, Victoria, 3001, Australia
- Present address: Graduate School, Southern Cross University, Lismore, New South Wales, Australia
| | - Les Christidis
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
| | - Paul Scofield
- Canterbury Museum, Rolleston Ave, Christchurch, 8001, New Zealand
| | - Oliver Haddrath
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, M5S 2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario, M5S 3B2, Canada
| | - Allan Baker
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, M5S 2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario, M5S 3B2, Canada
| | - David Lambert
- Environmental Futures Research Institute, Griffith University, 170 Kessels Road, Brisbane, Queensland, 4111, Australia
| | - Craig Millar
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
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Bian H, Wang P, Wang N, Tian Y, Bai P, Jiang H, Gao J. Dual-model analysis for improving the discrimination performance of human and nonhuman blood based on Raman spectroscopy. BIOMEDICAL OPTICS EXPRESS 2018; 9:3512-3522. [PMID: 30338136 PMCID: PMC6191633 DOI: 10.1364/boe.9.003512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/22/2018] [Accepted: 06/25/2018] [Indexed: 05/28/2023]
Abstract
The discrimination accuracy for human and nonhuman blood is important for customs inspection and forensic applications. Recently, Raman spectroscopy has shown effectiveness in analyzing blood droplets and stains with an excitation wavelength of 785 nm. However, the discrimination of liquid whole blood in a vacuum blood tube using Raman spectroscopy, which is a form of noncontact and nondestructive detection, has not been achieved. An excitation wavelength of 532 nm was chosen to avoid the fluorescent background of the blood tube, at the cost of reduced spectroscopic information and discrimination accuracy. To improve the accuracy and true positive rate (TPR) for human blood, a dual-model analysis method is proposed. First, model 1 was used to discriminate human-unlike nonhuman blood. Model 2 was then used to discriminate human-like nonhuman blood from the "human blood" obtained by model 1. A total of 332 Raman spectra from 10 species were used to build and validate the model. A blind test and external validation demonstrated the effectiveness of the model. Compared with the results obtained by the single partial least-squares model, the discrimination performance was improved. The total accuracy and TPR, which are highly important for practical applications, increased to 99.1% and 97.4% from 87.2% and 90.6%, respectively.
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Affiliation(s)
- Haiyi Bian
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
- Schott Glass Technologies (Suzhou) Co., Ltd., Suzhou 215009, China
| | - Peng Wang
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Ning Wang
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Yubing Tian
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Pengli Bai
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Jiangsu 215163, China
| | - Haowen Jiang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jing Gao
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
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Exploring hidden diversity in Southeast Asia's Dermogenys spp. (Beloniformes: Zenarchopteridae) through DNA barcoding. Sci Rep 2018; 8:10787. [PMID: 30018357 PMCID: PMC6050249 DOI: 10.1038/s41598-018-29049-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/26/2018] [Indexed: 11/15/2022] Open
Abstract
Members of the freshwater halfbeak genus Dermogenys are hard to identify to the species level, despite several previous attempts to isolate fixed meristic, morphometric and colour pattern differences. This has led to ongoing confusion in scientific literature, records of species occurrence, and entries in museum collections. Here, a DNA barcoding study was conducted on the genus to gain further understanding of its taxonomic status across the Southeast Asian region. Fish were collected from 33 localities, spanning freshwater and brackish habitats in Malaysia, Western Indonesia, Thailand and Vietnam. In total, 290 samples of Dermogenys spp. were amplified for a 651 base pair fragment of the mitochondrial cytochrome oxidase c subunit I (COI) gene. Analysis was able to successfully differentiate the three species: D. collettei, D. siamensis, D. sumatrana; reveal the presence of a new putative species, Dermogenys sp., that was sampled in sympatry with D. collettei at three locations; as well as uncovering two genetic lineages of a fifth species, D. bispina, that display non-overlapping geographical distributions in drainages of northern Borneo; Kudat and Sandakan. This study expands the barcode library for Zenarchopteridae, demonstrates the efficacy of DNA barcoding techniques for differentiating Dermogenys species, and the potential thereof in species discovery.
