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Chatzoglou E, Tsaousi N, Apostolidis AP, Exadactylos A, Sandaltzopoulos R, Giantsis IA, Gkafas GA, Malandrakis EE, Sarantopoulou J, Tokamani M, Triantaphyllidis G, Miliou H. High-Resolution Melting (HRM) Analysis for Rapid Molecular Identification of Sparidae Species in the Greek Fish Market. Genes (Basel) 2023; 14:1255. [PMID: 37372435 DOI: 10.3390/genes14061255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
The red porgy (Pagrus pagrus) and the common dentex (Dentex dentex) are Sparidae species of high commercial value, traded in the Greek market. In some cases, fish species identification from Greek fisheries is difficult for the consumer due to the strong morphological similarities with their imported counterparts or closely related species such as Pagrus major, Pagrus caeroleustictus, Dentex gibbosus and Pagellus erythrinus, especially when specimens are frozen, filleted or cooked. Techniques based on DNA sequencing, such as COI barcoding, accurately identify species substitution incidents; however, they are time consuming and expensive. In this study, regions of mtDNA were analyzed with RFLPs, multiplex PCR and HRM in order to develop a rapid method for species identification within the Sparidae family. HRM analysis of a 113 bp region of cytb and/or a 156 bp region of 16s could discriminate raw or cooked samples of P. pagrus and D. dentex from the aforementioned closely related species and P. pagrus specimens sampled in the Mediterranean Sea when compared to those fished in the eastern Atlantic. HRM analysis exhibited high accuracy and repeatability, revealing incidents of mislabeling. Multiple samples can be analyzed within three hours, rendering this method a useful tool in fish fraud monitoring.
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Affiliation(s)
- Evanthia Chatzoglou
- Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Nefeli Tsaousi
- Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Apostolos P Apostolidis
- Laboratory of Fish & Fisheries, Department of Animal Production, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Athanasios Exadactylos
- Hydrobiology-Ichthyology Lab, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Raphael Sandaltzopoulos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Ioannis A Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece
| | - Georgios A Gkafas
- Hydrobiology-Ichthyology Lab, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Emmanouil E Malandrakis
- Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Joanne Sarantopoulou
- Hydrobiology-Ichthyology Lab, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
| | - Maria Tokamani
- Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - George Triantaphyllidis
- Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
| | - Helen Miliou
- Laboratory of Applied Hydrobiology, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, 11855 Athens, Greece
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But GWC, Wu HY, Shao KT, Shaw PC. Rapid detection of CITES-listed shark fin species by loop-mediated isothermal amplification assay with potential for field use. Sci Rep 2020; 10:4455. [PMID: 32157111 PMCID: PMC7064571 DOI: 10.1038/s41598-020-61150-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/20/2020] [Indexed: 11/24/2022] Open
Abstract
Shark fin is a delicacy in many Asian countries. Overexploitation of sharks for shark fin trading has led to a drastic reduction in shark population. To monitor international trade of shark fin products and protect the endangered species from further population decline, we present rapid, user-friendly and sensitive diagnostic loop-mediated isothermal amplification (LAMP) and effective polymerase chain reaction (PCR) assays for all twelve CITES-listed shark species. Species-specific LAMP and PCR primers were designed based on cytochrome oxidase I (COI) and NADH2 regions. Our LAMP and PCR assays have been tested on 291 samples from 93 shark and related species. Target shark species could be differentiated from non-target species within three hours from DNA extraction to LAMP assay. The LAMP assay reported here is a simple and robust solution for on-site detection of CITES-listed shark species with shark fin products.
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Affiliation(s)
- Grace Wing-Chiu But
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Hoi-Yan Wu
- Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.,Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR
| | - Kwang-Tsao Shao
- Systematics and Biodiversity Information Division, Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Pang-Chui Shaw
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR. .,Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR. .,Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.
