1
|
Combination of Multiple Microsatellite Analysis and Genome-Wide SNP Genotyping Helps to Solve Wildlife Crime: A Case Study of Poaching of a Caucasian tur ( Capra caucasica) in Russian Mountain National Park. Animals (Basel) 2021; 11:ani11123416. [PMID: 34944192 PMCID: PMC8697997 DOI: 10.3390/ani11123416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/18/2021] [Accepted: 11/28/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary DNA molecular techniques, including multiple microsatellite analysis and genome-wide SNP-genotyping, were used to unlock and prove the poaching of wild goats (Capra caucasica) in an area of the Caucasian mountains in Russia. Abstract Poaching is one of the major types of wildlife crime in Russia. Remnants of goats (presumably the wild endemic species, the Caucasian tur) were found in an area of the Caucasian mountains. The case study involves a suspected poacher whose vehicle was found to have two duffel bags containing pieces of a carcass, which he claimed was that of a goat from his flock. The aim of the forensic genetic analysis for this case was to (i) establish individual identity and (ii) perform species identification. DNA typing based on fourteen microsatellites revealed that STR-genotypes generated from pieces of evidence found at crime scene fully matched those obtained from the evidence seized from the suspect. The results of genome-wide SNP-genotyping, using Illumina Goat SNP50 BeadChip, provided evidence that the poached animal was a wild Caucasian tur (Capra caucasica). Thus, based on comprehensive molecular genetic analysis, evidence of poaching was obtained and sent to local authorities. To our knowledge, this case study is the first to attempt to use DNA chips in wildlife forensics of ungulates.
Collapse
|
2
|
de Melo AA, Nunes R, Telles MPDC. Same information, new applications: revisiting primers for the avian COI gene and improving DNA barcoding identification. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00507-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
3
|
Kriangwanich W, Nganvongpanit K, Buddhachat K, Siengdee P, Chomdej S, Ponsuksili S, Thitaram C. Mammalian species identification using ISSR-HRM technique. Sci Prog 2021; 104:368504211026163. [PMID: 34143702 PMCID: PMC10455004 DOI: 10.1177/00368504211026163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Wildlife trading and the illegal hunting of wildlife are contributing factors to the biodiversity crisis that is presently unfolding across the world. The inability to control the trade of animal body parts or available biological materials is a major challenge for those who investigate wildlife crime. The effective management of this illegal trade is an important facet of wildlife forensic sciences and can be a key factor in the enforcement of effective legislation surrounding the illegal trade of protected and endangered species. However, the science of wildlife forensics is limited by the absence of a comprehensive database for wildlife investigations. Inter-simple sequence repeat markers (ISSR) coupled with high resolution melting analysis (HRM) have been effectively used for species identification of 38 mammalian species. Six primers of the ISSR markers were chosen for species identification analysis. From six ISSR primers resulting in a range of accuracy of 33.3%-100% and 100% in terms of precision in every primer. Furthermore, 161 mammalian samples were 100% distinguished to the correct species using these six ISSR primers. ISSR-HRM analysis was successfully employed in determining mammal identification among varying mammalian species, and thus could serve as an effective alternative tool or technique in the species identification process. This option would offer researchers a heightened level of convenience in terms of its performance and the ease with which researchers or field practice veterinarians would be able to interpret results in effectively identifying animal parts at wildlife investigation crime scenes.