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A protocol for obtaining DNA barcodes from plant and insect fragments isolated from forensic-type soils. Int J Legal Med 2018; 132:1515-1526. [PMID: 29423711 DOI: 10.1007/s00414-018-1772-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 01/09/2018] [Indexed: 10/18/2022]
Abstract
Soil is often collected from a suspect's tire, vehicle, or shoes during a criminal investigation and subsequently submitted to a forensic laboratory for analysis. Plant and insect material recovered in such samples is rarely analyzed, as morphological identification is difficult. In this study, DNA barcoding was used for taxonomic identifications by targeting the gene regions known to permit discrimination in plants [maturase K (matK) and ribulose 1,5-biphosphate carboxylase (rbcL)] and insects [cytochrome oxidase subunit I (COI)]. A DNA barcode protocol suitable for processing forensic-type biological fragments was developed and its utility broadly tested with forensic-type fragments (e.g., seeds, leaves, bark, head, legs; n, 213) isolated from soils collected within Virginia, USA (n, 11). Difficulties with PCR inhibitors in plant extracts and obtaining clean Sanger sequence data from insect amplicons were encountered during protocol development; however, the final protocol produced sequences specific to the expected locus and taxa. The overall quantity and quality of DNA extracted from the 213 forensic-type biological fragments was low (< 15 ng/μL). For plant fragments, only the rbcL sequence data was deemed reliable; thus, taxonomic identifications were limited to the family level. The majority of insect sequences matched COI in both GenBank and Barcode of Life DataSystems; however, they were identified as an undescribed environmental contaminant. Although limited taxonomic information was gleaned from the forensic-type fragments processed in this study, the new protocol shows promise for obtaining reliable and specific identifications through DNA barcoding, which could ultimately enhance the information gleaned from soil examinations.
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Kumar V, Sharma N, Sharma A. DNA barcoding of the Indian blackbuck (Antilope cervicapra) and their correlation with other closely related species. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2017. [DOI: 10.1186/s41935-017-0034-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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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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Geary J, Camicioli E, Bubela T. DNA barcoding in the media: does coverage of cool science reflect its social context? Genome 2016; 59:738-50. [PMID: 27463361 DOI: 10.1139/gen-2015-0210] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Paul Hebert and colleagues first described DNA barcoding in 2003, which led to international efforts to promote and coordinate its use. Since its inception, DNA barcoding has generated considerable media coverage. We analysed whether this coverage reflected both the scientific and social mandates of international barcoding organizations. We searched newspaper databases to identify 900 English-language articles from 2003 to 2013. Coverage of the science of DNA barcoding was highly positive but lacked context for key topics. Coverage omissions pose challenges for public understanding of the science and applications of DNA barcoding; these included coverage of governance structures and issues related to the sharing of genetic resources across national borders. Our analysis provided insight into how barcoding communication efforts have translated into media coverage; more targeted communication efforts may focus media attention on previously omitted, but important topics. Our analysis is timely as the DNA barcoding community works to establish the International Society for the Barcode of Life.
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Affiliation(s)
- Janis Geary
- School of Public Health, University of Alberta, Edmonton, AB, Canada.,School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Emma Camicioli
- School of Public Health, University of Alberta, Edmonton, AB, Canada.,School of Public Health, University of Alberta, Edmonton, AB, Canada
| | - Tania Bubela
- School of Public Health, University of Alberta, Edmonton, AB, Canada.,School of Public Health, University of Alberta, Edmonton, AB, Canada
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da Silva JM, Willows-Munro S. A review of over a decade of DNA barcoding in South Africa: a faunal perspective. AFRICAN ZOOLOGY 2016. [DOI: 10.1080/15627020.2016.1151377] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Adamowicz SJ, Steinke D. Increasing global participation in genetics research through DNA barcoding. Genome 2015; 58:519-26. [DOI: 10.1139/gen-2015-0130] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA barcoding—the sequencing of short, standardized DNA regions for specimen identification and species discovery—has promised to facilitate rapid access to biodiversity knowledge by diverse users. Here, we advance our opinion that increased global participation in genetics research is beneficial, both to scientists and for science, and explore the premise that DNA barcoding can help to democratize participation in genetics research. We examine publication patterns (2003–2014) in the DNA barcoding literature and compare trends with those in the broader, related domain of genomics. While genomics is the older and much larger field, the number of nations contributing to the published literature is similar between disciplines. Meanwhile, DNA barcoding exhibits a higher pace of growth in the number of publications as well as greater evenness among nations in their proportional contribution to total authorships. This exploration revealed DNA barcoding to be a highly international discipline, with growing participation by researchers in especially biodiverse nations. We briefly consider several of the challenges that may hinder further participation in genetics research, including access to training and molecular facilities as well as policy relating to the movement of genetic resources.
