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Martin B, Doane MP, Henkens J, Morgan JAT, Inglis L, Peddemors VM, Dinsdale EA, Huveneers C, Meyer L. Who bit the boat? New DNA collection and genomic methods enable species identification in suspected shark-related incidents. Forensic Sci Int Genet 2024; 72:103087. [PMID: 38996566 DOI: 10.1016/j.fsigen.2024.103087] [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: 05/03/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 07/14/2024]
Abstract
Species identification following shark-related incidents is critical for effective incident management and for collecting data to inform shark-bite mitigation strategies. Witness statements are not always reliable, and species identification is often ambiguous or missing. Alternative methods for species identification include morphological assessments of bite marks, analysis of collected teeth at the scene of the incident, and genetic approaches. However, access to appropriate collection media and robust genetic assays have limited the use of genetic technologies. Here, we present a case study that facilitated a unique opportunity to compare the effectiveness of medical gauze readily available in first-aid kits, and forensic-grade swabs in collecting genetic material for shark-species identification. Sterile medical gauze and forensic-grade swabs were used to collect transfer DNA from the bite margins on a bitten surf ski which were compared to a piece of shark tissue embedded along the bite margin. Witness accounts and the characteristics of the bite mark impressions inferred the involvement of a Carcharodon carcharias (white shark). The morphology of a tooth found on the boat that picked up the surf ski, however, suggested it belonged to an Orectolobus spp. (wobbegong). Genetic analysis of DNA transferred from the shark to the surf ski included the application of a broad-target nested PCR assay followed by Sanger sequencing, with white shark contribution to the 'total sample DNA' determined with a species-specific qPCR assay. The results of the genetic analyses were congruent between sampling methods with respect to species identification and the level of activity inferred by the donor-specific DNA contribution. These data also supported the inferences drawn from the bite mark morphology. DNA from the recovered tooth was PCR amplified with a wobbegong-specific primer pair designed for this study to corroborate the tooth's morphological identification. Following the confirmation of gauze used for sampling in the case study event, two additional isolated incidents occurred and were sampled in situ using gauze, as typically found in a first-aid kit, by external personnel. DNA extracted from these gauze samples resulted in the identification of a white shark as the donor of the DNA collected from the bite marks in both instances. This study, involving three incidents separated by time and location, represents the seminal application of gauze as a sampling media after critical human-shark interactions and strongly supports the practical implementation of these methods in the field.
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Affiliation(s)
- Belinda Martin
- Flinders University, Flinders Accelerator for Microbiome Exploration, Bedford Park, SA 5042, Australia; Flinders University, College of Science and Engineering, Bedford Park, SA 5042, Australia.
| | - Michael P Doane
- Flinders University, Flinders Accelerator for Microbiome Exploration, Bedford Park, SA 5042, Australia; Flinders University, College of Science and Engineering, Bedford Park, SA 5042, Australia.
| | - Jessica Henkens
- Flinders University, College of Science and Engineering, Bedford Park, SA 5042, Australia.
| | - Jess A T Morgan
- Queensland Department of Agriculture and Fisheries, Dutton Park, QLD 4102, Australia.
| | - Laura Inglis
- Flinders University, Flinders Accelerator for Microbiome Exploration, Bedford Park, SA 5042, Australia; Flinders University, College of Science and Engineering, Bedford Park, SA 5042, Australia.
| | - Victor M Peddemors
- New South Wales Department of Primary Industries, Sydney Institute of Marine Science, Mosman, NSW 2088, Australia.
| | - Elizabeth A Dinsdale
- Flinders University, Flinders Accelerator for Microbiome Exploration, Bedford Park, SA 5042, Australia; Flinders University, College of Science and Engineering, Bedford Park, SA 5042, Australia.
| | - Charlie Huveneers
- Flinders University, College of Science and Engineering, Bedford Park, SA 5042, Australia; Flinders University, Southern Shark Ecology Group, Bedford Park, SA 5042, Australia.
| | - Lauren Meyer
- Flinders University, College of Science and Engineering, Bedford Park, SA 5042, Australia; Flinders University, Southern Shark Ecology Group, Bedford Park, SA 5042, Australia; The Georgia Aquarium, Atlanta, GA 30313, United States.
