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Gayford JH, Whitehead DA. The biology and ecology of the Pacific sharpnose shark Rhizoprionodon longurio. Ecol Evol 2023; 13:e10600. [PMID: 37829178 PMCID: PMC10565905 DOI: 10.1002/ece3.10600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/04/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023] Open
Abstract
Amidst global declines in elasmobranch populations resulting predominantly from overfishing, the need to gather data regarding shark ecology is greater than ever. Many species remain data deficient or at risk of going extinct before sufficient conservation measures can be applied. In this review, we summarise existing knowledge regarding the biology and ecology of the Pacific sharpnose shark Rhizoprionodon longurio (Jordan & Hilbert, 1882), a small-bodied carcharhinid shark found in coastal waters of the Eastern Tropical Pacific Ocean that is of both commercial and ecological importance. We compare ecological parameters of this species with its closest extant relatives and identify major knowledge gaps and avenues for future research. In particular, additional studies investigating the behavioural and sensory ecology, as well as potential migratory patterns of the species are needed. Such studies will not only improve our understanding of R. longurio, but provide insight into the extent to which the numerous studies performed on a close relative-Rhizoprionodon terraenovae-provide an accurate representation of the biology and ecology of Rhizoprionodon and carcharhinids more generally.
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Affiliation(s)
- Joel H. Gayford
- Department of Life SciencesSilwood Park Campus, Imperial College LondonLondonUK
- Shark MeasurementsLondonUK
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Taking Advantage of the Genomics Revolution for Monitoring and Conservation of Chondrichthyan Populations. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11040049] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chondrichthyes (sharks, rays, skates and chimaeras) are among the oldest extant predators and are vital to top-down regulation of oceanic ecosystems. They are an ecologically diverse group occupying a wide range of habitats and are thus, exploited by coastal, pelagic and deep-water fishing industries. Chondrichthyes are among the most data deficient vertebrate species groups making design and implementation of regulatory and conservation measures challenging. High-throughput sequencing technologies have significantly propelled ecological investigations and understanding of marine and terrestrial species’ populations, but there remains a paucity of NGS based research on chondrichthyan populations. We present a brief review of current methods to access genomic and metagenomic data from Chondrichthyes and discuss applications of these datasets to increase our understanding of chondrichthyan taxonomy, evolution, ecology and population structures. Last, we consider opportunities and challenges offered by genomic studies for conservation and management of chondrichthyan populations.
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Johri S, Solanki J, Cantu VA, Fellows SR, Edwards RA, Moreno I, Vyas A, Dinsdale EA. 'Genome skimming' with the MinION hand-held sequencer identifies CITES-listed shark species in India's exports market. Sci Rep 2019; 9:4476. [PMID: 30872700 PMCID: PMC6418218 DOI: 10.1038/s41598-019-40940-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/22/2019] [Indexed: 12/31/2022] Open
Abstract
Chondrichthyes - sharks, rays, skates, and chimeras, are among the most threatened and data deficient vertebrate species. Global demand for shark and ray derived products, drives unregulated and exploitative fishing practices, which are in turn facilitated by the lack of ecological data required for effective conservation of these species. Here, we describe a Next Generation Sequencing method (using the MinION, a hand-held portable sequencing device from Oxford Nanopore Technologies), and analyses pipeline for molecular ecological studies in Chondrichthyes. Using this method, the complete mitochondrial genome and nuclear intergenic and protein-coding sequences were obtained by direct sequencing of genomic DNA obtained from shark fin tissue. Recovered loci include mitochondrial barcode sequences- Cytochrome oxidase I, NADH2, 16S rRNA and 12S rRNA- and nuclear genetic loci such as 5.8S rRNA, Internal Transcribed Spacer 2, and 28S rRNA regions, which are commonly used for taxonomic identification. Other loci recovered were the nuclear protein-coding genes for antithrombin or SerpinC, Immunoglobulin lambda light chain, Preprogehrelin, selenium binding protein 1(SBP1), Interleukin-1 beta (IL-1β) and Recombination-Activating Gene 1 (RAG1). The median coverage across all genetic loci was 20x and sequence accuracy was ≥99.8% compared to reference sequences. Analyses of the nuclear ITS2 region and the mitochondrial protein-encoding loci allowed accurate taxonomic identification of the shark specimen as Carcharhinus falciformis, a CITES Appendix II species. MinION sequencing provided 1,152,211 bp of new shark genome, increasing the number of sequenced shark genomes to five. Phylogenetic analyses using both mitochondrial and nuclear loci provided evidence that Prionace glauca is nested within Carcharhinus, suggesting the need for taxonomic reassignment of P. glauca. We increased genomic information about a shark species for ecological and population genetic studies, enabled accurate identification of the shark tissue for biodiversity indexing and resolved phylogenetic relationships among multiple taxa. The method was independent of amplification bias, and adaptable for field assessments of other Chondrichthyes and wildlife species in the future.
