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Daniel N, Nanaobi H, Praveenraj J, Balaji V, Stephen Sampath Kumar J. Unveiling the molecular identity of the diminutive cyprinid, Horadandia brittani (Teleostei: Cyprinidae), a species endemic to Southern India. Mol Biol Rep 2023; 50:9707-9714. [PMID: 37801277 DOI: 10.1007/s11033-023-08802-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
Abstract
BACKGROUND Horadandia brittani is a small cyprinid fish species initially discovered in the coastal floodplains of southern India. For almost 50 years, the genus Horadandia was monotypic with a single species confined to Sri Lanka. In 1992, a new species H. brittani was described from south-western India. Despite being described as a separate species, H. brittani was later considered a synonym of H. atukorali, but in 2013, researchers recognized it as a distinct species based on morphological differences. Despite this clarification, there was still a need to validate the identity of H. brittani and determine its evolutionary relationship with its closely related species using DNA sequences. METHODS To address the uncertainties surrounding the identity of H. brittani, the present study utilized molecular techniques to generate DNA sequences. Sample collection involved obtaining specimens of H. brittani from their natural habitats. Subsequently, DNA was extracted from the collected samples, and the mitochondrial cytochrome C oxidase (COI) gene was amplified using appropriate methods. RESULTS The analysis of DNA sequences obtained from the COI gene revealed significant genetic distinctions between H. brittani and H. atukorali. The genetic distance values between these two species ranged from 3.21 to 3.63%, clearly indicating that these two species are genetically separate entities. The study successfully established the phylogenetic relationships between H. brittani and H. atukorali based on the COI gene sequences, further confirming the validity of H. brittani as a distinct and separate species. CONCLUSION The findings of this study conclusively demonstrate that H. brittani is a valid and separate species, distinct from H. atukorali. The genetic analysis based on mitochondrial COI gene sequences provided strong evidence for the differentiation between these two species. The molecular data generated in this research can be used to identify H. brittani quickly and accurately in the future.
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Affiliation(s)
- N Daniel
- Kanyakumari Parakkai Centre for Sustainable Aquaculture, Tamil Nadu Dr. J. Jayalalithaa Fisheries University, Tamil Nadu, India.
| | - Hemam Nanaobi
- Department of Zoology, Manipur University, Imphal, India
| | - J Praveenraj
- ICAR-Central Island Agricultural Research Institute, Port Blair, India
| | - V Balaji
- A1101, Synchronicity CHS, Lok Milan Colony, Chandivali, Mumbai, Maharashtra, India
| | - J Stephen Sampath Kumar
- Directorate of Sustainable Aquaculture, Tamil Nadu Dr. J. Jayalalithaa Fisheries University, Tamil Nadu, India
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Filonzi L, Ardenghi A, Rontani PM, Voccia A, Ferrari C, Papa R, Bellin N, Nonnis Marzano F. Molecular Barcoding: A Tool to Guarantee Correct Seafood Labelling and Quality and Preserve the Conservation of Endangered Species. Foods 2023; 12:2420. [PMID: 37372635 DOI: 10.3390/foods12122420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
The recent increase in international fish trade leads to the need for improving the traceability of fishery products. In relation to this, consistent monitoring of the production chain focusing on technological developments, handling, processing and distribution via global networks is necessary. Molecular barcoding has therefore been suggested as the gold standard in seafood species traceability and labelling. This review describes the DNA barcoding methodology for preventing food fraud and adulteration in fish. In particular, attention has been focused on the application of molecular techniques to determine the identity and authenticity of fish products, to discriminate the presence of different species in processed seafood and to characterize raw materials undergoing food industry processes. In this regard, we herein present a large number of studies performed in different countries, showing the most reliable DNA barcodes for species identification based on both mitochondrial (COI, cytb, 16S rDNA and 12S rDNA) and nuclear genes. Results are discussed considering the advantages and disadvantages of the different techniques in relation to different scientific issues. Special regard has been dedicated to a dual approach referring to both the consumer's health and the conservation of threatened species, with a special focus on the feasibility of the different genetic and genomic approaches in relation to both scientific objectives and permissible costs to obtain reliable traceability.
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Affiliation(s)
- Laura Filonzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Alessia Ardenghi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Pietro Maria Rontani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Andrea Voccia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Claudio Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Riccardo Papa
- Department Biology, University of Puerto Rico, Rio Piedras, San Juan 00925, Puerto Rico
| | - Nicolò Bellin
- Department Biology, University of Puerto Rico, Rio Piedras, San Juan 00925, Puerto Rico
| | - Francesco Nonnis Marzano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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Klangnurak W, Arunrugstichai S, Manopawitr P, Krajangdara T. DNA-based species identification of shark fins traded in thai markets. CONSERV GENET 2023; 24:1-10. [PMID: 37363049 PMCID: PMC10105147 DOI: 10.1007/s10592-023-01519-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/21/2023] [Indexed: 06/28/2023]
Abstract
Shark fins are among the most highly prized seafood products in the world with massive consumption in Asia over the past several decades. The demand for shark fins is a major driver of the enormous population declines of elasmobranchs that are generally vulnerable to overexploitation. This study aims to better understand the species composition of shark fin products in Thailand and their conservation statuses by using DNA-based species identification. Various types and sizes of shark fins were collected from 4 locations in Thailand. DNA barcoding method based on a fragment of the cytochrome c oxidase subunit I (COI) gene was applied to species identification. Fins from at least 15 shark species were found from Thailand's markets. The spottail shark (Carcharhinus sorrah) and the night shark (Carcharhinus signatus) were the two dominant species presented in this study. 34% of identifiable samples are the species that have not been record in this region. 62% of species detected from the fin samples are categorized under the threatened categories of IUCN Red List. Species composition reported in shark fin products potentially helps indicate the appropriate conservation action and increases awareness from monitoring the trade in elasmobranch products. Supplementary Information The online version contains supplementary material available at 10.1007/s10592-023-01519-0.
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Affiliation(s)
- Wanlada Klangnurak
- Department of Animal Production Technology and Fishery, School of Agricultural Technology, King Mongkut’s Institute of Technology Ladkrabang, Ladkrabang, Bangkok, 10520 Thailand
| | - Sirachai Arunrugstichai
- Aow Thai Marine Ecology Center, FREC Bangkok, 77 Nakhon Sawan Rd, Wat Sommanat, Pom Prap Sattru Phai, Bangkok, 10100 Thailand
| | | | - Tassapon Krajangdara
- Phuket Marine Fisheries Research and Development Center, Department of Fisheries, Phuket, Thailand
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4
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Phillips JD, Athey TB, McNicholas PD, Hanner RH. VLF: An R package for the analysis of very low frequency variants in DNA sequences. Biodivers Data J 2023; 11:e96480. [PMID: 38327328 PMCID: PMC10848336 DOI: 10.3897/bdj.11.e96480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/30/2022] [Indexed: 01/27/2023] Open
Abstract
Here, we introduce VLF, an R package to determine the distribution of very low frequency variants (VLFs) in nucleotide and amino acid sequences for the analysis of errors in DNA sequence records. The package allows users to assess VLFs in aligned and trimmed protein-coding sequences by automatically calculating the frequency of nucleotides or amino acids in each sequence position and outputting those that occur under a user-specified frequency (default of p = 0.001). These results can then be used to explore fundamental population genetic and phylogeographic patterns, mechanisms and processes at the microevolutionary level, such as nucleotide and amino acid sequence conservation. Our package extends earlier work pertaining to an implementation of VLF analysis in Microsoft Excel, which was found to be both computationally slow and error prone. We compare those results to our own herein. Results between the two implementations are found to be highly consistent for a large DNA barcode dataset of bird species. Differences in results are readily explained by both manual human error and inadequate Linnean taxonomy (specifically, species synonymy). Here, VLF is also applied to a subset of avian barcodes to assess the extent of biological artifacts at the species level for Canada goose (Branta canadensis), as well as within a large dataset of DNA barcodes for fishes of forensic and regulatory importance. The novelty of VLF and its benefit over the previous implementation include its high level of automation, speed, scalability and ease-of-use, each desirable characteristics which will be extremely valuable as more sequence data are rapidly accumulated in popular reference databases, such as BOLD and GenBank.
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Affiliation(s)
- Jarrett D. Phillips
- School of Computer Science and Department of Integrative Biology, University of Guelph, Guelph, CanadaSchool of Computer Science and Department of Integrative Biology, University of GuelphGuelphCanada
| | - Taryn B.T. Athey
- Stollery Children's Hospital, Edmonton, CanadaStollery Children's HospitalEdmontonCanada
| | - Paul D. McNicholas
- Department of Mathematics and Statistics, McMaster University, Hamilton, CanadaDepartment of Mathematics and Statistics, McMaster UniversityHamiltonCanada
| | - Robert H. Hanner
- Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Guelph, CanadaBiodiversity Institute of Ontario and Department of Integrative Biology, University of GuelphGuelphCanada
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da Rocha RH, Fernandes CA, Bignotto TS, Margarido VP, Tencatt LFC, da Graça WJ, Gubiani ÉA. Integrated analysis reveals a new species of Corydoras Lacépède, 1803 (Siluriformes: Callichthyidae) in the lower Iguassu River, Brazil. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-021-00534-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Soares KDA, Mathubara K. Combined phylogeny and new classification of catsharks (Chondrichthyes: Elasmobranchii: Carcharhiniformes). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
This is the first study to combine morphological and molecular characters to infer the phylogenetic relationships among catsharks. All currently valid genera classified in the family Scyliorhinidae s.l. and representatives of other carcharhinoid families plus one lamnoid and two orectoloboids were included as terminal taxa. A total of 143 morphological characters and 44 NADH2 sequences were analysed. Parsimony analyses under different weighting schemes and strengths were used to generate hypotheses of phylogenetic relationships. The phylogenetic analysis of 78 terminal taxa, using the combined dataset and weighting each column separately (SEP; k = 3) resulted in one most-parsimonious cladogram of 4441 steps with the greatest internal resolution of clades and strongest support. The main changes in nomenclature and classification are the revised definition and scope of Scyliorhinidae, Apristurus and Pentanchus and the revalidation of Atelomycteridae. The monophyly of Pentanchidae is supported, as is that of most catshark genera. Two new subfamilies of the family Pentanchidae are defined: Halaelurinae subfam. nov. and Galeinae subfam. nov. Our analysis emphasizes the relevance of morphological characters in the inference of evolutionary history of carcharhinoids and sheds light on the taxonomic status of some genera in need of further exploration.