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2
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Wagner I, Smolina I, Koop MEL, Bal T, Lizano AM, Choo LQ, Hofreiter M, Gennari E, de Sabata E, Shivji MS, Noble LR, Jones CS, Hoarau G. Genome analysis reveals three distinct lineages of the cosmopolitan white shark. Curr Biol 2024; 34:3582-3590.e4. [PMID: 39047735 DOI: 10.1016/j.cub.2024.06.076] [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: 12/18/2023] [Revised: 03/22/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024]
Abstract
The white shark (Carcharodon carcharias) (Linnaeus, 1758), an iconic apex predator occurring in all oceans,1,2 is classified as Vulnerable globally3-with global abundance having dropped to 63% of 1970s estimates,4-and as Critically Endangered in Europe.5 Identification of evolutionary significant units and their management are crucial for conservation,6 especially as the white shark is facing various but often region-specific anthropogenic threats.7,8,9,10,11 Assessing connectivity in a cosmopolitan marine species requires worldwide sampling and high-resolution genetic markers.12 Both are lacking for the white shark, with studies to date typified by numerous but geographically limited sampling, and analyses relying largely on relatively small numbers of nuclear microsatellites,13,14,15,16,17,18,19 which can be plagued by various genotyping artefacts and thus require cautious interpretation.20 Sequencing and computational advances are finally allowing genomes21,22,23 to be leveraged into population studies,24,25,26,27 with datasets comprising thousands of single-nucleotide polymorphisms (SNPs). Here, combining target gene capture (TGC)28 sequencing (89 individuals, 4,000 SNPs) and whole-genome re-sequencing (17 individuals, 391,000 SNPs) with worldwide sampling across most of the distributional range, we identify three genetically distinct allopatric lineages (North Atlantic, Indo-Pacific, and North Pacific). These diverged 100,000-200,000 years ago during the Penultimate Glaciation, when low sea levels, different ocean currents, and water temperatures produced significant biogeographic barriers. Our results show that without high-resolution genomic analyses of samples representative of a species' range,12 the true extent of diversity, presence of past and contemporary barriers to gene flow, subsequent speciation, and local evolutionary events will remain enigmatic.
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Affiliation(s)
- Isabel Wagner
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Irina Smolina
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Martina E L Koop
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Thijs Bal
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
| | - Apollo M Lizano
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway; Marine Science Institute, University of the Philippines, Diliman Quezon City 1101, Philippines
| | - Le Qin Choo
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway; Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Enrico Gennari
- Oceans Research Institute, Mossel Bay 6500, South Africa
| | | | - Mahmood S Shivji
- Save Our Seas Shark Foundation Research Center and Guy Harvey Research Institute, Nova Southeastern University, Dania Beach, FL 33004, USA
| | - Leslie R Noble
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway; School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland AB24 2TZ, UK.
| | - Catherine S Jones
- School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland AB24 2TZ, UK.
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway.
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3
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Melis R, Di Crescenzo S, Cariani A, Ferrari A, Crobe V, Bellodi A, Mulas A, Carugati L, Coluccia E, Follesa MC, Cannas R. I Like This New Me: Unravelling Population Structure of Mediterranean Electric Rays and Taxonomic Uncertainties within Torpediniformes. Animals (Basel) 2023; 13:2899. [PMID: 37760300 PMCID: PMC10525375 DOI: 10.3390/ani13182899] [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: 08/01/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The present study focused on the three species of electric rays known to occur in the Mediterranean Sea: Torpedo torpedo, Torpedo marmorata and Tetronarce nobiliana. Correct identification of specimens is needed to properly assess the impact of fisheries on populations and species. Unfortunately, torpedoes share high morphological similarities, boosting episodes of field misidentification. In this context, genetic data was used (1) to identify specimens caught during fishing operations, (2) to measure the diversity among and within these species, and (3) to shed light on the possible occurrence of additional hidden species in the investigated area. New and already published sequences of COI and NADH2 mitochondrial genes were analyzed, both at a small scale along the Sardinian coasts (Western Mediterranean) and at a large scale in the whole Mediterranean Sea. High levels of genetic diversity were found in Sardinian populations, being significantly different from other areas of the Eastern Mediterranean Sea due to the biotic and abiotic factors here discussed. Sardinian torpedoes can hence be indicated as priority populations/areas to be protected within the Mediterranean Sea. Moreover, sequence data confirmed that only the three species occur in the investigated area. The application of several 'species-delimitation' methods found evidence of cryptic species in the three species outside the Mediterranean Sea, as well as in other genera/families, suggesting the urgent need for future studies and a comprehensive revision of the order Torpediniformes for its effective conservation.