Collapse
Affiliation(s)
- Wannapimol Kriangwanich
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Korakot Nganvongpanit
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand
| | - Kittisak Buddhachat
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Puntita Siengdee
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand
- Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Siriwadee Chomdej
- Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | | | - Chatchote Thitaram
- Center of Excellence in Elephant and Wildlife Research, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, Thailand
| |
Collapse
|
4
|
Dalton DL, de Bruyn M, Thompson T, Kotzé A. Assessing the utility of DNA barcoding in wildlife forensic cases involving South African antelope. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2020. [DOI: 10.1016/j.fsir.2020.100071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
5
|
Naseem A, Batool S, Abbas FI. Utility of mitochondrial COI gene for identification of wild ungulate species of conservational importance from Pakistan. Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1756476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Asif Naseem
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Sargodha, Pakistan
- Department of Zoology, University of Sargodha, Sargodha, Pakistan
| | - Sajida Batool
- Department of Zoology, University of Sargodha, Sargodha, Pakistan
| | - Fakhar- i- Abbas
- Zoology, Centre for Bioresource Research (CBR), Islamabad, Pakistan
| |
Collapse
|
6
|
Porter TM, Hajibabaei M. Over 2.5 million COI sequences in GenBank and growing. PLoS One 2018; 13:e0200177. [PMID: 30192752 PMCID: PMC6128447 DOI: 10.1371/journal.pone.0200177] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/24/2018] [Indexed: 01/20/2023] Open
Abstract
The increasing popularity of cytochrome c oxidase subunit 1 (COI) DNA metabarcoding warrants a careful look at the underlying reference databases used to make high-throughput taxonomic assignments. The objectives of this study are to document trends and assess the future usability of COI records for metabarcode identification. The number of COI records deposited to the NCBI nucleotide database has increased by a geometric average of 51% per year, from 8,137 records deposited in 2003 to a cumulative total of ~ 2.5 million by the end of 2017. About half of these records are fully identified to the species rank, 92% are at least 500 bp in length, 74% have a country annotation, and 51% have latitude-longitude annotations. To ensure the future usability of COI records in GenBank we suggest: 1) Improving the geographic representation of COI records, 2) Improving the cross-referencing of COI records in the Barcode of Life Data System and GenBank to facilitate consolidation and incorporation into existing bioinformatic pipelines, 3) Adherence to the minimum information about a marker gene sequence guidelines, and 4) Integrating metabarcodes from eDNA and mixed community studies with existing reference sequences. The growth of COI reference records over the past 15 years has been substantial and is likely to be a resource across many fields for years to come.
Collapse
Affiliation(s)
- Teresita M. Porter
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, Ontario, CANADA
- Great Lakes Forestry Centre, Natural Resources Canada, Sault Ste. Marie, Ontario, CANADA
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, Ontario, CANADA
| |
Collapse
|
7
|
|
8
|
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
|
9
|
Hou F, Wen L, Peng C, Guo J. Identification of marine traditional Chinese medicine dried seahorses in the traditional Chinese medicine market using DNA barcoding. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:107-112. [PMID: 27871217 DOI: 10.1080/24701394.2016.1248430] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Seahorse documented in Chinese pharmacopeia possess important medicinal efficacy and are used as an ingredient in traditional Chinese medicines. The growing international trade threatens the species. DNA barcoding holds a great application potentiality in wildlife conservation and might prevent the illegal trade of threatened species. The COI gene was used to identify seahorse, and nine Hippocampus species were found in the three large traditional Chinese medicines markets of China. All inter-specific genetic variations were larger than 2%. Mean genetic distances between species were 17-fold larger than those within the species. Phylogenetic tree showed that each species clustered in the appropriate branch. All results demonstrated that COI-based barcoding technique could be used to identify seahorse species and played a major role in monitoring the seahorse trade.
Collapse
Affiliation(s)
- Feixia Hou
- a Pharmacy College, Chengdu University of Traditional Chinese Medicine , Chengdu , China.,b The Ministry of Education Key Laboratory of Standardization of Chinese Herbal Medicine , Chengdu , China.,c Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province , Chengdu , China.,d Key Laboratory Breeding Base of Co-founded by Sichuan Province and MOST , Chengdu , China