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Affiliation(s)
- Karla D A Soares
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
| | - Kleber Mathubara
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, SP, Brazil
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Bellodi A, Benvenuto A, Melis R, Mulas A, Barone M, Barría C, Cariani A, Carugati L, Chatzispyrou A, Desrochers M, Ferrari A, Guallart J, Hemida F, Mancusi C, Mazzoldi C, Ramírez-Amaro S, Rey J, Scannella D, Serena F, Tinti F, Vella A, Follesa MC, Cannas R. Call me by my name: unravelling the taxonomy of the gulper shark genus Centrophorus in the Mediterranean Sea through an integrated taxonomic approach. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab110] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The current shift of fishery efforts towards the deep sea is raising concern about the vulnerability of deep-water sharks, which are often poorly studied and characterized by problematic taxonomy. For instance, in the Mediterranean Sea the taxonomy of genus Centrophorus has not been clearly unravelled yet. Since proper identification of the species is fundamental for their correct assessment and management, this study aims at clarifying the taxonomy of this genus in the Mediterranean Basin through an integrated taxonomic approach. We analysed a total of 281 gulper sharks (Centrophorus spp.) collected from various Mediterranean, Atlantic and Indian Ocean waters. Molecular data obtained from cytochrome c oxidase subunit I (COI), 16S ribosomal RNA (16S), NADH dehydrogenase subunit 2 (ND2) and a portion of a nuclear 28S ribosomal DNA gene region (28S) have highlighted the presence of a unique mitochondrial clade in the Mediterranean Sea. The morphometric results confirmed these findings, supporting the presence of a unique and distinct morphological group comprising all Mediterranean individuals. The data strongly indicate the occurrence of a single Centrophorus species in the Mediterranean, ascribable to C. cf. uyato, and suggest the need for a revision of the systematics of the genus in the area.
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Affiliation(s)
- Andrea Bellodi
- Department of Life and Environmental Sciences – University of Cagliari, Via T. Via Fiorelli 1, 09126 Cagliari, Italy
- CoNISMa Consorzio Nazionale Interuniversitario per le Scienze Mare, Piazzale Flaminio 9, 00196 Rome, Italy
| | - Anna Benvenuto
- CoNISMa Consorzio Nazionale Interuniversitario per le Scienze Mare, Piazzale Flaminio 9, 00196 Rome, Italy
- Department of Biological, Geological and Environmental Sciences – Alma Mater Studiorum University of Bologna, Via Sant’alberto 163, 48123 Ravenna, Italy
| | - Riccardo Melis
- Department of Life and Environmental Sciences – University of Cagliari, Via T. Via Fiorelli 1, 09126 Cagliari, Italy
- CoNISMa Consorzio Nazionale Interuniversitario per le Scienze Mare, Piazzale Flaminio 9, 00196 Rome, Italy
| | - Antonello Mulas
- Department of Life and Environmental Sciences – University of Cagliari, Via T. Via Fiorelli 1, 09126 Cagliari, Italy
- CoNISMa Consorzio Nazionale Interuniversitario per le Scienze Mare, Piazzale Flaminio 9, 00196 Rome, Italy
| | - Monica Barone
- Food and Agriculture Organization of the United Nations – Fisheries Division, Viale delle Terme di Caracalla, 00153 Rome, Italy
| | - Claudio Barría
- Institut de Ciències del Mar, Passeig Marítim de la Barceloneta 37, 08003 Barcelona, Spain
| | - Alessia Cariani
- CoNISMa Consorzio Nazionale Interuniversitario per le Scienze Mare, Piazzale Flaminio 9, 00196 Rome, Italy
- Department of Biological, Geological and Environmental Sciences – Alma Mater Studiorum University of Bologna, Via Sant’alberto 163, 48123 Ravenna, Italy
| | - Laura Carugati
- Department of Life and Environmental Sciences – University of Cagliari, Via T. Via Fiorelli 1, 09126 Cagliari, Italy
- CoNISMa Consorzio Nazionale Interuniversitario per le Scienze Mare, Piazzale Flaminio 9, 00196 Rome, Italy
| | - Archontia Chatzispyrou
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 576A Vouliagmenis Ave., 16452 Argyroupoli, Greece
| | - Monique Desrochers
- Northeastern University College of Science, 360 Huntington Ave, Boston, MA 02115, Massachusetts, USA
| | - Alice Ferrari
- CoNISMa Consorzio Nazionale Interuniversitario per le Scienze Mare, Piazzale Flaminio 9, 00196 Rome, Italy
- Department of Biological, Geological and Environmental Sciences – Alma Mater Studiorum University of Bologna, Via Sant’alberto 163, 48123 Ravenna, Italy
| | - Javier Guallart
- Marine Biology Laboratory, Zoology Department, Universitat de València, Burjassot E-46100 València, Spain
| | - Farid Hemida
- Ecole Nationale Supérieure des Sciences de la Mer et de l’Amenagement du Littoral, Dely Ibrahim 16320, Algiers, Algeria
| | - Cecilia Mancusi
- Environmental Protection Agency of Tuscany Region, Marine Division, Operational Unit Fisheries Resources and Marine Biodiversity, Via Marradi 114, 56127 Livorno, Italy
| | - Carlotta Mazzoldi
- University of Padova, Department of Biology, Via U. Bassi 58/B, 35131 Padova, Italy
| | - Sergio Ramírez-Amaro
- Instituto Español de Oceanografía, Centre Oceanogràfic de les Balears, Moll de Ponent s/n, 07015 Palma, Spain
| | - Javier Rey
- Instituto Español de Oceanografía, Centro Oceanográfico de Malaga, Muelle Pesquero s/n, 29640 Fuengirola, Spain
| | - Danilo Scannella
- Institute for Marine Biological Resources and Biotechnologies, National Research Council, Via Vaccara, 61, 91026, Mazara del Vallo, Italy
| | - Fabrizio Serena
- Institute for Marine Biological Resources and Biotechnologies, National Research Council, Via Vaccara, 61, 91026, Mazara del Vallo, Italy
| | - Fausto Tinti
- CoNISMa Consorzio Nazionale Interuniversitario per le Scienze Mare, Piazzale Flaminio 9, 00196 Rome, Italy
- Department of Biological, Geological and Environmental Sciences – Alma Mater Studiorum University of Bologna, Via Sant’alberto 163, 48123 Ravenna, Italy
| | - Adriana Vella
- Conservation Biology Research Group, Department of Biology, University of Malta, Msida, MSD2080, Malta
| | - Maria Cristina Follesa
- Department of Life and Environmental Sciences – University of Cagliari, Via T. Via Fiorelli 1, 09126 Cagliari, Italy
- CoNISMa Consorzio Nazionale Interuniversitario per le Scienze Mare, Piazzale Flaminio 9, 00196 Rome, Italy
| | - Rita Cannas
- Department of Life and Environmental Sciences – University of Cagliari, Via T. Via Fiorelli 1, 09126 Cagliari, Italy
- CoNISMa Consorzio Nazionale Interuniversitario per le Scienze Mare, Piazzale Flaminio 9, 00196 Rome, Italy
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Gonzalez C, Postaire B, Domingues RR, Feldheim KA, Caballero S, Chapman D. Phylogeography and population genetics of the cryptic bonnethead shark Sphyrna aff. tiburo in Brazil and the Caribbean inferred from mtDNA markers. JOURNAL OF FISH BIOLOGY 2021; 99:1899-1911. [PMID: 34476811 DOI: 10.1111/jfb.14896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/19/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Resolving the identity, phylogeny and distribution of cryptic species within species complexes is an essential precursor to management. The bonnethead shark, Sphyrna tiburo, is a small coastal shark distributed in the Western Atlantic from North Carolina (U.S.A.) to southern Brazil. Genetic analyses based on mitochondrial markers revealed that bonnethead sharks comprise a species complex with at least two lineages in the Northwestern Atlantic and the Caribbean (S. tiburo and Sphyrna aff. tiburo, respectively). The phylogeographic and phylogenetic analysis of two mitochondrial markers [control region (mtCR) and cytochrome oxidase I (COI)] showed that bonnethead sharks from southeastern Brazil correspond to S. aff. tiburo, extending the distribution of this cryptic species >5000 km. Bonnethead shark populations are only managed in the U.S.A. and in the 2000s were considered to be regionally extinct or collapsed in southeast Brazil. The results indicate that there is significant genetic differentiation between S. aff. tiburo from Brazil and other populations from the Caribbean (ΦST = 0.9053, P < 0.000), which means that collapsed populations in the former are unlikely to be replenished from Caribbean immigration. The species identity of bonnethead sharks in the Southwest Atlantic and their relationship to North Atlantic and Caribbean populations still remains unresolved. Taxonomic revision and further sampling are required to reevaluate the status of the bonnethead shark complex through its distribution range.