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Affiliation(s)
- Riccardo Melis
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
| | - Simone Di Crescenzo
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
| | - Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy; (A.C.); (A.F.); (V.C.)
| | - Alice Ferrari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy; (A.C.); (A.F.); (V.C.)
| | - Valentina Crobe
- Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy; (A.C.); (A.F.); (V.C.)
| | - Andrea Bellodi
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
| | - Antonello Mulas
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
| | - Laura Carugati
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
| | - Elisabetta Coluccia
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
| | - Maria Cristina Follesa
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
| | - Rita Cannas
- Department of Life and Environmental Sciences, University of Cagliari, 09126 Cagliari, Italy; (R.M.); (S.D.C.); (A.B.); (A.M.); (L.C.); (E.C.); (M.C.F.)
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Doane MP, Johnson CJ, Johri S, Kerr EN, Morris MM, Desantiago R, Turnlund AC, Goodman A, Mora M, Lima LFO, Nosal AP, Dinsdale EA. The Epidermal Microbiome Within an Aggregation of Leopard Sharks (Triakis semifasciata) Has Taxonomic Flexibility with Gene Functional Stability Across Three Time-points. MICROBIAL ECOLOGY 2023; 85:747-764. [PMID: 35129649 PMCID: PMC9957878 DOI: 10.1007/s00248-022-01969-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/17/2022] [Indexed: 05/06/2023]
Abstract
The epidermis of Chondrichthyan fishes consists of dermal denticles with production of minimal but protein-rich mucus that collectively, influence the attachment and biofilm development of microbes, facilitating a unique epidermal microbiome. Here, we use metagenomics to provide the taxonomic and functional characterization of the epidermal microbiome of the Triakis semifasciata (leopard shark) at three time-points collected across 4 years to identify links between microbial groups and host metabolism. Our aims include (1) describing the variation of microbiome taxa over time and identifying recurrent microbiome members (present across all time-points); (2) investigating the relationship between the recurrent and flexible taxa (those which are not found consistently across time-points); (3) describing the functional compositions of the microbiome which may suggest links with the host metabolism; and (4) identifying whether metabolic processes are shared across microbial genera or are unique to specific taxa. Microbial members of the microbiome showed high similarity between all individuals (Bray-Curtis similarity index = 82.7, where 0 = no overlap, 100 = total overlap) with the relative abundance of those members varying across sampling time-points, suggesting flexibility of taxa in the microbiome. One hundred and eighty-eight genera were identified as recurrent, including Pseudomonas, Erythrobacter, Alcanivorax, Marinobacter, and Sphingopxis being consistently abundant across time-points, while Limnobacter and Xyella exhibited switching patterns with high relative abundance in 2013, Sphingobium and Sphingomona in 2015, and Altermonas, Leeuwenhoekiella, Gramella, and Maribacter in 2017. Of the 188 genera identified as recurrent, the top 19 relatively abundant genera formed three recurrent groups. The microbiome also displayed high functional similarity between individuals (Bray-Curtis similarity index = 97.6) with gene function composition remaining consistent across all time-points. These results show that while the presence of microbial genera exhibits consistency across time-points, their abundances do fluctuate. Microbial functions however remain stable across time-points; thus, we suggest the leopard shark microbiomes exhibit functional redundancy. We show coexistence of microbes hosted in elasmobranch microbiomes that encode genes involved in utilizing nitrogen, but not fixing nitrogen, degrading urea, and resistant to heavy metal.
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Affiliation(s)
- Michael P. Doane
- College of Science and Engineering, Flinders University, Bedford Park, South Australia Australia
| | - Colton J. Johnson
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Shaili Johri
- Hopkins Marine Station, Stanford University, Pacific Grove, CA USA
| | - Emma N. Kerr
- College of Science and Engineering, Flinders University, Bedford Park, South Australia Australia
| | | | - Ric Desantiago
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Abigail C. Turnlund
- Australian Centre for Ecogenomics, University of Queensland, St Lucia, QLD Australia
| | - Asha Goodman
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Maria Mora
- Department of Biology, San Diego State University, San Diego, CA USA
| | | | - Andrew P. Nosal
- Department of Environmental and Ocean Sciences, University of San Diego, San Diego, CA USA
- Scripps Institution of Oceanography, University of California – San Diego, CA La Jolla, USA
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5
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Manuzzi A, Jiménez-Mena B, Henriques R, Holmes BJ, Pepperell J, Edson J, Bennett MB, Huveneers C, Ovenden JR, Nielsen EE. Retrospective genomics highlights changes in genetic composition of tiger sharks (Galeocerdo cuvier) and potential loss of a south-eastern Australia population. Sci Rep 2022; 12:6582. [PMID: 35449439 PMCID: PMC9023511 DOI: 10.1038/s41598-022-10529-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/06/2022] [Indexed: 11/08/2022] Open
Abstract
Over the last century, many shark populations have declined, primarily due to overexploitation in commercial, artisanal and recreational fisheries. In addition, in some locations the use of shark control programs also has had an impact on shark numbers. Still, there is a general perception that populations of large ocean predators cover wide areas and therefore their diversity is less susceptible to local anthropogenic disturbance. Here we report on temporal genomic analyses of tiger shark (Galeocerdo cuvier) DNA samples that were collected from eastern Australia over the past century. Using Single Nucleotide Polymorphism (SNP) loci, we documented a significant change in genetic composition of tiger sharks born between ~1939 and 2015. The change was most likely due to a shift over time in the relative contribution of two well-differentiated, but hitherto cryptic populations. Our data strongly indicate a dramatic shift in the relative contribution of these two populations to the overall tiger shark abundance on the east coast of Australia, possibly associated with differences in direct or indirect exploitation rates.