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Fotedar S, Lukehurst S, Jackson G, Snow M. Molecular tools for identification of shark species involved in depredation incidents in Western Australian fisheries. PLoS One 2019; 14:e0210500. [PMID: 30633772 PMCID: PMC6329513 DOI: 10.1371/journal.pone.0210500] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/23/2018] [Indexed: 11/19/2022] Open
Abstract
Shark depredation is an issue of concern in some Western Australian recreational and commercial fisheries where it can have economic, social and ecological consequences. Knowledge of the shark species involved is fundamental to developing effective management strategies to mitigate the impacts of depredation. Identification of the species responsible is difficult as direct observation of depredation events is uncommon and evaluating bite marks on fish has a high degree of uncertainty. The use of trace DNA techniques has provided an alternative method for species identification. We demonstrate proof of concept for a targeted DNA barcoding approach to identify shark species using trace DNA found at bite marks on recovered remains of hooked fish. Following laboratory validation, forensic analysis of swabs collected from samples of bitten demersal fish, led to the definitive identification of shark species involved in 100% of the incidences of depredation (n = 16).
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Affiliation(s)
- Seema Fotedar
- Department of Primary Industries and Regional Development, Government of Western Australia, Hillarys, Western Australia, Australia
- * E-mail:
| | - Sherralee Lukehurst
- Department of Primary Industries and Regional Development, Government of Western Australia, Hillarys, Western Australia, Australia
- Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Gary Jackson
- Department of Primary Industries and Regional Development, Government of Western Australia, Hillarys, Western Australia, Australia
| | - Michael Snow
- Department of Primary Industries and Regional Development, Government of Western Australia, Hillarys, Western Australia, Australia
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Maduna SN, Rossouw C, da Silva C, Soekoe M, Bester‐van der Merwe AE. Species identification and comparative population genetics of four coastal houndsharks based on novel NGS-mined microsatellites. Ecol Evol 2017; 7:1462-1486. [PMID: 28261458 PMCID: PMC5330897 DOI: 10.1002/ece3.2770] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 11/14/2016] [Accepted: 12/21/2016] [Indexed: 11/06/2022] Open
Abstract
The common smooth-hound (Mustelus mustelus) is the topmost bio-economically and recreationally important shark species in southern Africa, western Africa, and Mediterranean Sea. Here, we used the Illumina HiSeq™ 2000 next-generation sequencing (NGS) technology to develop novel microsatellite markers for Mustelus mustelus. Two microsatellite multiplex panels were constructed from 11 polymorphic loci and characterized in two populations of Mustelus mustelus representative of its South African distribution. The markers were then tested for cross-species utility in Galeorhinus galeus, Mustelus palumbes, and Triakis megalopterus, three other demersal coastal sharks also subjected to recreational and/or commercial fishery pressures in South Africa. We assessed genetic diversity (NA, AR, HO, HE, and PIC) and differentiation (FST and Dest) for each species and also examined the potential use of these markers in species assignment. In each of the four species, all 11 microsatellites were variable with up to a mean NA of 8, AR up to 7.5, HE and PIC as high as 0.842. We were able to reject genetic homogeneity for all species investigated here except for T. megalopterus. We found that the panel of the microsatellite markers developed in this study could discriminate between the study species, particularly for those that are morphologically very similar. Our study provides molecular tools to address ecological and evolutionary questions vital to the conservation and management of these locally and globally exploited shark species.