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Affiliation(s)
- Cindy Gonzalez
- Predator Ecology and Conservation Lab, Biological Sciences Department, Florida International University, Miami, Florida, 33181, USA
| | - Bautisse Postaire
- Predator Ecology and Conservation Lab, Biological Sciences Department, Florida International University, Miami, Florida, 33181, USA
| | - Rodrigo R Domingues
- Departamento de Ciências do Mar, Universidade Federal de São Paulo, Instituto do Mar, São Paulo, Brazil
| | - Kevin A Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, Chicago, Illinois, USA
| | - Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia
| | - Demian Chapman
- Predator Ecology and Conservation Lab, Biological Sciences Department, Florida International University, Miami, Florida, 33181, USA
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Villate‐Moreno M, Pollerspöck J, Kremer‐Obrock F, Straube N. Molecular analyses of confiscated shark fins reveal shortcomings of CITES implementations in Germany. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
| | | | | | - Nicolas Straube
- Department of Natural History University Museum of Bergen Bergen Norway
- SNSB ‐ Bavarian State Collection of Zoology Munich Germany
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Domingues RR, Bunholi IV, Pinhal D, Antunes A, Mendonça FF. From molecule to conservation: DNA-based methods to overcome frontiers in the shark and ray fin trade. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01194-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Ferrari A, Di Crescenzo S, Cariani A, Crobe V, Benvenuto A, Piattoni F, Mancusi C, Bonnici L, Bonello JJ, Schembri PJ, Serena F, Massi D, Titone A, Tinti F. Puzzling over spurdogs: molecular taxonomy assessment of the Squalus species in the Strait of Sicily. THE EUROPEAN ZOOLOGICAL JOURNAL 2021. [DOI: 10.1080/24750263.2020.1849436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- A. Ferrari
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, Ravenna, Italy
| | - S. Di Crescenzo
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, Ravenna, Italy
| | - A. Cariani
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, Ravenna, Italy
| | - V. Crobe
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, Ravenna, Italy
| | - A. Benvenuto
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, Ravenna, Italy
| | - F. Piattoni
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, Ravenna, Italy
| | - C. Mancusi
- Environmental Protection Agency of Tuscany Region (ARPAT), Livorno, Italy
| | - L. Bonnici
- Department of Biology, University of Malta, Msida, Malta
| | - J. J. Bonello
- Department of Biology, University of Malta, Msida, Malta
| | - P. J. Schembri
- Department of Biology, University of Malta, Msida, Malta
| | - F. Serena
- Institute for Marine Biological Resources and Biotechnologies (IRBIM), National Research Council – (CNR), Mazara del Vallo, Italy
| | - D. Massi
- Institute for Marine Biological Resources and Biotechnologies (IRBIM), National Research Council – (CNR), Mazara del Vallo, Italy
| | - A. Titone
- Institute for Marine Biological Resources and Biotechnologies (IRBIM), National Research Council – (CNR), Mazara del Vallo, Italy
| | - F. Tinti
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, Ravenna, Italy
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12
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Corrêa de Barros R, Moreira da Rocha R. Genetic analyses reveal cryptic diversity in the widely distributed Styela canopus (Ascidiacea:Styelidae). INVERTEBR SYST 2021. [DOI: 10.1071/is20058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The routine use of DNA sequencing techniques and phylogenetic analysis has resulted in the discovery of many cryptic species, especially in the oceans. The common, globally introduced species Styela canopus is suspected to be a complex of cryptic species because of its widespread distribution and variable external morphology. We tested this possibility using COI and ANT marker sequences to uncover the phylogenetic relationship among 19 populations, and to examine genetic variability as well as gene flow. We obtained 271 COI and 67 ANT sequences and found surprising diversity among the 19 populations (COI: π = 0.18, hd = 0.99; ANT: π = 0.13, hd = 0.95). Corresponding topologies were found using Bayesian inference and maximum likelihood for both simple locus (COI) and multilocus (COI + ANT) analyses and so the clades received strong support. We used simple (ABGD, bPTP, GMYC) and multiple (BSD) locus methods to delimit species. The simple locus methods indicated that the current Styela canopus comprises at least 15 species. The BSD method for concatenated data supported 7 of the 15 species. We suggest that S. canopus should be treated as the Styela canopus complex. The large number of cryptic species found, often with more than one clade found in sympatry, creates opportunities for better understanding reproductive isolation, hybridisation or speciation. As several lineages have already been introduced widely around the world, we must quickly understand their diversity and invasive abilities.
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13
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DNA barcoding and species delimitation of butterflies (Lepidoptera) from Nigeria. Mol Biol Rep 2020; 47:9441-9457. [PMID: 33200313 DOI: 10.1007/s11033-020-05984-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/05/2020] [Indexed: 10/23/2022]
Abstract
Accurate identification of species is a prerequisite for successful biodiversity management and further genetic studies. Species identification techniques often require both morphological diagnostics and molecular tools, such as DNA barcoding, for correct identification. In particular, the use of the subunit I of the mitochondrial cytochrome c oxidase (COI) gene for DNA barcoding has proven useful in species identification for insects. However, to date, no studies have been carried out on the DNA barcoding of Nigerian butterflies. We evaluated the utility of DNA barcoding applied for the first time to 735 butterfly specimens from southern Nigeria. In total, 699 DNA barcodes, resulting in a record of 116 species belonging to 57 genera, were generated. Our study sample comprised 807 DNA barcodes based on sequences generated from our current study and 108 others retrieved from BOLD. Different molecular analyses, including genetic distance-based evaluation (Neighbor-Joining, Maximum Likelihood and Bayesian trees) and species delimitation tests (TaxonDNA, Automated Barcode Gap Discovery, General Mixed Yule-Coalescent, and Bayesian Poisson Tree Processes) were performed to accurately identify and delineate species. The genetic distance-based analyses resulted in 163 well-separated clusters consisting of 147 described and 16 unidentified species. Our findings indicate that about 90.20% of the butterfly species were explicitly discriminated using DNA barcodes. Also, our field collections reported the first country records of ten butterfly species-Acraea serena, Amauris cf. dannfelti, Aterica galena extensa, Axione tjoane rubescens, Charaxes galleyanus, Papilio lormieri lormeri, Pentila alba, Precis actia, Precis tugela, and Tagiades flesus. Further, DNA barcodes revealed a high mitochondrial intraspecific divergence of more than 3% in Bicyclus vulgaris vulgaris and Colotis evagore. Furthermore, our result revealed an overall high haplotype (gene) diversity (0.9764), suggesting that DNA barcoding can provide information at a population level for Nigerian butterflies. The present study confirms the efficiency of DNA barcoding for identifying butterflies from Nigeria. To gain a better understanding of regional variation in DNA barcodes of this biogeographically complex area, future work should expand the DNA barcode reference library to include all butterfly species from Nigeria as well as surrounding countries. Also, further studies, involving relevant genetic and eco-morphological datasets, are required to understand processes governing mitochondrial intraspecific divergences reported in some species complexes.
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Parapar J, Capa M, Nygren A, Moreira J. To name but a few: descriptions of five new species of Terebellides (Annelida, Trichobranchidae) from the North East Atlantic. Zookeys 2020; 992:1-58. [PMID: 33223905 PMCID: PMC7677295 DOI: 10.3897/zookeys.992.55977] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/06/2020] [Indexed: 11/18/2022] Open
Abstract
The number of described species of the genus Terebellides Sars, 1835 (Annelida, Trichobranchidae) has greatly increased in the last years, particularly in the North East Atlantic. In this context, this paper deals with several putative species recently delineated by molecular means within a well delimited clade of Terebellides. Species are characterised here by a combination of morphological characters, and a complementary nucleotide diagnostic approach. Three species were identified as the nominal species T.stroemii Sars, 1835, T.bigeniculatus Parapar, Moreira & Helgason, 2011 and T.europaeaLavesque et al., 2019. Five species are described as new: T.bakkenisp. nov., T.kongsrudisp. nov., T.norvegicasp. nov., T.ronningaesp. nov. and T.scoticasp. nov. The distinctive morphological characters refer to the branchial shape, absence or presence of papillae on lamellae of anterior margin of branchial dorsal lobes, absence or presence of ciliated papillae dorsal to thoracic notopodia, geniculate chaetae in one or two chaetigers, and the morphology of thoracic and abdominal uncini teeth. Furthermore, the description of T.bigeniculatus is revised and complemented after examination of type specimens. An updated identification key to all species of the genus in NE Atlantic and a proposal of a classification of different types of abdominal uncini to be used in taxonomy are also included.
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Affiliation(s)
- Julio Parapar
- Departamento de Bioloxía, Universidade da Coruña, Spain Universidade da Coruña Coruña Spain
| | - María Capa
- Departament de Biologia, Universitat de les Illes Balears, Spain Universitat de les Illes Balears Mallorca Spain
| | - Arne Nygren
- Sjöfartmuseet Akvariet, Göteborg, Sweden and Institutionen för marina vetenskaper, Göteborgs Universitet, Sweden Göteborgs Universitet Göteborg Sweden
| | - Juan Moreira
- Departamento de Biología (Zoología) & Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Facultad de Ciencias, Universidad Autónoma de Madrid, Spain Universidad Autónoma de Madrid Madrid Spain
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Tiktak GP, Butcher D, Lawrence PJ, Norrey J, Bradley L, Shaw K, Preziosi R, Megson D. Are concentrations of pollutants in sharks, rays and skates (Elasmobranchii) a cause for concern? A systematic review. MARINE POLLUTION BULLETIN 2020; 160:111701. [PMID: 33181965 DOI: 10.1016/j.marpolbul.2020.111701] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
This review represents a comprehensive analysis on pollutants in elasmobranchs including meta-analysis on the most studied pollutants: mercury, cadmium, PCBs and DDTs, in muscle and liver tissue. Elasmobranchs are particularly vulnerable to pollutant exposure which may pose a risk to the organism as well as humans that consume elasmobranch products. The highest concentrations of pollutants were found in sharks occupying top trophic levels (Carcharhiniformes and Lamniformes). A human health risk assessment identified that children and adults consuming shark once a week are exposed to over three times more mercury than is recommended by the US EPA. This poses a risk to local fishing communities and international consumers of shark-based products, as well as those subject to the widespread mislabelling of elasmobranch products. Wider screening studies are recommended to determine the risk to elasmobranchs from emerging pollutants and more robust studies are recommended to assess the risks to human health.
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Affiliation(s)
- Guuske P Tiktak
- Ecology & Environment Research Centre, Manchester Metropolitan University, Manchester M1 5GD, UK.
| | - Demi Butcher
- School of Geography, Earth and Environmental Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK
| | - Peter J Lawrence
- Bangor University, School of Ocean Sciences, Askew St, Menai Bridge, Wales LL59 5AB, UK
| | - John Norrey
- Ecology & Environment Research Centre, Manchester Metropolitan University, Manchester M1 5GD, UK
| | - Lee Bradley
- Ecology & Environment Research Centre, Manchester Metropolitan University, Manchester M1 5GD, UK
| | - Kirsty Shaw
- Ecology & Environment Research Centre, Manchester Metropolitan University, Manchester M1 5GD, UK
| | - Richard Preziosi
- Ecology & Environment Research Centre, Manchester Metropolitan University, Manchester M1 5GD, UK
| | - David Megson
- Ecology & Environment Research Centre, Manchester Metropolitan University, Manchester M1 5GD, UK
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16
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Determining the Authenticity of Shark Meat Products by DNA Sequencing. Foods 2020; 9:foods9091194. [PMID: 32872285 PMCID: PMC7555804 DOI: 10.3390/foods9091194] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 01/25/2023] Open
Abstract
Given that the global shark meat market is poised to grow in future years, the aim of this study was to use DNA sequencing of the cytochrome c oxidase I (COI) and NADH dehydrogenase subunit 2 (NADH2) mitochondrial genes to examine the market of shark meat products in Italy. This made it possible to analyze patterns of species utilization and commercialization of threatened, endangered and/or prohibited species, focusing on fraudulent activities in the shark food chain in order to propose seafood safety and environmental sustainability solutions. The study shows that the labeling of shark meat products generally lacks comprehensive information, thus making it difficult for consumers to make informed purchasing decisions and fails to comply with European Union (EU) legislation regarding seafood labelling. Molecular investigation reveals a high mislabeling rate (45.4%), highlighting widespread use of cheaper species either in order to replace species that are better known and more popular, or else in order to sell various threatened species. Considering that seafood mislabeling can circumvent the management of sustainable fisheries and facilitate Illegal, Unreported and Unregulated (IUU) fishing, the routine use of genetic analysis should be encouraged among control and enforcement agencies in order to implement effective management measures. This would help to build a species-specific reporting system for all catches, and enhance control measures, in order to prevent illegal activities connected with shark catches and trade around the world.