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Affiliation(s)
- Sarah J. Adamowicz
- Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Dirk Steinke
- Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
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Gonçalves PFM, Oliveira-Marques AR, Matsumoto TE, Miyaki CY. DNA Barcoding Identifies Illegal Parrot Trade: Figure 1. J Hered 2015; 106 Suppl 1:560-4. [DOI: 10.1093/jhered/esv035] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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Bertolini F, Ghionda MC, D’Alessandro E, Geraci C, Chiofalo V, Fontanesi L. A next generation semiconductor based sequencing approach for the identification of meat species in DNA mixtures. PLoS One 2015; 10:e0121701. [PMID: 25923709 PMCID: PMC4414512 DOI: 10.1371/journal.pone.0121701] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 02/14/2015] [Indexed: 11/18/2022] Open
Abstract
The identification of the species of origin of meat and meat products is an important issue to prevent and detect frauds that might have economic, ethical and health implications. In this paper we evaluated the potential of the next generation semiconductor based sequencing technology (Ion Torrent Personal Genome Machine) for the identification of DNA from meat species (pig, horse, cattle, sheep, rabbit, chicken, turkey, pheasant, duck, goose and pigeon) as well as from human and rat in DNA mixtures through the sequencing of PCR products obtained from different couples of universal primers that amplify 12S and 16S rRNA mitochondrial DNA genes. Six libraries were produced including PCR products obtained separately from 13 species or from DNA mixtures containing DNA from all species or only avian or only mammalian species at equimolar concentration or at 1:10 or 1:50 ratios for pig and horse DNA. Sequencing obtained a total of 33,294,511 called nucleotides of which 29,109,688 with Q20 (87.43%) in a total of 215,944 reads. Different alignment algorithms were used to assign the species based on sequence data. Error rate calculated after confirmation of the obtained sequences by Sanger sequencing ranged from 0.0003 to 0.02 for the different species. Correlation about the number of reads per species between different libraries was high for mammalian species (0.97) and lower for avian species (0.70). PCR competition limited the efficiency of amplification and sequencing for avian species for some primer pairs. Detection of low level of pig and horse DNA was possible with reads obtained from different primer pairs. The sequencing of the products obtained from different universal PCR primers could be a useful strategy to overcome potential problems of amplification. Based on these results, the Ion Torrent technology can be applied for the identification of meat species in DNA mixtures.
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Affiliation(s)
- Francesca Bertolini
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Marco Ciro Ghionda
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
- Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, 98168, Messina, Italy
| | - Enrico D’Alessandro
- Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, 98168, Messina, Italy
| | - Claudia Geraci
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Vincenzo Chiofalo
- Department of Veterinary Sciences, Animal Production Unit, University of Messina, Polo Universitario dell'Annunziata, 98168, Messina, Italy
- Meat Research Consortium, Polo Universitario dell’Annunziata, 98168, Messina, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
- * E-mail:
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Chen J, Jiang Z, Li C, Ping X, Cui S, Tang S, Chu H, Liu B. Identification of ungulates used in a traditional Chinese medicine with DNA barcoding technology. Ecol Evol 2015; 5:1818-25. [PMID: 26140198 PMCID: PMC4485963 DOI: 10.1002/ece3.1457] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/12/2015] [Accepted: 02/16/2015] [Indexed: 11/22/2022] Open
Abstract
Horns of Saiga antelope (Saiga tatarica) have always been an ingredient of “Lingyangjiao”, a traditional Chinese medicine (TCM). Persistent hunting for Saiga antelope has already threatened the survival of critical endangered populations in wild. To control the growing pressure, CITES and Chinese government have legislated for monitoring the trade of Saiga horns. However, similar ungulate horns are difficult to identify by their morphological characteristics, which has impeded the law enforcement. Besides Saiga antelope, other seven ungulate species which have similar horns are also sold and marked as “Lingyangjiao” in TCM markets to offset shortage of Saiga antelope horns. Such species are Gazella subgutturosa, Pantholops hodgsonii, Procapra picticaudata, Procapra gutturosa, Procapra przewalskii, Capra hircus, and Ovis aries. Our study aimed at implementing DNA barcoding technology to diagnose Saiga horns and the substitutes. We successfully extracted genomic DNA from horn samples. We recovered COI sequences of 644 bp with specific primers and 349 bp with nested PCR primers designed for degraded horn samples. The mean interspecific genetic distance of data set of the 644-bp full barcodes and the 349-bp mini-barcodes was 14.96% and 15.38%, respectively, and the mean intraspecific distance was 0.24% and 0.20%, respectively. Each species formed independent clades in neighbor-joining (NJ) phylogenetic tree of the two data sets with >99% supporting values, except P. gutturosa and P. przewalskii. The deep genetic distances gap and clear species clades in NJ tree of either full barcodes or mini-barcodes suggest that barcoding technology is an effective tool to diagnose Saiga horns and their substitutes. Barcoding diagnosis protocol developed here will simplify diagnosis of “Lingyangjiao” species and will facilitate conservation of endangered ungulates involved in TCM “Lingyangjiao” markets, especially the Saiga antelope.