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Affiliation(s)
- Alice Manuzzi
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark.
| | - Belen Jiménez-Mena
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Romina Henriques
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Bonnie J Holmes
- School of Science, Technology & Engineering, University of the Sunshine Coast, Sippy Downs, QLD, 4556, Australia
| | - Julian Pepperell
- Pepperell Research and Consulting, PO Box 1475, Noosaville DC, QLD, 4566, Australia
| | - Janette Edson
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mike B Bennett
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Charlie Huveneers
- College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Jennifer R Ovenden
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Einar E Nielsen
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
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6
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Perry CT, Pratte ZA, Clavere-Graciette A, Ritchie KB, Hueter RE, Newton AL, Fischer GC, Dinsdale EA, Doane MP, Wilkinson KA, Bassos-Hull K, Lyons K, Dove ADM, Hoopes LA, Stewart FJ. Elasmobranch microbiomes: emerging patterns and implications for host health and ecology. Anim Microbiome 2021; 3:61. [PMID: 34526135 PMCID: PMC8444439 DOI: 10.1186/s42523-021-00121-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/21/2021] [Indexed: 12/20/2022] Open
Abstract
Elasmobranchs (sharks, skates and rays) are of broad ecological, economic, and societal value. These globally important fishes are experiencing sharp population declines as a result of human activity in the oceans. Research to understand elasmobranch ecology and conservation is critical and has now begun to explore the role of body-associated microbiomes in shaping elasmobranch health. Here, we review the burgeoning efforts to understand elasmobranch microbiomes, highlighting microbiome variation among gastrointestinal, oral, skin, and blood-associated niches. We identify major bacterial lineages in the microbiome, challenges to the field, key unanswered questions, and avenues for future work. We argue for prioritizing research to determine how microbiomes interact mechanistically with the unique physiology of elasmobranchs, potentially identifying roles in host immunity, disease, nutrition, and waste processing. Understanding elasmobranch–microbiome interactions is critical for predicting how sharks and rays respond to a changing ocean and for managing healthy populations in managed care.
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Affiliation(s)
- Cameron T Perry
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Zoe A Pratte
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Kim B Ritchie
- Department of Natural Sciences, University of South Carolina Beaufort, Beaufort, SC, USA
| | - Robert E Hueter
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,OCEARCH, Park City, UT, USA
| | - Alisa L Newton
- Disney's Animals, Science and Environment, Orlando, FL, USA
| | - G Christopher Fischer
- OCEARCH, Park City, UT, USA.,Marine Science Research Institute, Jacksonville University, Jacksonville, FL, USA
| | - Elizabeth A Dinsdale
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Michael P Doane
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Krystan A Wilkinson
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA.,Chicago Zoological Society's Sarasota Dolphin Research Program ℅ Mote Marine Laboratory, Sarasota, FL, USA
| | - Kim Bassos-Hull
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, Sarasota, FL, USA
| | - Kady Lyons
- Research and Conservation Department, Georgia Aquarium, Atlanta, GA, USA
| | - Alistair D M Dove
- Research and Conservation Department, Georgia Aquarium, Atlanta, GA, USA
| | - Lisa A Hoopes
- Research and Conservation Department, Georgia Aquarium, Atlanta, GA, USA
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
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7
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Diversity of Seahorse Species (Hippocampus spp.) in the International Aquarium Trade. DIVERSITY 2021. [DOI: 10.3390/d13050187] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Seahorses (Hippocampus spp.) are threatened as a result of habitat degradation and overfishing. They have commercial value as traditional medicine, curio objects, and pets in the aquarium industry. There are 48 valid species, 27 of which are represented in the international aquarium trade. Most species in the aquarium industry are relatively large and were described early in the history of seahorse taxonomy. In 2002, seahorses became the first marine fishes for which the international trade became regulated by CITES (Convention for the International Trade in Endangered Species of Wild Fauna and Flora), with implementation in 2004. Since then, aquaculture has been developed to improve the sustainability of the seahorse trade. This review provides analyses of the roles of wild-caught and cultured individuals in the international aquarium trade of various Hippocampus species for the period 1997–2018. For all species, trade numbers declined after 2011. The proportion of cultured seahorses in the aquarium trade increased rapidly after their listing in CITES, although the industry is still struggling to produce large numbers of young in a cost-effective way, and its economic viability is technically challenging in terms of diet and disease. Whether seahorse aquaculture can benefit wild populations will largely depend on its capacity to provide an alternative livelihood for subsistence fishers in the source countries. For most species, CITES trade records of live animals in the aquarium industry started a few years earlier than those of dead bodies in the traditional medicine trade, despite the latter being 15 times higher in number. The use of DNA analysis in the species identification of seahorses has predominantly been applied to animals in the traditional medicine market, but not to the aquarium trade. Genetic tools have already been used in the description of new species and will also help to discover new species and in various other kinds of applications.