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17
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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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18
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Zahn RJ, Silva AJ, Hellberg RS. Development of a DNA mini-barcoding protocol targeting COI for the identification of elasmobranch species in shark cartilage pills. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106918] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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19
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Gonzalez C, Gallagher AJ, Caballero S. Conservation genetics of the bonnethead shark Sphyrna tiburo in Bocas del Toro, Panama: Preliminary evidence of a unique stock. PLoS One 2019; 14:e0220737. [PMID: 31415593 PMCID: PMC6695166 DOI: 10.1371/journal.pone.0220737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/21/2019] [Indexed: 12/04/2022] Open
Abstract
The bonnethead shark, Sphyrna tiburo, is a small elasmobranch distributed in the Eastern Pacific from southern California to Ecuador, and along the Western Atlantic, with preferences for continental margins of North, Central and South America, the Gulf of Mexico, and the Caribbean. Recent studies have suggested that it could be under a process of cryptic speciation, with the possibility to find different species in similar geographic locations. Here we assessed the population structure and genetic diversity of this highly philopatric and non-dispersive species in the Bocas del Toro Archipelago, Panama. Fragments of the mitochondrial genes cytochrome oxidase I and control region, were used to test the genetic structure of adult and juvenile S. tiburo in this area, and were compared with other locations of the Western Atlantic and Belize. We found significant genetic differentiation between Caribbean bonnethead sharks from Bocas del Toro and Belize, when compared to bonnetheads from other locations of the Western Atlantic. These results also suggest that Bocas del Toro could constitute a different genetic population unit for this species, whereby bonnethead sharks in this area could belong to a unique stock. The information obtained in this study could improve our understanding of the population dynamics of the bonnethead shark throughout its distribution range, and may be used as a baseline for future conservation initiatives for coastal sharks in Central America, a poorly studied an often overlooked region for shark conservation and research.
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Affiliation(s)
- Cindy Gonzalez
- Departamento de Ciencias Biológicas, Universidad de los Andes, Laboratorio de Ecología Molecular de Vertebrados Acuáticos—LEMVA, Bogota, Colombia
| | - Austin J. Gallagher
- Beneath the Waves Inc, Herndon, Virginia, United States of America
- Smithsonian Tropical Research Institute, Balboa, Panama City, Republic of Panama
- Rosentiel School of Marine and Atmospheric Sciences, University of Miami, Miami, Florida, United States of America
| | - Susana Caballero
- Departamento de Ciencias Biológicas, Universidad de los Andes, Laboratorio de Ecología Molecular de Vertebrados Acuáticos—LEMVA, Bogota, Colombia
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20
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Azpelicueta MDLM, Delpiani SM, Cione AL, Oliveira C, Marceniuk AP, Díaz de Astarloa JM. Morphology and molecular evidence support the validity of Pogonias courbina (Lacepède, 1803) (Teleostei: Sciaenidae), with a redescription and neotype designation. PLoS One 2019; 14:e0216280. [PMID: 31216281 PMCID: PMC6584015 DOI: 10.1371/journal.pone.0216280] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 04/17/2019] [Indexed: 11/18/2022] Open
Abstract
The family Sciaenidae comprises about 300 species. The black drum Pogonias cromis was the only valid species of the genus. Herein, Pogonias courbina Lacepède 1803 is redescribed based on morphological and molecular evidence and a neotype is designated. Pogonias courbina is distinguished by the following characters: the occurrence of characteristic thickening of the dorsal spines VII to XI in all specimens larger than 250 mm SL; all pterygiophores in the dorsal-fin laminar, thin; anal-fin pterygiophores slender excluded those of spines; lateral projections of gas bladder with few finger-like projections; genetic distance between both species 1%; exclusive occurrence of characters in six informative sites of COI (58 G; 214 G; 328 A; 331 A; 553C; 580 G). The method Automatic Barcode gap Discovery detected gaps in nucleotid distance congruent with the NJ, MP, and ML tree analysis. Also, advertisement calls are three times shorter in duration in P. courbina than in P. cromis. In addition, two monophyletic groups for P. cromis and P. courbina appear in trees obtained with different methodologies, emphasizing the absence of shared haplotypes. A gap of about 8000 km occurs in the distribution of both species along coastal areas of the Atlantic Ocean.
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Affiliation(s)
- María de las Mercedes Azpelicueta
- CONICET, División Zoología Vertebrados, Museo de La Plata, Facultad de Ciencias Naturales, La Plata, provincia de Buenos Aires, Argentina
| | - Sergio Matías Delpiani
- CONICET, Laboratorio iBOL de referencia de Mar del Plata, Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Mar del Plata, provincia de Buenos Aires, Argentina
| | - Alberto Luis Cione
- CONICET, División Paleontología, Museo de La Plata, Facultad de Ciencias Naturales, La Plata, provincia de Buenos Aires, Argentina
| | - Claudio Oliveira
- Departamento de Morfologia Instituto de Biociências, UNESP, São Paulo, Brazil
| | | | - Juan Martín Díaz de Astarloa
- CONICET, Laboratorio de Biotaxonomía Morfólogica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Mar del Plata, provincia de Buenos Aires, Argentina
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21
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Pirog A, Jaquemet S, Ravigné V, Cliff G, Clua E, Holmes BJ, Hussey NE, Nevill JEG, Temple AJ, Berggren P, Vigliola L, Magalon H. Genetic population structure and demography of an apex predator, the tiger shark Galeocerdo cuvier. Ecol Evol 2019; 9:5551-5571. [PMID: 31160982 PMCID: PMC6540675 DOI: 10.1002/ece3.5111] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 01/20/2019] [Accepted: 02/26/2019] [Indexed: 12/16/2022] Open
Abstract
Population genetics has been increasingly applied to study large sharks over the last decade. Whilst large shark species are often difficult to study with direct methods, improved knowledge is needed for both population management and conservation, especially for species vulnerable to anthropogenic and climatic impacts. The tiger shark, Galeocerdo cuvier, is an apex predator known to play important direct and indirect roles in tropical and subtropical marine ecosystems. While the global and Indo-West Pacific population genetic structure of this species has recently been investigated, questions remain over population structure and demographic history within the western Indian (WIO) and within the western Pacific Oceans (WPO). To address the knowledge gap in tiger shark regional population structures, the genetic diversity of 286 individuals sampled in seven localities was investigated using 27 microsatellite loci and three mitochondrial genes (CR,COI, and cytb). A weak genetic differentiation was observed between the WIO and the WPO, suggesting high genetic connectivity. This result agrees with previous studies and highlights the importance of the pelagic behavior of this species to ensure gene flow. Using approximate Bayesian computation to couple information from both nuclear and mitochondrial markers, evidence of a recent bottleneck in the Holocene (2,000-3,000 years ago) was found, which is the most probable cause for the low genetic diversity observed. A contemporary effective population size as low as 111 [43,369] was estimated during the bottleneck. Together, these results indicate low genetic diversity that may reflect a vulnerable population sensitive to regional pressures. Conservation measures are thus needed to protect a species that is classified as Near Threatened.
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Affiliation(s)
- Agathe Pirog
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint Denis, La RéunionFrance
| | - Sébastien Jaquemet
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint Denis, La RéunionFrance
| | | | - Geremy Cliff
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Eric Clua
- EPHE‐CNRS‐UPVDCNRS UPVDUSR 3278 CRIOBEPSL Research UniversityPerpignanFrance
- Laboratoire d'Excellence CORAILPerpignanFrance
| | - Bonnie J. Holmes
- School of Biological SciencesUniversity of Queensland, St LuciaBrisbaneQueenslandAustralia
| | - Nigel E. Hussey
- Biological SciencesUniversity of WindsorWindsorOntarioCanada
| | | | - Andrew J. Temple
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Per Berggren
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Laurent Vigliola
- Laboratoire d'Excellence CORAILPerpignanFrance
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Institut de Recherche pour le DéveloppementNouméaNouvelle CalédonieFrance
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint Denis, La RéunionFrance
- Laboratoire d'Excellence CORAILPerpignanFrance
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Gangan SS, Pavan-Kumar A, K JA. Multigene barcoding and phylogeny of selected Engraulidae species. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:548-555. [PMID: 30892983 DOI: 10.1080/24701394.2019.1570175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Anchovies (Engraulidae) are one of the ecologically important groups and often difficult to identify due to their small size and overlapping morphological characters. In the present study, reference DNA barcodes were generated for 82 individuals representing 13 species of Engraulidae family using mitochondrial Cytochrome c oxidase subunit I (COI) and 16S rRNA genes. The average genetic distance value of COI gene for conspecific, congeneric and confamilial is 0.25, 20.45 and 22.28%, respectively. Mitochondrial 16S rRNA showed an average divergence value of 0.60, 10.28 and 14.37% for within species, between species and within families, respectively. Comparison of the present study reference barcodes with the reported sequences revealed high frequency of misidentification of species and possible occurrence of cryptic species in this family. Phylogenetic tree reconstructed using different methodologies revealed monophyletic nature of genus Stolephorus and the evolutionary relationship within genus Stolephorus is defined as ([S. insularis: S. tamilensis] S. dubiosus (S. waitei [S. commersonnii: S. indicus])).