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Affiliation(s)
- Jing Chen
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China ; University of Chinese Academy of Sciences No. 19 (A) Yuquan Road, Beijing, 100049, China
| | - Zhigang Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China ; University of Chinese Academy of Sciences No. 19 (A) Yuquan Road, Beijing, 100049, China ; Endangered Species Scientific Commission of the People's Republic of China Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China
| | - Chunlin Li
- School of Resources and Environmental Engineering, Anhui University No. 111 Jiu Long Road, Hefei, 230601, Anhui Province, China
| | - Xiaoge Ping
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China
| | - Shaopeng Cui
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China ; University of Chinese Academy of Sciences No. 19 (A) Yuquan Road, Beijing, 100049, China
| | - Songhua Tang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Chaoyang District, No. 1 Beichen West Road, Beijing, 100101, China
| | - Hongjun Chu
- Wildlife Conservation Office of Altay Prefecture 836500, Altay, Xinjiang, China
| | - Binwan Liu
- College of Wildlife Resources, Northeast Forestry University, No. 26 Hexing Road Xiangfang District Harbin, 150040, Heilongjiang Province, China
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Khedkar GD, Abhayankar SB, Nalage D, Ahmed SN, Khedkar CD. DNA barcode based wildlife forensics for resolving the origin of claw samples using a novel primer cocktail. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:3932-3935. [PMID: 25492536 DOI: 10.3109/19401736.2014.987270] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Excessive wildlife hunting for commercial purposes can have negative impacts on biodiversity and may result in species extinction. To ensure compliance with legal statutes, forensic identification approaches relying on molecular markers may be used to identify the species of origin of animal material from hairs, claw, blood, bone, or meat. Using this approach, DNA sequences from the COI "barcoding" gene have been used to identify material from a number of domesticated animal species. However, many wild species of carnivores still present great challenges in generating COI barcodes using standard "universal" primer pairs. In the work presented here, the mitochondrial COI gene was successfully amplified using a novel primer cocktail, and the products were sequenced to determine the species of twenty one unknown samples of claw material collected as part of forensic wildlife case investigations. Sixteen of the unknown samples were recognized to have originated from either Panthera leo or P. pardus individuals. The remaining five samples could be identified only to the family level due to the absence of reference animal sequences. This is the first report on the use of COI sequences for the identification of P. pardus and P. leo from claw samples as part of forensic investigations in India. The study also highlights the need for adequate reference material to aid in the resolution of suspected cases of illegal wildlife harvesting.
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Affiliation(s)
- Gulab D Khedkar
- a Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University , Aurangabad , Maharashtra , India
| | - Shil Bapurao Abhayankar
- a Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University , Aurangabad , Maharashtra , India
| | - Dinesh Nalage
- a Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University , Aurangabad , Maharashtra , India
| | - Shaikh Nadeem Ahmed
- b Ministry of Food Processing Industries, Live Stock Products, Panchsheel Bhavan , August Kranti Marg , New Delhi , India , and
| | - Chandraprakash D Khedkar
- c College of Dairy Technology, Maharashtra Animal and Fisheries Sciences University , Nagpur , Maharashtra , India
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Ferri G, Corradini B, Ferrari F, Santunione AL, Palazzoli F, Alu' M. Forensic botany II, DNA barcode for land plants: Which markers after the international agreement? Forensic Sci Int Genet 2014; 15:131-6. [PMID: 25457632 DOI: 10.1016/j.fsigen.2014.10.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/23/2014] [Accepted: 10/03/2014] [Indexed: 11/17/2022]
Abstract
The ambitious idea of using a short piece of DNA for large-scale species identification (DNA barcoding) is already a powerful tool for scientists and the application of this standard technique seems promising in a range of fields including forensic genetics. While DNA barcoding enjoyed a remarkable success for animal identification through cytochrome c oxidase I (COI) analysis, the attempts to identify a single barcode for plants remained a vain hope for a longtime. From the beginning, the Consortium for the Barcode of Life (CBOL) showed a lack of agreement on a core plant barcode, reflecting the diversity of viewpoints. Different research groups advocated various markers with divergent set of criteria until the recent publication by the CBOL-Plant Working Group. After a four-year effort, in 2009 the International Team concluded to agree on standard markers promoting a multilocus solution (rbcL and matK), with 70-75% of discrimination to the species level. In 2009 our group firstly proposed the broad application of DNA barcoding principles as a tool for identification of trace botanical evidence through the analysis of two chloroplast loci (trnH-psbA and trnL-trnF) in plant species belonging to local flora. Difficulties and drawbacks that were encountered included a poor coverage of species in specific databases and the lack of authenticated reference sequences for the selected markers. Successful preliminary results were obtained providing an approach to progressively identify unknown plant specimens to a given taxonomic rank, usable by any non-specialist botanist or in case of a shortage of taxonomic expertise. Now we considered mandatory to update and to compare our previous findings with the new selected plastid markers (matK+rbcL), taking into account forensic requirements. Features of all the four loci (the two previously analyzed trnH-psbA+trnL-trnF and matK+rbcL) were compared singly and in multilocus solutions to assess the most suitable combination for forensic botany. Based on obtained results, we recommend the adoption of a two-locus combination with rbcL+trnH-psbA plastid markers, which currently best satisfies forensic needs for botanical species identification.