| | - Longlian Wen
- e Dujiangyan Traditional Chinese Medicine Hospital , Chengdu , Sichuan , China
| | - Cheng Peng
- a Pharmacy College, Chengdu University of Traditional Chinese Medicine , Chengdu , China.,b The Ministry of Education Key Laboratory of Standardization of Chinese Herbal Medicine , Chengdu , China.,c Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province , Chengdu , China.,d Key Laboratory Breeding Base of Co-founded by Sichuan Province and MOST , Chengdu , China
| | - Jinlin Guo
- a Pharmacy College, Chengdu University of Traditional Chinese Medicine , Chengdu , China.,b The Ministry of Education Key Laboratory of Standardization of Chinese Herbal Medicine , Chengdu , China.,c Key Laboratory of Systematic Research, Development and Utilization of Chinese Medicine Resources in Sichuan Province , Chengdu , China.,d Key Laboratory Breeding Base of Co-founded by Sichuan Province and MOST , Chengdu , China
| |
Collapse
|
10
|
Staats M, Arulandhu AJ, Gravendeel B, Holst-Jensen A, Scholtens I, Peelen T, Prins TW, Kok E. Advances in DNA metabarcoding for food and wildlife forensic species identification. Anal Bioanal Chem 2016; 408:4615-30. [PMID: 27178552 PMCID: PMC4909793 DOI: 10.1007/s00216-016-9595-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 04/19/2016] [Accepted: 04/20/2016] [Indexed: 12/18/2022]
Abstract
Species identification using DNA barcodes has been widely adopted by forensic scientists as an effective molecular tool for tracking adulterations in food and for analysing samples from alleged wildlife crime incidents. DNA barcoding is an approach that involves sequencing of short DNA sequences from standardized regions and comparison to a reference database as a molecular diagnostic tool in species identification. In recent years, remarkable progress has been made towards developing DNA metabarcoding strategies, which involves next-generation sequencing of DNA barcodes for the simultaneous detection of multiple species in complex samples. Metabarcoding strategies can be used in processed materials containing highly degraded DNA e.g. for the identification of endangered and hazardous species in traditional medicine. This review aims to provide insight into advances of plant and animal DNA barcoding and highlights current practices and recent developments for DNA metabarcoding of food and wildlife forensic samples from a practical point of view. Special emphasis is placed on new developments for identifying species listed in the Convention on International Trade of Endangered Species (CITES) appendices for which reliable methods for species identification may signal and/or prevent illegal trade. Current technological developments and challenges of DNA metabarcoding for forensic scientists will be assessed in the light of stakeholders' needs.
Collapse
Affiliation(s)
- Martijn Staats
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands.
| | - Alfred J Arulandhu
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, Sylviusweg 72, P.O. Box 9517, Leiden, The Netherlands
| | - Arne Holst-Jensen
- Norwegian Veterinary Institute, Ullevaalsveien 68, P.O. Box 750, Sentrum, 0106, Oslo, Norway
| | - Ingrid Scholtens
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Tamara Peelen
- Dutch Customs Laboratory, Kingsfordweg 1, 1043 GN, Amsterdam, The Netherlands
| | - Theo W Prins
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Esther Kok
- RIKILT Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| |
Collapse
|
11
|
Kvie KS, Heggenes J, Røed KH. Merging and comparing three mitochondrial markers for phylogenetic studies of Eurasian reindeer (Rangifer tarandus). Ecol Evol 2016; 6:4347-58. [PMID: 27386080 PMCID: PMC4893353 DOI: 10.1002/ece3.2199] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 04/25/2016] [Accepted: 05/02/2016] [Indexed: 01/12/2023] Open
Abstract
Phylogenetic analyses provide information that can be useful in the conservation of genetic variation by identifying intraspecific genetic structure. Reconstruction of phylogenetic relationships requires the use of markers with the appropriate amount of variation relative to the timeframe and purpose of the study. Here, genetic structure and clustering are inferred from comparative analyses of three widely used mitochondrial markers, the CR, cytb and the COI region, merged and separately, using Eurasian reindeer as a model. A Bayesian phylogeny and a MJ network, both based on the merged dataset, indicate several distinct maternal haplotype clusters within Eurasian reindeer. In addition to confirm previously described clusters, two new subclusters were found. When comparing the results from the merged dataset with the results from analyses of the three markers separately, similar clustering was found in the CR and COI phylogenies, whereas the cytb region showed poor resolution. Phylogenetic analyses of the merged dataset and the CR revealed congruent results, implying that single sequencing analysis of the CR is an applicable method for studying the haplotype structure in Eurasian reindeer.