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Affiliation(s)
- Shardul S Gangan
- a Fisheries Resources Harvest & Post-Harvest Division , ICAR - Central Institute of Fisheries Education , Mumbai , India
| | - A Pavan-Kumar
- b Fish Genetics and Biotechnology Division , ICAR - Central Institute of Fisheries Education , Mumbai , India
| | - Jaiswar A K
- a Fisheries Resources Harvest & Post-Harvest Division , ICAR - Central Institute of Fisheries Education , Mumbai , India
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23
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Phillips JD, Gillis DJ, Hanner RH. Incomplete estimates of genetic diversity within species: Implications for DNA barcoding. Ecol Evol 2019; 9:2996-3010. [PMID: 30891232 PMCID: PMC6406011 DOI: 10.1002/ece3.4757] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/03/2018] [Accepted: 10/12/2018] [Indexed: 02/01/2023] Open
Abstract
DNA barcoding has greatly accelerated the pace of specimen identification to the species level, as well as species delineation. Whereas the application of DNA barcoding to the matching of unknown specimens to known species is straightforward, its use for species delimitation is more controversial, as species discovery hinges critically on present levels of haplotype diversity, as well as patterning of standing genetic variation that exists within and between species. Typical sample sizes for molecular biodiversity assessment using DNA barcodes range from 5 to 10 individuals per species. However, required levels that are necessary to fully gauge haplotype variation at the species level are presumed to be strongly taxon-specific. Importantly, little attention has been paid to determining appropriate specimen sample sizes that are necessary to reveal the majority of intraspecific haplotype variation within any one species. In this paper, we present a brief outline of the current literature and methods on intraspecific sample size estimation for the assessment of COI DNA barcode haplotype sampling completeness. The importance of adequate sample sizes for studies of molecular biodiversity is stressed, with application to a variety of metazoan taxa, through reviewing foundational statistical and population genetic models, with specific application to ray-finned fishes (Chordata: Actinopterygii). Finally, promising avenues for further research in this area are highlighted.
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Affiliation(s)
- Jarrett D. Phillips
- School of Computer ScienceUniversity of GuelphGuelphOntarioCanada
- Centre for Biodiversity GenomicsBiodiversity Institute of OntarioUniversity of GuelphGuelphOntarioCanada
| | - Daniel J. Gillis
- School of Computer ScienceUniversity of GuelphGuelphOntarioCanada
| | - Robert H. Hanner
- Centre for Biodiversity GenomicsBiodiversity Institute of OntarioUniversity of GuelphGuelphOntarioCanada
- Department of Integrative BiologyUniversity of GuelphGuelphOntarioCanada
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24
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Young MK, Smith RJ, Pilgrim KL, Fairchild MP, Schwartz MK. Integrative taxonomy refutes a species hypothesis: The asymmetric hybrid origin of Arsapnia arapahoe (Plecoptera, Capniidae). Ecol Evol 2019; 9:1364-1377. [PMID: 30805166 PMCID: PMC6374720 DOI: 10.1002/ece3.4852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/02/2018] [Accepted: 11/29/2018] [Indexed: 11/23/2022] Open
Abstract
Molecular tools are commonly directed at refining taxonomies and the species that constitute their fundamental units. This has been especially insightful for groups for which species hypotheses are ambiguous and have largely been based on morphological differences between certain life stages or sexes, and has added importance when taxa are a focus of conservation efforts. Here, we examine the taxonomic status of Arsapnia arapahoe, a winter stonefly in the family Capniidae that is a species of conservation concern because of its limited abundance and restricted range in northern Colorado, USA. Phylogenetic analyses of sequences of mitochondrial and nuclear genes of this and other capniid stoneflies from this region and elsewhere in western North America indicated extensive haplotype sharing, limited genetic differences, and a lack of reciprocal monophyly between A. arapahoe and the sympatric A. decepta, despite distinctive and consistent morphological differences in the sexual apparatus of males of both species. Analyses of autosomal and sex-linked single nucleotide polymorphisms detected using genotyping by sequencing indicated that all individuals of A. arapahoe consisted of F1 hybrids between female A. decepta and males of another sympatric stonefly, Capnia gracilaria. Rather than constitute a self-sustaining evolutionary lineage, A. arapahoe appears to represent the product of nonintrogressive hybridization in the limited area of syntopy between two widely distributed taxa. This offers a cautionary tale for taxonomists and conservation biologists working on the less-studied components of the global fauna.
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Affiliation(s)
- Michael K. Young
- U.S. Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontana
| | - Rebecca J. Smith
- U.S. Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontana
| | - Kristine L. Pilgrim
- U.S. Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontana
| | | | - Michael K. Schwartz
- U.S. Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish ConservationMissoulaMontana
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25
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Artisanal shark fishing in Milne Bay Province, Papua New Guinea: biomass estimation from genetically identified shark and ray fins. Sci Rep 2018; 8:6693. [PMID: 29703988 PMCID: PMC5923204 DOI: 10.1038/s41598-018-25101-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 04/13/2018] [Indexed: 11/08/2022] Open
Abstract
Our study is the first detailed examination of species composition using DNA COI barcoding of elasmobranchs from an artisanal fishery of Papua New Guinea. The study is the first in the region to provide biomass estimates based on species confirmation following examination of dried fins. Over 20 species of elasmobranchs were identified from 623 fins from the artisanal fishery in Milne Bay Province of PNG, with Carcharhinus amblyrhynchos and Carcharhinus melanopterus the most abundant species in the catches. Of concern, 21% of fins examined were from IUCN listed threatened species (Vulnerable or Endangered) with 8% of fins from the Endangered scalloped hammerhead (Sphyrna lewini). Following species identifications and use of species-specific length and weight extrapolations, we estimated over 9 t of elasmobranchs contributed to the fin batch. Importantly, the vast majority of the elasmobranchs in this batch were from immature animals. Genetic identification has an important role to play in the ongoing sustainable management of elasmobranchs in artisanal fisheries in PNG and more widely. However in the absence of ongoing genetic testing, recording the species (if known) at the time of catch is more achievable and would provide more robust data for fisheries managers in PNG over the longer term.
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Kornilios P, Kumlutaş Y, Lymberakis P, Ilgaz Ç. Cryptic diversity and molecular systematics of the Aegean Ophiomorus
skinks (Reptilia: Squamata), with the description of a new species. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12205] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | - Yusuf Kumlutaş
- Department of Biology; Faculty of Science; Dokuz Eylül University; Buca-Izmir Turkey
| | - Petros Lymberakis
- Natural History Museum of Crete; University of Crete; Irakleio, Crete Greece
| | - Çetin Ilgaz
- Department of Biology; Faculty of Science; Dokuz Eylül University; Buca-Izmir Turkey
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Kolmann MA, Elbassiouny AA, Liverpool EA, Lovejoy NR. DNA barcoding reveals the diversity of sharks in Guyana coastal markets. NEOTROPICAL ICHTHYOLOGY 2017. [DOI: 10.1590/1982-0224-20170097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
ABSTRACT A fundamental challenge for both sustainable fisheries and biodiversity protection in the Neotropics is the accurate determination of species identity. The biodiversity of the coastal sharks of Guyana is poorly understood, but these species are subject to both artisanal fishing as well as harvesting by industrialized offshore fleets. To determine what species of sharks are frequently caught and consumed along the coastline of Guyana, we used DNA barcoding to identify market specimens. We sequenced the mitochondrial co1 gene for 132 samples collected from six markets, and compared our sequences to those available in the Barcode of Life Database (BOLD) and GenBank. Nearly 30% of the total sample diversity was represented by two species of Hammerhead Sharks (Sphyrna mokarran and S. lewini), both listed as Endangered by the International Union for Conservation of Nature (IUCN). Other significant portions of the samples included Sharpnose Sharks (23% - Rhizoprionodon spp.), considered Vulnerable in Brazilian waters due to unregulated gillnet fisheries, and the Smalltail Shark (17% - Carcharhinus porosus). We found that barcoding provides efficient and accurate identification of market specimens in Guyana, making this study the first in over thirty years to address Guyana’s coastal shark biodiversity.
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Steinke D, Bernard AM, Horn RL, Hilton P, Hanner R, Shivji MS. DNA analysis of traded shark fins and mobulid gill plates reveals a high proportion of species of conservation concern. Sci Rep 2017; 7:9505. [PMID: 28842669 PMCID: PMC5573315 DOI: 10.1038/s41598-017-10123-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 08/04/2017] [Indexed: 12/05/2022] Open
Abstract
Continuously increasing demand for plant and animal products causes unsustainable depletion of biological resources. It is estimated that one-quarter of sharks and rays are threatened worldwide and although the global fin trade is widely recognized as a major driver, demand for meat, liver oil, and gill plates also represents a significant threat. This study used DNA barcoding and 16 S rRNA sequencing as a method to identify shark and ray species from dried fins and gill plates, obtained in Canada, China, and Sri Lanka. 129 fins and gill plates were analysed and searches on BOLD produced matches to 20 species of sharks and five species of rays or – in two cases – to a species pair. Twelve of the species found are listed or have been approved for listing in 2017 in the appendices of the Convention on International Trade in Endangered Species of Fauna and Flora (CITES), including the whale shark (Rhincodon typus), which was surprisingly found among both shark fin and gill plate samples. More than half of identified species fall under the IUCN Red List categories ‘Endangered’ and ‘Vulnerable’, raising further concerns about the impacts of this trade on the sustainability of these low productivity species.
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Affiliation(s)
- Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada.
| | - Andrea M Bernard
- Save Our Seas Shark Research Center USA and Department of Biological Sciences, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA.,Guy Harvey Research Institute and Department of Biological Sciences, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA
| | - Rebekah L Horn
- Save Our Seas Shark Research Center USA and Department of Biological Sciences, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA.,Guy Harvey Research Institute and Department of Biological Sciences, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA
| | | | - Robert Hanner
- Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Mahmood S Shivji
- Save Our Seas Shark Research Center USA and Department of Biological Sciences, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA. .,Guy Harvey Research Institute and Department of Biological Sciences, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL, 33004, USA.
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A new species of Tometes Valenciennes 1850 (Characiformes: Serrasalmidae) from Tocantins-Araguaia River Basin based on integrative analysis of molecular and morphological data. PLoS One 2017; 12:e0170053. [PMID: 28422969 PMCID: PMC5396854 DOI: 10.1371/journal.pone.0170053] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 12/24/2016] [Indexed: 11/19/2022] Open
Abstract
A new large serrasalmid species of Tometes is described from the Tocantins-Araguaia River Basin. Tometes siderocarajensissp. nov. is currently found in the rapids of the Itacaiúnas River Basin, and formerly inhabited the lower Tocantins River. The new species can be distinguished from all congeners, except from T. ancylorhynchus, by the presence of lateral space between 1st and 2nd premaxillary teeth, and by the absence of lateral cusps in these two teeth. However, T. siderocarajensissp. nov. can be differentiated from syntopic congener T. ancylorhynchus by an entirely black with mottled red body in live specimens, densely pigmented pelvic fins with a high concentration of dark chromatophores, and the presence of 39 to 41 rows of circumpeduncular scales (vs. silvery body coloration with slightly reddish overtones on middle flank during breeding period in live specimens, hyaline to slightly pale coloration on distalmost region of pelvic fins, and 30 to 36 rows of circumpeduncular scales). Additionally, molecular sequence shows that T. siderocarajensissp. nov. is reciprocally monophyletic, and diagnosable from all congeners by having two autapomorphic molecular characters in the mitochondrial gene COI. The phylogenetic reconstruction still show that T. siderocarajensissp. nov. is closely related to T. trilobatus. This is the first molecular study using an integrative taxonomic approach based on morphological and molecular sequence data for all described species of Tometes. These findings increase the number of formally described species of Tometes to seven. A key to the Tometes species is provided.