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Affiliation(s)
- G Ferri
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy.
| | - B Corradini
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - F Ferrari
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - A L Santunione
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - F Palazzoli
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
| | - M Alu'
- Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Italy
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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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21
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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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22
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Yang C, Xiao Z, Zou Y, Zhang X, Yang B, Hao Y, Moermond T, Yue B. DNA barcoding revises a misidentification on musk deer. ACTA ACUST UNITED AC 2014; 26:605-12. [DOI: 10.3109/19401736.2014.880887] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Johnson RN, Wilson-Wilde L, Linacre A. Current and future directions of DNA in wildlife forensic science. Forensic Sci Int Genet 2013; 10:1-11. [PMID: 24680123 DOI: 10.1016/j.fsigen.2013.12.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 12/13/2013] [Accepted: 12/18/2013] [Indexed: 12/22/2022]
Abstract
Wildlife forensic science may not have attained the profile of human identification, yet the scale of criminal activity related to wildlife is extensive by any measure. Service delivery in the arena of wildlife forensic science is often ad hoc, unco-ordinated and unregulated, yet many of those currently dedicated to wildlife conservation and the protection of endangered species are striving to ensure that the highest standards are met. The genetic markers and software used to evaluate data in wildlife forensic science are more varied than those in human forensic identification and are rarely standardised between species. The time and resources required to characterise and validate each genetic maker is considerable and in some cases prohibitive. Further, issues are regularly encountered in the construction of allelic databases and allelic ladders; essential in human identification studies, but also applicable to wildlife criminal investigations. Accreditation and certification are essential in human identification and are currently being strived for in the forensic wildlife community. Examples are provided as to how best practice can be demonstrated in all areas of wildlife crime analysis and ensure that this field of forensic science gains and maintains the respect it deserves. This review is aimed at those conducting human identification to illustrate how research concepts in wildlife forensic science can be used in the criminal justice system, as well as describing the real importance of this type of forensic analysis.
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Affiliation(s)
- Rebecca N Johnson
- Australian Museum Research Institute, Australian Centre for Wildlife Genomics, Science and Learning Division, Australian Museum, Sydney, Australia.
| | - Linzi Wilson-Wilde
- Australia New Zealand Policing Advisory Agency - National Institute of Forensic Science, Melbourne, Australia
| | - Adrian Linacre
- School of Biological Sciences, Flinders University, Bedford Park, Adelaide, Australia
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Aliabadian M, Beentjes KK, Roselaar C(K, van Brandwijk H, Nijman V, Vonk R. DNA barcoding of Dutch birds. Zookeys 2013; 365:25-48. [PMID: 24453549 PMCID: PMC3890669 DOI: 10.3897/zookeys.365.6287] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 12/06/2013] [Indexed: 12/01/2022] Open
Abstract
The mitochondrial cytochrome c oxidase subunit I (COI) can serve as a fast and accurate marker for the identification of animal species, and has been applied in a number of studies on birds. We here sequenced the COI gene for 387 individuals of 147 species of birds from the Netherlands, with 83 species being represented by > 2 sequences. The Netherlands occupies a small geographic area and 95% of all samples were collected within a 50 km radius from one another. The intraspecific divergences averaged 0.29% among this assemblage, but most values were lower; the interspecific divergences averaged 9.54%. In all, 95% of species were represented by a unique barcode, with 6 species of gulls and skua (Larus and Stercorarius) having at least one shared barcode. This is best explained by these species representing recent radiations with ongoing hybridization. In contrast, one species, the Lesser Whitethroat Sylvia curruca showed deep divergences, averaging 5.76% and up to 8.68% between individuals. These possibly represent two distinct taxa, S. curruca and S. blythi, both clearly separated in a haplotype network analysis. Our study adds to a growing body of DNA barcodes that have become available for birds, and shows that a DNA barcoding approach enables to identify known Dutch bird species with a very high resolution. In addition some species were flagged up for further detailed taxonomic investigation, illustrating that even in ornithologically well-known areas such as the Netherlands, more is to be learned about the birds that are present.