Collapse
Affiliation(s)
- Kjersti S Kvie
- Department of Environmental Studies University College of Southeast Norway Bø in Telemark Norway; Department of Basic Sciences and Aquatic Medicine Norwegian University of Life Sciences Oslo Norway
| | - Jan Heggenes
- Department of Environmental Studies University College of Southeast Norway Bø in Telemark Norway
| | - Knut H Røed
- Department of Basic Sciences and Aquatic Medicine Norwegian University of Life Sciences Oslo Norway
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
King SRB, McCain CM. Robust discrimination ofReithrodontomys megalotisandR. montanus(Mammalia: Rodentia) from Colorado, using cranial morphology and external characteristics within age classes. P BIOL SOC WASH 2015. [DOI: 10.2988/0006-324x-128.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
|
14
|
Ermakov OA, Simonov E, Surin VL, Titov SV, Brandler OV, Ivanova NV, Borisenko AV. Implications of hybridization, NUMTs, and overlooked diversity for DNA Barcoding of Eurasian ground squirrels. PLoS One 2015; 10:e0117201. [PMID: 25617768 PMCID: PMC4305304 DOI: 10.1371/journal.pone.0117201] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 12/19/2014] [Indexed: 11/30/2022] Open
Abstract
The utility of DNA Barcoding for species identification and discovery has catalyzed a concerted effort to build the global reference library; however, many animal groups of economical or conservational importance remain poorly represented. This study aims to contribute DNA barcode records for all ground squirrel species (Xerinae, Sciuridae, Rodentia) inhabiting Eurasia and to test efficiency of this approach for species discrimination. Cytochrome c oxidase subunit 1 (COI) gene sequences were obtained for 97 individuals representing 16 ground squirrel species of which 12 were correctly identified. Taxonomic allocation of some specimens within four species was complicated by geographically restricted mtDNA introgression. Exclusion of individuals with introgressed mtDNA allowed reaching a 91.6% identification success rate. Significant COI divergence (3.5-4.4%) was observed within the most widespread ground squirrel species (Spermophilus erythrogenys, S. pygmaeus, S. suslicus, Urocitellus undulatus), suggesting the presence of cryptic species. A single putative NUMT (nuclear mitochondrial pseudogene) sequence was recovered during molecular analysis; mitochondrial COI from this sample was amplified following re-extraction of DNA. Our data show high discrimination ability of 100 bp COI fragments for Eurasian ground squirrels (84.3%) with no incorrect assessments, underscoring the potential utility of the existing reference librariy for the development of diagnostic 'mini-barcodes'.
Collapse
Affiliation(s)
- Oleg A. Ermakov
- Department of Zoology and Ecology, Penza State University, Penza, Russia
| | - Evgeniy Simonov
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Tomsk State University, Tomsk, Russia
| | - Vadim L. Surin
- Hematological Research Center, Russian Academy of Medical Sciences, Moscow, Russia
| | - Sergey V. Titov
- Department of Zoology and Ecology, Penza State University, Penza, Russia
| | - Oleg V. Brandler
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Alex V. Borisenko
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Canada
| |
Collapse
|
15
|
Chao Z, Liao J, Liang Z, Huang S, Zhang L, Li J. Cytochrome C oxidase subunit I barcodes provide an efficient tool for Jinqian Baihua She (Bungarus parvus) authentication. Pharmacogn Mag 2014; 10:449-57. [PMID: 25422545 PMCID: PMC4239722 DOI: 10.4103/0973-1296.141816] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 10/01/2013] [Accepted: 09/26/2014] [Indexed: 01/21/2023] Open
Abstract
Objective: To test the feasibility of DNA barcoding for accurate identification of Jinqian Baihua She and its adulterants. Materials and Methods: Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of 39 samples from 9 snake species, including Bungarus multicinctus, the officially recognized origin animal by Chinese Pharmacopoeia, and other 8 adulterate species. The aligned sequences, 658 base pairs in length, were analyzed for divergence using the Kimura-2-parameter (K2P) distance model with MEGA5.0. Results: The mean intraspecific K2P distance was 0.0103 and the average interspecific genetic distance was 0.2178 in B. multicinctus, far greater than the minimal interspecific genetic distance of 0.027 recommended for species identification. A neighbor-joining (NJ) tree was constructed, in which each species formed a monophyletic clade with bootstrap supports of 100%. All the data were submitted to Barcode of Life Data system version 3.0 (BOLD, http://www.barcodinglife.org) under the project title “DNA barcoding Bungarus multicinctus and its adulterants”. Ten samples of commercially available crude drugs of JBS were identified using the identification engine provided by BOLD. All the samples were clearly identified at the species level, among which five were found to be the adulterants and identified as Dinodon rufozonatum. Conclusion: DNA barcoding using the standard COI gene fragments provides an effective and accurate means for JBS identification and authentication.