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Identification of wood-boring beetles (Cerambycidae and Buprestidae) intercepted in trade-associated solid wood packaging material using DNA barcoding and morphology. Sci Rep 2017; 7:40316. [PMID: 28091577 PMCID: PMC5238391 DOI: 10.1038/srep40316] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 12/05/2016] [Indexed: 11/09/2022] Open
Abstract
Global trade facilitates the inadvertent movement of insect pests and subsequent establishment of populations outside their native ranges. Despite phytosanitary measures, nonnative insects arrive at United States (U.S.) ports of entry as larvae in solid wood packaging material (SWPM). Identification of wood-boring larval insects is important for pest risk analysis and management, but is difficult beyond family level due to highly conserved morphology. Therefore, we integrated DNA barcoding and rearing of larvae to identify wood-boring insects in SWPM. From 2012 to 2015, we obtained larvae of 338 longhorned beetles (Cerambycidae) and 38 metallic wood boring beetles (Buprestidae) intercepted in SWPM associated with imported products at six U.S. ports. We identified 265 specimens to species or genus using DNA barcodes. Ninety-three larvae were reared to adults and identified morphologically. No conflict was found between the two approaches, which together identified 275 cerambycids (23 genera) and 16 buprestids (4 genera). Our integrated approach confirmed novel DNA barcodes for seven species (10 specimens) of woodborers not in public databases. This study demonstrates the utility of DNA barcoding as a tool for regulatory agencies. We provide important documentation of potential beetle pests that may cross country borders through the SWPM pathway.
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White fish authentication by COIBar-RFLP: Toward a common strategy for the rapid identification of species in convenience seafood. Food Control 2016. [DOI: 10.1016/j.foodcont.2016.05.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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32
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A New Species of Tiger Pleco Panaqolus (Siluriformes: Loricariidae) from the Xingu Basin, Brazil. PLoS One 2016; 11:e0165388. [PMID: 27828981 PMCID: PMC5102395 DOI: 10.1371/journal.pone.0165388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 10/10/2016] [Indexed: 11/30/2022] Open
Abstract
Panaqolus tankei is described from the Xingu River, Brazil. The new species is diagnosed from P. albomaculatus, P. dentex, P. nix, P. nocturnus, and P. koko by its color pattern consisting of dark and light diagonal bars on the body and bands on the fins (vs. body and fins without bars or bands); from P. albivermis, P. maccus, and P. purusiensis by the width of the dark bars being more or less the same of the light bars (vs. dark bars at least two or three times wider than light bars) and from P. changae by the absence of vermiculation on the head (vs. vermiculation present on head). The new species differs from P. gnomus by the orientation of the bars from posterodorsal to anteroventral direction (vs. anterodorsal to posteroventral direction), and from P. claustellifer by the orientation of the bands in the dorsal fin that are not parallel to the margin (vs. parallel to the margin). The barcoding region (COI) was sequenced for the new species, sequences were deposited in GenBank and were compared with congeners from other drainages. With regard to the current construction of a hydroelectric power plant (a so-called mega dam) in the Xingu River, herewith we increase knowledge of the river Xingu’s ichthyofauna and, thus improve the assessment of the impacts of that construction on the river.
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Bernard AM, Feldheim KA, Heithaus MR, Wintner SP, Wetherbee BM, Shivji MS. Global population genetic dynamics of a highly migratory, apex predator shark. Mol Ecol 2016; 25:5312-5329. [DOI: 10.1111/mec.13845] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 08/09/2016] [Accepted: 08/25/2016] [Indexed: 01/19/2023]
Affiliation(s)
- Andrea M. Bernard
- Save Our Seas Shark Research Center Halmos College of Natural Sciences & Oceanography Nova Southeastern University 8000 N. Ocean Drive Dania Beach FL 33004 USA
| | - Kevin A. Feldheim
- The Field Museum of Natural History Pritzker Laboratory for Molecular Systematics and Evolution 1400 South Lake Shore Drive Chicago IL 60605 USA
| | - Michael R. Heithaus
- School of Environment and Society Florida International University Miami FL USA
| | - Sabine P. Wintner
- KwaZulu‐Natal Sharks Board Private Bag 2 Umhlanga Rocks 4320 South Africa
- Biomedical Resource Unit University of KwaZulu‐Natal Durban 4000 South Africa
| | - Bradley M. Wetherbee
- Department of Biological Sciences University of Rhode Island Kingston RI USA
- Guy Harvey Research Institute Dania Beach, FL 33004 USA
| | - Mahmood S. Shivji
- Save Our Seas Shark Research Center and Guy Harvey Research Institute Halmos College of Natural Sciences & Oceanography Nova Southeastern University 8000 N. Ocean Drive Dania Beach FL 33004 USA
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Breman FC, Loix S, Jordaens K, Snoeks J, Van Steenberge M. Testing the potential of DNA barcoding in vertebrate radiations: the case of the littoral cichlids (Pisces, Perciformes, Cichlidae) from Lake Tanganyika. Mol Ecol Resour 2016; 16:1455-1464. [DOI: 10.1111/1755-0998.12523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/26/2016] [Accepted: 02/26/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Floris C. Breman
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
| | - Sara Loix
- Laboratory of Biodiversity and Evolutionary Genomics; KU Leuven; Charles Debériotstraat 32 B-3000 Leuven Belgium
| | - Kurt Jordaens
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
| | - Jos Snoeks
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
- Laboratory of Biodiversity and Evolutionary Genomics; KU Leuven; Charles Debériotstraat 32 B-3000 Leuven Belgium
| | - Maarten Van Steenberge
- Biology Department; Royal Museum for Central Africa; Leuvensesteenweg 13 B-3080 Tervuren Belgium
- Laboratory of Biodiversity and Evolutionary Genomics; KU Leuven; Charles Debériotstraat 32 B-3000 Leuven Belgium
- Institute of Zoology; University of Graz; Universitätsplatz 2 8010 Graz Austria
- Operational Directorate Taxonomy and Phylogeny; Royal Belgian Institute of Natural Sciences; Vautierstraat 29 1000 Brussels Belgium
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35
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Chuang PS, Hung TC, Chang HA, Huang CK, Shiao JC. The Species and Origin of Shark Fins in Taiwan's Fishing Ports, Markets, and Customs Detention: A DNA Barcoding Analysis. PLoS One 2016; 11:e0147290. [PMID: 26799827 PMCID: PMC4723227 DOI: 10.1371/journal.pone.0147290] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 01/01/2016] [Indexed: 11/19/2022] Open
Abstract
The increasing consumption of shark products, along with the shark's fishing vulnerabilities, has led to the decrease in certain shark populations. In this study we used a DNA barcoding method to identify the species of shark landings at fishing ports, shark fin products in retail stores, and shark fins detained by Taiwan customs. In total we identified 23, 24, and 14 species from 231 fishing landings, 316 fin products, and 113 detained shark fins, respectively. All the three sample sources were dominated by Prionace glauca, which accounted for more than 30% of the collected samples. Over 60% of the species identified in the fin products also appeared in the port landings, suggesting the domestic-dominance of shark fin products in Taiwan. However, international trade also contributes a certain proportion of the fin product markets, as four species identified from the shark fin products are not found in Taiwan's waters, and some domestic-available species were also found in the customs-detained sample. In addition to the species identification, we also found geographical differentiation in the cox1 gene of the common thresher sharks (Alopias vulpinus), the pelagic thresher shark (A. pelagicus), the smooth hammerhead shark (Sphyrna zygaena), and the scalloped hammerhead shark (S. lewini). This result might allow fishing authorities to more effectively trace the origins as well as enforce the management and conservation of these sharks.
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Affiliation(s)
- Po-Shun Chuang
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Tzu-Chiao Hung
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Hung-An Chang
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Chien-Kang Huang
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Jen-Chieh Shiao
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
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36
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González-Castro M, Rosso JJ, Mabragaña E, Díaz de Astarloa JM. Surfing among species, populations and morphotypes: Inferring boundaries between two species of new world silversides (Atherinopsidae). C R Biol 2015; 339:10-23. [PMID: 26705969 DOI: 10.1016/j.crvi.2015.11.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 11/16/2022]
Abstract
Atherinopsidae are widespread freshwater and shallow marine fish with singular economic importance. Morphological, genetical and life cycles differences between marine and estuarine populations were already reported in this family, suggesting ongoing speciation. Also, coexistence and interbreeding between closely related species were documented. The aim of this study was to infer boundaries among: (A) Odontesthes bonariensis and O. argentinensis at species level, and intermediate morphs; (B) the population of O. argentinensis of Mar Chiquita Lagoon and its marine conspecifics. To achieve this, we integrated, meristic, Geometrics Morphometrics and DNA Barcode approaches. Four groups were discriminated and subsequently characterized according to their morphological traits, shape and meristic characters. No shared haplotypes between O. bonariensis and O. argentinensis were found. Significative-meristic and body shape differences between the Mar Chiquita and marine individuals of O. argentinensis were found, suggesting they behave as well differentiated populations, or even incipient ecological species. The fact that the Odontesthes morphotypes shared haplotypes with both, O. argentinensis and O. bonariensis, but also possess meristic and morphometric distinctive traits open new questions related to the origin of this morphogroup.