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Affiliation(s)
- Shaili Johri
- Department of Biology, 5500 Campanile Dr., San Diego State University, San Diego, CA, 92128, USA
| | - Jitesh Solanki
- College of Fisheries Science, Rajendra Bhuvan Road, Junagadh Agricultural University, Veraval, Gujarat, 362266, India
| | - Vito Adrian Cantu
- Computational Sciences Research Center, 5500 Campanile Drive, San Diego State University, San Diego, CA, 92128, USA
| | - Sam R Fellows
- Department of Biology, 5500 Campanile Dr., San Diego State University, San Diego, CA, 92128, USA
| | - Robert A Edwards
- Computational Sciences Research Center, 5500 Campanile Drive, San Diego State University, San Diego, CA, 92128, USA
| | - Isabel Moreno
- Department of Biology, 5500 Campanile Dr., San Diego State University, San Diego, CA, 92128, USA
| | - Asit Vyas
- College of Fisheries Science, Rajendra Bhuvan Road, Junagadh Agricultural University, Veraval, Gujarat, 362266, India
| | - Elizabeth A Dinsdale
- Department of Biology, 5500 Campanile Dr., San Diego State University, San Diego, CA, 92128, USA.
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DNA-based identification reveals illegal trade of threatened shark species in a global elasmobranch conservation hotspot. Sci Rep 2018; 8:3347. [PMID: 29463851 PMCID: PMC5820252 DOI: 10.1038/s41598-018-21683-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/01/2018] [Indexed: 02/07/2023] Open
Abstract
Here, we report trading of endangered shark species in a world hotspot for elasmobranch conservation in Brazil. Data on shark fisheries are scarce in Brazil, although the northern and northeastern regions have the highest indices of shark bycatch. Harvest is made primarily with processed carcasses lacking head and fins, which hampers reliable species identification and law enforcement on illegal catches. We used partial sequences of two mitochondrial genes (COI and/or NADH2) to identify 17 shark species from 427 samples being harvested and marketed on the northern coast of Brazil. Nine species (53%) are listed under some extinction threat category according to Brazilian law and international authorities (IUCN – International Union for Conservation of Nature; CITES – Convention on International Trade of Endangered Species of Wild Fauna and Flora). The number increases to 13 (76%) if we also consider the Near Threatened category. Hammerhead sharks are under threat worldwide, and composed 18.7% of samples, with Sphyrna mokarran being the fourth most common species among samples. As illegal trade of threatened shark species is a worldwide conservation problem, molecular identification of processed meat or specimens lacking diagnostic body parts is a highly effective tool for species identification and law enforcement.
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Nachtigall PG, Rodrigues-Filho LFS, Sodré DCA, Vallinoto M, Pinhal D. A multiplex PCR approach for the molecular identification and conservation of the Critically Endangered daggernose shark. ENDANGER SPECIES RES 2017. [DOI: 10.3354/esr00798] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Wyffels J, King BL, Vincent J, Chen C, Wu CH, Polson SW. SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes. F1000Res 2014; 3:191. [PMID: 25309735 PMCID: PMC4184313 DOI: 10.12688/f1000research.4996.1] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/12/2014] [Indexed: 12/02/2022] Open
Abstract
Chondrichthyan fishes are a diverse class of gnathostomes that provide a valuable perspective on fundamental characteristics shared by all jawed and limbed vertebrates. Studies of phylogeny, species diversity, population structure, conservation, and physiology are accelerated by genomic, transcriptomic and protein sequence data. These data are widely available for many sarcopterygii (coelacanth, lungfish and tetrapods) and actinoptergii (ray-finned fish including teleosts) taxa, but limited for chondrichthyan fishes. In this study, we summarize available data for chondrichthyes and describe resources for one of the largest projects to characterize one of these fish,
Leucoraja erinacea, the little skate. SkateBase (
http://skatebase.org) serves as the skate genome project portal linking data, research tools, and teaching resources.
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Affiliation(s)
- Jennifer Wyffels
- Department of Computer and Information Sciences, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Benjamin L King
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, 04672, USA
| | - James Vincent
- Vermont Genetics Network, University of Vermont, Burlington, VT, 05405, USA
| | - Chuming Chen
- Department of Computer and Information Sciences, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Cathy H Wu
- Department of Computer and Information Sciences, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Shawn W Polson
- Department of Computer and Information Sciences, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
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