Collapse
Affiliation(s)
- Zhi Chao
- Department of Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Jing Liao
- Department of Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China ; Beijing Royal Intergrative Medicine Hospital, Beijing, China
| | - Zhenbiao Liang
- Department of Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China ; Department of Pharmacy, Zhongshan People's Hospital, Zhongshan, China
| | - Suhua Huang
- Department of Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Liang Zhang
- South China Institute of Endangered Animals, Guangzhou, China
| | - Junde Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| |
Collapse
|
16
|
Gaubert P, Njiokou F, Olayemi A, Pagani P, Dufour S, Danquah E, Nutsuakor MEK, Ngua G, Missoup AD, Tedesco PA, Dernat R, Antunes A. Bushmeat genetics: setting up a reference framework for the DNA typing of African forest bushmeat. Mol Ecol Resour 2014; 15:633-51. [DOI: 10.1111/1755-0998.12334] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 09/17/2014] [Accepted: 09/19/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier - UM2-CNRS-IRD; Université Montpellier 2; Place Eugène Bataillon - CC 64 34095 Montpellier Cedex 05 France
| | - Flobert Njiokou
- Laboratoire de Parasitologie et d'Ecologie; Faculté des Sciences; Université de Yaoundé I; BP 812 Yaoundé Cameroon
| | - Ayodeji Olayemi
- Natural History Museum; Obafemi Awolowo University; Ho 220005 Ile-Ife Osun State Nigeria
| | - Paolo Pagani
- Dutch Wildlife Health Centre; Faculty of Veterinary Medicine; Yalelaan 1 3584 CL Utrecht The Netherlands
| | | | - Emmanuel Danquah
- Department of Wildlife and Range Management; Faculty of Renewable Natural Resources; Kwame Nkrumah University of Science and Technology; University Post Office; Kumasi Ghana
| | - Mac Elikem K. Nutsuakor
- Department of Wildlife and Range Management; Faculty of Renewable Natural Resources; Kwame Nkrumah University of Science and Technology; University Post Office; Kumasi Ghana
| | - Gabriel Ngua
- Amigos de la Naturaleza y del Desarrollo de Guinea Ecuatorial (ANDEGE); Barrió Ukomba, S/N Bata Equatorial Guinea
| | - Alain-Didier Missoup
- Biologie de l'Evolution - Mammalogie; Département de Biologie des Organismes Animaux; Faculté des Sciences; Université de Douala; BP 24157 Douala Cameroon
| | - Pablo A. Tedesco
- Département Milieux et Peuplements Aquatiques; Muséum National d'Histoire Naturelle; UMR Biologie des ORganismes et des Ecosystèmes Aquatiques (UMR BOREA IRD 207-CNRS 7208-UPMC-MNHN); 43 rue Cuvier FR-75231 Paris Cedex France
| | - Rémy Dernat
- Institut des Sciences de l'Evolution - CNRS UMR 5554; Plateforme Bioinformatique LabEx; Université Montpellier 2; Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental; Universidade do Porto; Rua dos Bragas, 177 4050-123 Porto Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre 4169-007 Porto Portugal
| |
Collapse
|
17
|
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]
|
18
|
A strategy for trade monitoring and substitution of the organs of threatened animals. Sci Rep 2013; 3:3108. [PMID: 24173429 PMCID: PMC3813934 DOI: 10.1038/srep03108] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 10/16/2013] [Indexed: 12/14/2022] Open
Abstract
The use of threatened animals as a source of traditional medicines is accelerating the extinction of such species and imposes great challenges to animal conservation. In this study, we propose a feasible strategy for the conservation of threatened medicinal animals that combines trade monitoring and the search for substitutes. First, DNA barcoding provides a powerful technique for monitoring the trade of animal species, which helps in restricting the excessive use and illegal trade of such species. Second, pharmacological tests have been adopted to evaluate the biological equivalence of threatened and domestic animals; based on such testing, potential substitutes are recommended. Based on a review of threatened animal species and their substitutes, we find that the search for substitutes deserves special attention; however, this work is far from complete. These results may be of great value for the conservation of threatened animals and maintaining the heritage of traditional medicine.