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Affiliation(s)
- Mariano González-Castro
- Grupo de Biotaxonomía Morfológica y molecular de peces, IIMyC-CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Juan José Rosso
- Grupo de Biotaxonomía Morfológica y molecular de peces, IIMyC-CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ezequiel Mabragaña
- Grupo de Biotaxonomía Morfológica y molecular de peces, IIMyC-CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juan Martín Díaz de Astarloa
- Grupo de Biotaxonomía Morfológica y molecular de peces, IIMyC-CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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37
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Pappalardo AM, Federico C, Sabella G, Saccone S, Ferrito V. A COI Nonsynonymous Mutation as Diagnostic Tool for Intraspecific Discrimination in the European Anchovy Engraulis encrasicolus (Linnaeus). PLoS One 2015; 10:e0143297. [PMID: 26599908 PMCID: PMC4657973 DOI: 10.1371/journal.pone.0143297] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 11/03/2015] [Indexed: 12/01/2022] Open
Abstract
The European anchovy, Engraulis encrasicolus, is currently one of the principal target species for commercial fisheries in Europe. In this study, the mitochondrial Control Region (CR) and the Cytochrome Oxidase I (COI) mitochondrial gene were analyzed in 74 specimens of E. encrasicolus from four localities in the central Mediterranean. In both populations, the two markers revealed the presence of two main haplogroups, A and B, already detected in previous investigations of different classes of molecular markers. Both CR and COI markers consistently identified two haplogroups. The COI sequence analysis identified a non-synonymous transversion (T to G) at position 116 of the translated sequence, resulting in an amino acid change. All COI sequences of haplogroup A had an amino acid sequence with alanine in this position, while serine was present in the same position in haplogroup B. The two haplogroups A and B were also discriminated by the variable number of TACA elements at the 5’-end of the mitochondrial CR. The selection tests applied to the COI dataset revealed that codon 116 was not under positive selection, that seven amino acid changes were under purifying selection, and that two amino acids were under episodic positive selection.
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Affiliation(s)
- Anna Maria Pappalardo
- Department of Biological, Geological and Environmental Sciences, Sec. Animal Biology “M. La Greca”, University of Catania, Catania, Italy
| | - Concetta Federico
- Department of Biological, Geological and Environmental Sciences, Sec. Animal Biology “M. La Greca”, University of Catania, Catania, Italy
| | - Giorgio Sabella
- Department of Biological, Geological and Environmental Sciences, Sec. Animal Biology “M. La Greca”, University of Catania, Catania, Italy
| | - Salvatore Saccone
- Department of Biological, Geological and Environmental Sciences, Sec. Animal Biology “M. La Greca”, University of Catania, Catania, Italy
| | - Venera Ferrito
- Department of Biological, Geological and Environmental Sciences, Sec. Animal Biology “M. La Greca”, University of Catania, Catania, Italy
- * E-mail:
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38
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Pappalardo AM, Ferrito V. A COIBar-RFLP strategy for the rapid detection of Engraulis encrasicolus in processed anchovy products. Food Control 2015. [DOI: 10.1016/j.foodcont.2015.03.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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39
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Wang XB, Deng J, Zhang JT, Zhou QS, Zhang YZ, Wu SA. DNA barcoding of common soft scales (Hemiptera: Coccoidea: Coccidae) in China. BULLETIN OF ENTOMOLOGICAL RESEARCH 2015; 105:545-554. [PMID: 25989705 DOI: 10.1017/s0007485315000413] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The soft scales (Hemiptera: Coccoidea: Coccidae) are a group of sap-sucking plant parasites, many of which are notorious agricultural pests. The quarantine and economic importance of soft scales necessitates rapid and reliable identification of these taxa. Nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene (barcoding region) and 28S rDNA were generated from 340 individuals of 36 common soft scales in China. Distance-based [(best match, Automated Barcode Gap Discovery (ABGD)], tree-based (neighbor-joining, Bayesian inference), Klee diagrams, and general mixed Yule coalescent (GMYC) models were used to evaluate barcoding success rates in the data set. Best match showed that COI and 28S sequences could provide 100 and 95.52% correct identification, respectively. The average interspecific divergences were 19.81% for COI data and 20.38% for 28S data, and mean intraspecific divergences were 0.56 and 0.07%, respectively. For COI data, multiple methods (ABGD, Klee, and tree-based methods) resulted in general congruence with morphological identifications. However, GMYC analysis tended to provide more molecular operational taxonomic units (MOTUs). Twelve MOTUs derived from five morphospecies (Rhodococcus sariuoni, Pulvinaria vitis, Pulvinaria aurantii, Parasaissetia nigra, and Ceroplastes rubens) were observed using the GMYC approach. In addition, tree-based methods showed that 28S sequences could be used for species-level identification (except for Ceroplastes ceriferus - Ceroplastes pseudoceriferus), even with low genetic variation (<1%). This report demonstrates the robustness of DNA barcoding for species discrimination of soft scales with two molecular markers (COI and 28S) and provides a reliable barcode library and rapid diagnostic tool for common soft scales in China.
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Affiliation(s)
- X-B Wang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education,Beijing Forestry University,Beijing 100083,China
| | - J Deng
- The Key Laboratory for Silviculture and Conservation of Ministry of Education,Beijing Forestry University,Beijing 100083,China
| | - J-T Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education,Beijing Forestry University,Beijing 100083,China
| | - Q-S Zhou
- Key Laboratory of Zoological Systematics and Evolution,Institute of Zoology,Chinese Academy of Sciences,Beijing 100101,China
| | - Y-Z Zhang
- Key Laboratory of Zoological Systematics and Evolution,Institute of Zoology,Chinese Academy of Sciences,Beijing 100101,China
| | - S-A Wu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education,Beijing Forestry University,Beijing 100083,China
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40
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Bester-van der Merwe AE, Gledhill KS. Molecular species identification and population genetics of chondrichthyans in South Africa: current challenges, priorities and progress. AFRICAN ZOOLOGY 2015. [DOI: 10.1080/15627020.2015.1063408] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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41
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Paknia O, Bergmann T, Hadrys H. Some ‘ant’swers: Application of a layered barcode approach to problems in ant taxonomy. Mol Ecol Resour 2015; 15:1262-74. [DOI: 10.1111/1755-0998.12395] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/03/2015] [Accepted: 02/18/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Omid Paknia
- Institut für Tierökologie und Zellbiologie; Stiftung Tierärztliche Hochschule Hannover; Hannover Germany
| | - Tjard Bergmann
- Institut für Tierökologie und Zellbiologie; Stiftung Tierärztliche Hochschule Hannover; Hannover Germany
| | - Heike Hadrys
- Institut für Tierökologie und Zellbiologie; Stiftung Tierärztliche Hochschule Hannover; Hannover Germany
- EEB; Yale University; New Haven Connecticut 06511 USA
- Sackler Institute for Comparative Genomics; American Museum of Natural History; New York New York 10024 USA
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42
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Fields AT, Abercrombie DL, Eng R, Feldheim K, Chapman DD. A novel mini-DNA barcoding assay to identify processed fins from internationally protected shark species. PLoS One 2015; 10:e0114844. [PMID: 25646789 PMCID: PMC4315593 DOI: 10.1371/journal.pone.0114844] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 10/09/2014] [Indexed: 11/25/2022] Open
Abstract
There is a growing need to identify shark products in trade, in part due to the recent listing of five commercially important species on the Appendices of the Convention on International Trade in Endangered Species (CITES; porbeagle, Lamna nasus, oceanic whitetip, Carcharhinus longimanus scalloped hammerhead, Sphyrna lewini, smooth hammerhead, S. zygaena and great hammerhead S. mokarran) in addition to three species listed in the early part of this century (whale, Rhincodon typus, basking, Cetorhinus maximus, and white, Carcharodon carcharias). Shark fins are traded internationally to supply the Asian dried seafood market, in which they are used to make the luxury dish shark fin soup. Shark fins usually enter international trade with their skin still intact and can be identified using morphological characters or standard DNA-barcoding approaches. Once they reach Asia and are traded in this region the skin is removed and they are treated with chemicals that eliminate many key diagnostic characters and degrade their DNA ("processed fins"). Here, we present a validated mini-barcode assay based on partial sequences of the cytochrome oxidase I gene that can reliably identify the processed fins of seven of the eight CITES listed shark species. We also demonstrate that the assay can even frequently identify the species or genus of origin of shark fin soup (31 out of 50 samples).
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Affiliation(s)
- Andrew T. Fields
- School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, New York, 11794, United States of America
| | | | - Rowena Eng
- School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, New York, 11794, United States of America
| | - Kevin Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, Illinois, 60605, United States of America
| | - Demian D. Chapman
- School of Marine and Atmospheric Science, Stony Brook University, Stony Brook, New York, 11794, United States of America
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43
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Wienerroither RM, Bjelland O, Bachmann L, Junge C. Northernmost record of the little gulper shark Centrophorus uyato in the north-eastern Atlantic Ocean, with taxonomical notes on Centrophorus zeehaani. JOURNAL OF FISH BIOLOGY 2015; 86:834-844. [PMID: 25605421 DOI: 10.1111/jfb.12602] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 11/10/2014] [Indexed: 06/04/2023]
Abstract
A specimen of the little gulper shark Centrophorus uyato was collected in the Norwegian Sea off the coast of northern Norway, marking the northernmost record of the species in the eastern North Atlantic Ocean. Morphological characteristics collected from the specimen indicate a close relationship to the Australian species Centrophorus zeehaani. DNA barcoding analysis of the mitochondrial cytochrome oxidase subunit I (coI) gene for species of Centrophorus suggests conspecificity of C. uyato and C. zeehaani.
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Affiliation(s)
- R M Wienerroither
- Institute of Marine Research, P. O. Box 1870 Nordnes, 5817 Bergen, Norway
| | - O Bjelland
- Institute of Marine Research, P. O. Box 1870 Nordnes, 5817 Bergen, Norway
| | - L Bachmann
- Natural History Museum, University of Oslo, P. O. Box 1172 Blindern, 0318 Oslo, Norway
| | - C Junge
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P. O. Box 1066 Blindern, 0316 Oslo, Norway
- Southern Seas Ecology Laboratories, School of Earth & Environmental Sciences, University of Adelaide, SA 5005, Australia
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44
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Avelino GS, Britski HA, Foresti F, Oliveira C. Molecular identification of Leporinus from the south portion of South America. ACTA ACUST UNITED AC 2015. [DOI: 10.1515/dna-2015-0013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractAnostomidae is a widely distributed group that includes the species rich Leporinus. This genus is widespread in South America, including its south portion where they are mainly distributed in the São Francisco and La Plata basins. Here we obtained sequences of mitochondrial and nuclear genes of 19 species of Leporinus with the objective of testing our methods of molecular species identification and to test the similarities between species of Leporinus of the São Francisco and La Plata basins. Results show that two species pair have a genetic distance below 2% (L. paranensis x L. obtusidens and L. paranensis x L. aff. paranensis). Our results also show that a high genetic distance occurs in L. obtusidens and L. striatus suggesting a possible local differentiation of these species. An interesting finding of our study is that the genetic similarities observed among species does not corroborate the division of species of Leporinus in groups according to color patterns. Additionally, our results show that the species of Leporinus from the La Plata and São Francisco are not more similar among themselves than to species of other drainages which could be explained by the occurrence of recent fauna exchanges between these two basins and adjacent basins.