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Affiliation(s)
- Simo N. Maduna
- Department of GeneticsMolecular Breeding and Biodiversity GroupStellenbosch UniversityStellenboschSouth Africa
| | - Charné Rossouw
- Department of GeneticsMolecular Breeding and Biodiversity GroupStellenbosch UniversityStellenboschSouth Africa
| | - Charlene da Silva
- Department of Agriculture, Forestry and FisheriesFisheries ResearchRogge BaySouth Africa
| | - Michelle Soekoe
- Department of Ichthyology and Fisheries ScienceRhodes UniversityGrahamstownSouth Africa
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Johnson GJ, Buckworth RC, Lee H, Morgan JAT, Ovenden JR, McMahon CR. A novel field method to distinguish between cryptic carcharhinid sharks, Australian blacktip shark Carcharhinus tilstoni and common blacktip shark C. limbatus, despite the presence of hybrids. JOURNAL OF FISH BIOLOGY 2017; 90:39-60. [PMID: 27774596 DOI: 10.1111/jfb.13102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/04/2016] [Indexed: 06/06/2023]
Abstract
Multivariate and machine-learning methods were used to develop field identification techniques for two species of cryptic blacktip shark. From 112 specimens, precaudal vertebrae (PCV) counts and molecular analysis identified 95 Australian blacktip sharks Carcharhinus tilstoni and 17 common blacktip sharks Carcharhinus limbatus. Molecular analysis also revealed 27 of the 112 were C. tilstoni × C. limbatus hybrids, of which 23 had C. tilstoni PCV counts and four had C. limbatus PCV counts. In the absence of further information about hybrid phenotypes, hybrids were assigned as either C. limbatus or C. tilstoni based on PCV counts. Discriminant analysis achieved 80% successful identification, but machine-learning models were better, achieving 100% successful identification, using six key measurements (fork length, caudal-fin peduncle height, interdorsal space, second dorsal-fin height, pelvic-fin length and pelvic-fin midpoint to first dorsal-fin insertion). Furthermore, pelvic-fin markings could be used for identification: C. limbatus has a distinct black mark >3% of the total pelvic-fin area, while C. tilstoni has markings with diffuse edges, or has smaller or no markings. Machine learning and pelvic-fin marking identification methods were field tested achieving 87 and 90% successful identification, respectively. With further refinement, the techniques developed here will form an important part of a multi-faceted approach to identification of C. tilstoni and C. limbatus and have a clear management and conservation application to these commercially important sharks. The methods developed here are broadly applicable and can be used to resolve species identities in many fisheries where cryptic species exist.
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Affiliation(s)
- G J Johnson
- Department of Primary Industry and Fisheries, Aquatic Resource Research Unit, G. P. O Box 3000, Darwin, NT, 0801, Australia
| | - R C Buckworth
- CSIRO Oceans and Atmosphere Flagship, PMB 44 Winnellie, Darwin, NT, 0822, Australia
| | - H Lee
- Department of Primary Industry and Fisheries, Aquatic Resource Research Unit, G. P. O Box 3000, Darwin, NT, 0801, Australia
| | - J A T Morgan
- Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, P. O. Box 6097, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - J R Ovenden
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - C R McMahon
- Sydney Institute of Marine Science, 19 Chowder Bay Road, Mosman, NSW, 2088, Australia
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 2001, Australia
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Ramón-Laca A, Gleeson D, Yockney I, Perry M, Nugent G, Forsyth DM. Reliable discrimination of 10 ungulate species using high resolution melting analysis of faecal DNA. PLoS One 2014; 9:e92043. [PMID: 24637802 PMCID: PMC3956866 DOI: 10.1371/journal.pone.0092043] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/18/2014] [Indexed: 11/18/2022] Open
Abstract
Identifying species occupying an area is essential for many ecological and conservation studies. Faecal DNA is a potentially powerful method for identifying cryptic mammalian species. In New Zealand, 10 species of ungulate (Order: Artiodactyla) have established wild populations and are managed as pests because of their impacts on native ecosystems. However, identifying the ungulate species present within a management area based on pellet morphology is unreliable. We present a method that enables reliable identification of 10 ungulate species (red deer, sika deer, rusa deer, fallow deer, sambar deer, white-tailed deer, Himalayan tahr, Alpine chamois, feral sheep, and feral goat) from swabs of faecal pellets. A high resolution melting (HRM) assay, targeting a fragment of the 12S rRNA gene, was developed. Species-specific primers were designed and combined in a multiplex PCR resulting in fragments of different length and therefore different melting behaviour for each species. The method was developed using tissue from each of the 10 species, and was validated in blind trials. Our protocol enabled species to be determined for 94% of faecal pellet swabs collected during routine monitoring by the New Zealand Department of Conservation. Our HRM method enables high-throughput and cost-effective species identification from low DNA template samples, and could readily be adapted to discriminate other mammalian species from faecal DNA.