Collapse
|
19
|
D’Amato ME, Alechine E, Cloete KW, Davison S, Corach D. Where is the game? Wild meat products authentication in South Africa: a case study. INVESTIGATIVE GENETICS 2013; 4:6. [PMID: 23452350 PMCID: PMC3621286 DOI: 10.1186/2041-2223-4-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 02/14/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Wild animals' meat is extensively consumed in South Africa, being obtained either from ranching, farming or hunting. To test the authenticity of the commercial labels of meat products in the local market, we obtained DNA sequence information from 146 samples (14 beef and 132 game labels) for barcoding cytochrome c oxidase subunit I and partial cytochrome b and mitochondrial fragments. The reliability of species assignments were evaluated using BLAST searches in GenBank, maximum likelihood phylogenetic analysis and the character-based method implemented in BLOG. The Kimura-2-parameter intra- and interspecific variation was evaluated for all matched species. RESULTS The combined application of similarity, phylogenetic and character-based methods proved successful in species identification. Game meat samples showed 76.5% substitution, no beef samples were substituted. The substitutions showed a variety of domestic species (cattle, horse, pig, lamb), common game species in the market (kudu, gemsbok, ostrich, impala, springbok), uncommon species in the market (giraffe, waterbuck, bushbuck, duiker, mountain zebra) and extra-continental species (kangaroo). The mountain zebra Equus zebra is an International Union for Conservation of Nature (IUCN) red listed species. We also detected Damaliscus pygargus, which is composed of two subspecies with one listed by IUCN as 'near threatened'; however, these mitochondrial fragments were insufficient to distinguish between the subspecies. The genetic distance between African ungulate species often overlaps with within-species distance in cases of recent speciation events, and strong phylogeographic structure determines within-species distances that are similar to the commonly accepted distances between species. CONCLUSIONS The reliability of commercial labeling of game meat in South Africa is very poor. The extensive substitution of wild game has important implications for conservation and commerce, and for the consumers making decisions on the basis of health, religious beliefs or personal choices.Distance would be a poor indicator for identification of African ungulates species. The efficiency of the character-based method is reliant upon availability of large reference data. The current higher availability of cytochrome b data would make this the marker of choice for African ungulates. The encountered problems of incomplete or erroneous information in databases are discussed.
Collapse
Affiliation(s)
- Maria Eugenia D’Amato
- Biotechnology Department, Forensic DNA Lab, University of the Western Cape, Modderdam Road, Bellville, 7535, South Africa
| | - Evguenia Alechine
- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina
| | - Kevin Wesley Cloete
- Biotechnology Department, Forensic DNA Lab, University of the Western Cape, Modderdam Road, Bellville, 7535, South Africa
| | - Sean Davison
- Biotechnology Department, Forensic DNA Lab, University of the Western Cape, Modderdam Road, Bellville, 7535, South Africa
| | - Daniel Corach
- Servicio de Huellas Digitales Genéticas, School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina
| |
Collapse
|
20
|
Forensic DNA barcoding and bio-response studies of animal horn products used in traditional medicine. PLoS One 2013; 8:e55854. [PMID: 23409064 PMCID: PMC3568084 DOI: 10.1371/journal.pone.0055854] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 01/03/2013] [Indexed: 12/21/2022] Open
Abstract
Background Animal horns (AHs) have been applied to traditional medicine for more than thousands of years, of which clinical effects have been confirmed by the history. But now parts of AHs have been listed in the items of wildlife conservation, which limits the use for traditional medicine. The contradiction between the development of traditional medicine and the protection of wild resources has already become the common concern of zoophilists, traditional medical professionals, economists, sociologists. We believe that to strengthen the identification for threatened animals, to prevent the circulation of them, and to seek fertile animals of corresponding bioactivities as substitutes are effective strategies to solve this problem. Methodology/Principal Findings A powerful technique of DNA barcoding based on the mitochondrial gene cytochrome c oxidase I (COI) was used to identify threatened animals of Bovidae and Cervidae, as well as their illegal adulterants (including 10 species and 47 specimens). Meanwhile, the microcalorimetric technique was used to characterize the differences of bio-responses when those animal specimens acted on model organism (Escherichia coli). We found that the COI gene could be used as a universal primer to identify threatened animals and illegal adulterants mentioned above. By analyzing 223 mitochondrial COI sequences, a 100% identification success rate was achieved. We further found that the horns of Mongolian Gazelle and Red Deer could be exploited as a substitute for some functions of endangered Saiga Antelope and Sika Deer in traditional medicine, respectively. Conclusion/Significance Although it needs a more comprehensive evaluation of bioequivalence in order to completely solve the problem of substitutes for threatened animals, we believe that the identification (DNA barcoding) of threatened animals combined with seeking substitutions (bio-response) can yet be regarded as a valid strategy for establishing a balance between the protection of threatened animals and the development of traditional medicine.
Collapse
|
21
|
Lassen SB, Nielsen SA, Skovgård H, Kristensen M. Molecular differentiation of Culicoides biting midges (Diptera: Ceratopogonidae) from the subgenus Culicoides Latreille in Denmark. Parasitol Res 2011; 110:1765-71. [DOI: 10.1007/s00436-011-2697-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 10/12/2011] [Indexed: 10/15/2022]
|