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Affiliation(s)
- Mansour Aliabadian
- Department of Biology, Ferdowsi University of Mashhad, Mashhad, Iran
- Naturalis Biodiversity Center, Leiden, the Netherlands
| | | | | | | | - Vincent Nijman
- Department of Social Sciences, Oxford Brookes University, Oxford, UK
| | - Ronald Vonk
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
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Potrich C, Santini GC, Lunelli L, Pasquardini L, Bertorelli R, De Sanctis V, Quattrone A, Pederzolli C. The Making of “on-Chip PCR in Real-Time” for Food Quality Control. BIONANOSCIENCE 2013. [DOI: 10.1007/s12668-013-0080-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Sampling strategy and potential utility of indels for DNA barcoding of closely related plant species: a case study in taxus. Int J Mol Sci 2012; 13:8740-8751. [PMID: 22942731 PMCID: PMC3430262 DOI: 10.3390/ijms13078740] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 06/23/2012] [Accepted: 06/27/2012] [Indexed: 11/30/2022] Open
Abstract
Although DNA barcoding has become a useful tool for species identification and biodiversity surveys in plant sciences, there remains little consensus concerning appropriate sampling strategies and the treatment of indels. To address these two issues, we sampled 39 populations for nine Taxus species across their entire ranges, with two to three individuals per population randomly sampled. We sequenced one core DNA barcode (matK) and three supplementary regions (trnH-psbA, trnL-trnF and ITS) for all samples to test the effects of sampling design and the utility of indels. Our results suggested that increasing sampling within-population did not change the clustering of individuals, and that meant within-population P-distances were zero for most populations in all regions. Based on the markers tested here, comparison of methods either including or excluding indels indicated that discrimination and nodal support of monophyletic groups were significantly increased when indels were included. Thus we concluded that one individual per population was adequate to represent the within-population variation in these species for DNA barcoding, and that intra-specific sampling was best focused on representing the entire ranges of certain taxa. We also found that indels occurring in the chloroplast trnL-trnF and trnH-psbA regions were informative to differentiate among for closely related taxa barcoding, and we proposed that indel-coding methods should be considered for use in future for closed related plant species DNA barcoding projects on or below generic level.
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Chiellini C, Iannelli R, Modeo L, Bianchi V, Petroni G. Biofouling of reverse osmosis membranes used in river water purification for drinking purposes: analysis of microbial populations. BIOFOULING 2012; 28:969-984. [PMID: 22971211 DOI: 10.1080/08927014.2012.724679] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Biofouling in water treatment processes represents one of the most frequent causes of plant performance decline. Investigation of clogged membranes (reverse osmosis membranes, microfiltration membranes and ultrafiltration membranes) is generally performed on fresh membranes. In the present study, a multidisciplinary autopsy of a reverse osmosis membrane (ROM) was conducted. The membrane, which was used in sulfate-rich river water purification for drinking purposes, had become inoperative after 6 months because of biofouling and was later stored for 18 months in dry conditions before analysis. SSU rRNA gene library construction, clone sequencing, T-RFLP, light microscope, and scanning electron microscope (SEM) observations were used to identify the microorganisms present on the membrane and possibly responsible for biofouling at the time of removal. The microorganisms were mainly represented by bacteria belonging to the phylum Actinobacteria and by a single protozoan species belonging to the Lobosea group. The microbiological analysis was interpreted in the context of the treatment plant operations to hypothesize as to the possible mechanisms used by microorganisms to enter the plant and colonize the ROM surface.
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Affiliation(s)
- Carolina Chiellini
- Department of Biology, Unit of Protistology-Zoology, University of Pisa, Via Volta 4/6, Pisa, 56126, Italy
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