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45
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Wang YJ, Li ZH, Zhang SF, Varadínová Z, Jiang F, Kučerová Z, Stejskal V, Opit G, Cao Y, Li FJ. DNA barcoding of five common stored-product pest species of genus Cryptolestes (Coleoptera: Laemophloeidae). BULLETIN OF ENTOMOLOGICAL RESEARCH 2014; 104:671-678. [PMID: 24725375 DOI: 10.1017/s0007485314000224] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Several species of the genus Cryptolestes Ganglbauer, 1899 (Coleoptera: Laemophloeidae) are commonly found in stored products. In this study, five species of Cryptolestes, with almost worldwide distribution, were obtained from laboratories in China, Czech Republic and the USA: Cryptolestes ferrugineus (Stephens, 1831), Cryptolestes pusillus (Schönherr, 1817), Cryptolestes turcicus (Grouvelle, 1876), Cryptolestes pusilloides (Steel & Howe, 1952) and Cryptolestes capensis (Waltl, 1834). Molecular identification based on a 658 bp fragment from the mitochondrial DNA cytochrome c oxidase subunit I (COI) was adopted to overcome some problems of morphological identification of Cryptolestes species. The utility of COI sequences as DNA barcodes in discriminating the five Cryptolestes species was evaluated on adults and larvae by analysing Kimura 2-parameter distances, phylogenetic tree and haplotype networks. The results showed that molecular approaches based on DNA barcodes were able to accurately identify these species. This is the first study using DNA barcoding to identify Cryptolestes species and the gathered DNA sequences will complement the biological barcode database.
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Affiliation(s)
- Y J Wang
- Department of Entomology, College of Agriculture and Biotechnology,China Agricultural University,No. 2 Yuanmingyuan West Road, Beijing,China
| | - Z H Li
- Department of Entomology, College of Agriculture and Biotechnology,China Agricultural University,No. 2 Yuanmingyuan West Road, Beijing,China
| | - S F Zhang
- Institute of Animal and Plant Quarantine,Chinese Academy of Inspection and Quarantine,Beijing,China
| | - Z Varadínová
- Department of Zoology, Faculty of Science,Charles University in Prague,Viničná 7, Prague,Czech Republic
| | - F Jiang
- Department of Entomology, College of Agriculture and Biotechnology,China Agricultural University,No. 2 Yuanmingyuan West Road, Beijing,China
| | - Z Kučerová
- Department of Pest Control of Stored Products and Food Safety,Crop Research Institute,Drnovská 507, Prague,Czech Republic
| | - V Stejskal
- Department of Pest Control of Stored Products and Food Safety,Crop Research Institute,Drnovská 507, Prague,Czech Republic
| | - G Opit
- Department of Entomology and Plant Pathology,Oklahoma State University,Stillwater, OK,USA
| | - Y Cao
- Academy of State Administration of Grain,No. 11 Baiwanzhuang Street, Beijing,China
| | - F J Li
- Academy of State Administration of Grain,No. 11 Baiwanzhuang Street, Beijing,China
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46
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Authentication of raw and processed tuna from Indonesian markets using DNA barcoding, nuclear gene and character-based approach. Eur Food Res Technol 2014. [DOI: 10.1007/s00217-014-2266-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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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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Cox K, Thomaes A, Antonini G, Zilioli M, De Gelas K, Harvey D, Solano E, Audisio P, McKeown N, Shaw P, Minetti R, Bartolozzi L, Mergeay J. Testing the performance of a fragment of the COI gene to identify western Palaearctic stag beetle species (Coleoptera, Lucanidae). Zookeys 2013; 365:105-26. [PMID: 24453554 PMCID: PMC3890674 DOI: 10.3897/zookeys.365.5526] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 10/16/2013] [Indexed: 11/12/2022] Open
Abstract
THE TAXONOMY OF STAG BEETLES (COLEOPTERA Lucanidae) remains challenging, mainly due to the sexual dimorphism and the strong allometry in males. Such conjecture confounds taxonomic based conservation efforts that are urgently needed due to numerous threats to stag beetle biodiversity. Molecular tools could help solve the problem of identification of the different recognized taxa in the "Lucanus cervus complex" and in some related Palaearctic species. We investigated the potential use of a 670 bp region at the 3' end of the mitochondrial cytochrome c oxidase subunit I gene (COI) for barcoding purposes (different from the standard COI barcoding region). Well resolved species and subspecies were L. tetraodon, L. cervusakbesianus, L. c. laticornis, as well as the two eastern Asian outgroup taxa L. formosanus and L. hermani. Conversely, certain taxa could not be distinguished from each other based on K2P-distances and tree topologies: L. c. fabiani / L. (P.) barbarossa, L. c. judaicus / an unknown Lucanus species, L. c. cervus / L. c. turcicus / L. c. pentaphyllus / L. (P.) macrophyllus / L. ibericus. The relative roles of phenotypic plasticity, recurrent hybridisation and incomplete lineage sorting underlying taxonomic and phylogenetic discordances are discussed.
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Affiliation(s)
- Karen Cox
- Research Institute for Nature and Forest, Gaverstraat 4, B-9500 Geraardsbergen, Belgium
| | - Arno Thomaes
- Research Institute for Nature and Forest, Gaverstraat 4, B-9500 Geraardsbergen, Belgium
| | - Gloria Antonini
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza - University of Rome, via A. Borelli 50, I-00161 Rome, Italy
| | - Michele Zilioli
- Natural History Museum, Entomological section, Corso Venezia 55, I-20121 Milano, Italy
| | - Koen De Gelas
- Research Institute for Nature and Forest, Gaverstraat 4, B-9500 Geraardsbergen, Belgium
- Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, Belgium
| | - Deborah Harvey
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, UK
| | - Emanuela Solano
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza - University of Rome, via A. Borelli 50, I-00161 Rome, Italy
| | - Paolo Audisio
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza - University of Rome, via A. Borelli 50, I-00161 Rome, Italy
| | - Niall McKeown
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, UK
| | - Paul Shaw
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, UK
| | | | - Luca Bartolozzi
- Natural History Museum, Zoological Section “La Specola”, via Romana 17, 50125 Firenze, Italy
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Gaverstraat 4, B-9500 Geraardsbergen, Belgium
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Liu SYV, Chan CLC, Lin O, Hu CS, Chen CA. DNA barcoding of shark meats identify species composition and CITES-listed species from the markets in Taiwan. PLoS One 2013; 8:e79373. [PMID: 24260209 PMCID: PMC3832526 DOI: 10.1371/journal.pone.0079373] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 09/29/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND An increasing awareness of the vulnerability of sharks to exploitation by shark finning has contributed to a growing concern about an unsustainable shark fishery. Taiwan's fleet has the 4th largest shark catch in the world, accounting for almost 6% of the global figures. Revealing the diversity of sharks consumed by Taiwanese is important in designing conservation plans. However, fins make up less than 5% of the total body weight of a shark, and their bodies are sold as filets in the market, making it difficult or impossible to identify species using morphological traits. METHODS In the present study, we adopted a DNA barcoding technique using a 391-bp fragment of the mitochondrial cytochrome oxidase I (COI) gene to examine the diversity of shark filets and fins collected from markets and restaurants island-wide in Taiwan. RESULTS Amongst the 548 tissue samples collected and sequenced, 20 major clusters were apparent by phylogenetic analyses, each of them containing individuals belonging to the same species (most with more than 95% bootstrap values), corresponding to 20 species of sharks. Additionally, Alopias pelagicus, Carcharhinus falciformis, Isurus oxyrinchus, and Prionace glauca consisted of 80% of the samples we collected, indicating that these species might be heavily consumed in Taiwan. Approximately 5% of the tissue samples used in this study were identified as species listed in CITES Appendix II, including two species of Sphyrna, C. longimanus and Carcharodon carcharias. CONCLUSION DNA barcoding provides an alternative method for understanding shark species composition when species-specific data is unavailable. Considering the global population decline, stock assessments of Appendix II species and highly consumed species are needed to accomplish the ultimate goal of shark conservation.
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Affiliation(s)
- Shang-Yin Vanson Liu
- Biodiversity Research Center, Academia Sinica, Nangang, Taipei, Taiwan
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, United States of America
| | | | - Oceana Lin
- The Society of Wilderness, Taipei, Taiwan
| | | | - Chaolun Allen Chen
- Biodiversity Research Center, Academia Sinica, Nangang, Taipei, Taiwan
- Taiwan International Graduate Program-Biodiversity, Academia Sinica, Nangang, Taipei, Taiwan
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
- * E-mail:
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50
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Viswambharan D, Pavan-Kumar A, Singh DP, Jaiswar AK, Chakraborty SK, Nair JR, Lakra WS. DNA barcoding of gobiid fishes (Perciformes, Gobioidei). ACTA ACUST UNITED AC 2013; 26:15-9. [DOI: 10.3109/19401736.2013.834438] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Divya Viswambharan
- Division of Fish Genetics and Biotechnology, Central Institute of Fisheries Education, Mumbai, Maharashtra, India and
| | - A. Pavan-Kumar
- Division of Fish Genetics and Biotechnology, Central Institute of Fisheries Education, Mumbai, Maharashtra, India and
| | - Dhirendra P. Singh
- Division of Fish Genetics and Biotechnology, Central Institute of Fisheries Education, Mumbai, Maharashtra, India and
| | - A. K. Jaiswar
- Division of Fish Genetics and Biotechnology, Central Institute of Fisheries Education, Mumbai, Maharashtra, India and
| | - S. K. Chakraborty
- Division of Fish Genetics and Biotechnology, Central Institute of Fisheries Education, Mumbai, Maharashtra, India and
| | - J. Rajashekharan Nair
- Department of Fishery Biology, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - W. S. Lakra
- Division of Fish Genetics and Biotechnology, Central Institute of Fisheries Education, Mumbai, Maharashtra, India and
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