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Affiliation(s)
- Ana Ramón-Laca
- EcoGene®, Landcare Research, Auckland, New Zealand
- * E-mail:
| | - Dianne Gleeson
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Ivor Yockney
- Landcare Research, Lincoln, Canterbury, New Zealand
| | - Michael Perry
- Landcare Research, Palmerston North, Manawatu, New Zealand
| | | | - David M. Forsyth
- Arthur Rylah Institute for Environmental Research, Department of Environment and Primary Industries, Heidelberg, Victoria, Australia
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Harry AV, Morgan JAT, Ovenden JR, Tobin AJ, Welch DJ, Simpfendorfer CA. Comparison of the reproductive ecology of two sympatric blacktip sharks (Carcharhinus limbatus and Carcharhinus tilstoni) off north-eastern Australia with species identification inferred from vertebral counts. JOURNAL OF FISH BIOLOGY 2012; 81:1225-1233. [PMID: 22957866 DOI: 10.1111/j.1095-8649.2012.03400.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Precaudal vertebral counts were used to distinguish between 237 morphologically similar Carcharhinus limbatus and Carcharhinus tilstoni and were congruent with differences in reproductive ecology between the species. In addition to differing lengths at maturity and adult body size, the two species had asynchronous parturition, were born at different sizes and the relative frequencies of neonates differed in two coastal nursery areas. Despite evidence that hybridization can occur, these differences suggest the species are largely reproductively isolated.
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Affiliation(s)
- A V Harry
- Centre for Sustainable Tropical Fisheries and Aquaculture & School of Earth and Environmental Sciences, James Cook University, Townsville, Qld 4811, Australia.
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Portnoy DS, Heist EJ. Molecular markers: progress and prospects for understanding reproductive ecology in elasmobranchs. JOURNAL OF FISH BIOLOGY 2012; 80:1120-40. [PMID: 22497375 DOI: 10.1111/j.1095-8649.2011.03206.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Application of modern molecular tools is expanding the understanding of elasmobranch reproductive ecology. High-resolution molecular markers provide information at scales ranging from the identification of reproductively isolated populations in sympatry (i.e. cryptic species) to the relationships among parents, offspring and siblings. This avenue of study has not only augmented the current understanding of the reproductive biology of elasmobranchs but has also provided novel insights that could not be obtained through experimental or observational techniques. Sharing of genetic polymorphisms across ocean basins indicates that for some species there may be gene flow on global scales. The presence, however, of morphologically similar but genetically distinct entities in sympatry suggests that reproductive isolation can occur with minimal morphological differentiation. This review discusses the recent findings in elasmobranch reproductive biology like philopatry, hybridization and polyandry while highlighting important molecular and analytical techniques. Furthermore, the review examines gaps in current knowledge and discusses how new technologies may be applied to further the understanding of elasmobranch reproductive ecology.
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Affiliation(s)
- D S Portnoy
- Department of Wildlife and Fisheries Sciences, Center for Biosystematics and Biodiversity, Texas A&M University, College Station, TX 77843-2258, USA.
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Dudgeon CL, Blower DC, Broderick D, Giles JL, Holmes BJ, Kashiwagi T, Krück NC, Morgan JAT, Tillett BJ, Ovenden JR. A review of the application of molecular genetics for fisheries management and conservation of sharks and rays. JOURNAL OF FISH BIOLOGY 2012; 80:1789-1843. [PMID: 22497408 DOI: 10.1111/j.1095-8649.2012.03265.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Since the first investigation 25 years ago, the application of genetic tools to address ecological and evolutionary questions in elasmobranch studies has greatly expanded. Major developments in genetic theory as well as in the availability, cost effectiveness and resolution of genetic markers were instrumental for particularly rapid progress over the last 10 years. Genetic studies of elasmobranchs are of direct importance and have application to fisheries management and conservation issues such as the definition of management units and identification of species from fins. In the future, increased application of the most recent and emerging technologies will enable accelerated genetic data production and the development of new markers at reduced costs, paving the way for a paradigm shift from gene to genome-scale research, and more focus on adaptive rather than just neutral variation. Current literature is reviewed in six fields of elasmobranch molecular genetics relevant to fisheries and conservation management (species identification, phylogeography, philopatry, genetic effective population size, molecular evolutionary rate and emerging methods). Where possible, examples from the Indo-Pacific region, which has been underrepresented in previous reviews, are emphasized within a global perspective.
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Affiliation(s)
- C L Dudgeon
- The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.
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Detection of interspecies hybridisation in Chondrichthyes: hybrids and hybrid offspring between Australian (Carcharhinus tilstoni) and common (C. limbatus) blacktip shark found in an Australian fishery. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0298-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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