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8
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Jorgensen SJ, Micheli F, White TD, Van Houtan KS, Alfaro-Shigueto J, Andrzejaczek S, Arnoldi NS, Baum JK, Block B, Britten GL, Butner C, Caballero S, Cardeñosa D, Chapple TK, Clarke S, Cortés E, Dulvy NK, Fowler S, Gallagher AJ, Gilman E, Godley BJ, Graham RT, Hammerschlag N, Harry AV, Heithaus M, Hutchinson M, Huveneers C, Lowe CG, Lucifora LO, MacKeracher T, Mangel JC, Barbosa Martins AP, McCauley DJ, McClenachan L, Mull C, Natanson LJ, Pauly D, Pazmiño DA, Pistevos JCA, Queiroz N, Roff G, Shea BD, Simpfendorfer CA, Sims DW, Ward-Paige C, Worm B, Ferretti F. Emergent research and priorities for shark and ray conservation. ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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9
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Schwanck TN, Schweinsberg M, Lampert KP, Guttridge TL, Tollrian R, O'Shea O. Linking local movement and molecular analysis to explore philopatry and population connectivity of the southern stingray Hypanus americanus. JOURNAL OF FISH BIOLOGY 2020; 96:1475-1488. [PMID: 32191344 DOI: 10.1111/jfb.14325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/05/2020] [Accepted: 03/17/2020] [Indexed: 06/10/2023]
Abstract
Limited data pertaining to life history and population connectivity of the data-deficient southern stingray (Hypanus americanus) are available. To determine potential vulnerabilities of their populations, this study aimed to analyse their movement patterns and genetic variability. A population of southern stingrays encompassing nine sites around Cape Eleuthera, the Bahamas, has been monitored using mark-recapture, spanning a 2.5 year period. Out of 200 individual stingrays, more than a third were encountered again. The home range of the females appears to be restricted, which supports the notion of high site residency. As resident populations of stingrays could suffer from a lack of population connectivity and be predestined for genetic isolation and local extirpation, this study further investigated the genetic connectivity of four sample sites in the central and western Bahamas. A haplotype analysis from the mitochondrial D-loop region showed that no distinct population structure strictly correlated with the sample site. These findings were complemented by five microsatellite loci that revealed high degrees in genotypic variability and little population differentiation. The results suggest gene flow mediated by both males and females.
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Affiliation(s)
- Tanja N Schwanck
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, 44801 Bochum, Germany
- School of Biological Sciences, University of Aberdeen, AB24 2TZ Aberdeen, United Kingdom
| | - Maximilian Schweinsberg
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, 44801 Bochum, Germany
| | - Kathrin P Lampert
- Institute for Zoology, University of Cologne, 50674 Cologne, Germany
| | - Tristan L Guttridge
- Bimini Biological Field Station Foundation, 15 Elizabeth Drive, South Bimini, The Bahamas
- Saving the Blue, Kendall, Miami, Florida, USA
| | - Ralph Tollrian
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr University Bochum, 44801 Bochum, Germany
| | - Owen O'Shea
- The Centre for Ocean Research and Education, Gregory Town, Eleuthera, The Bahamas
- Shark Research and Conservation Program, Cape Eleuthera Institute, Eleuthera, The Bahamas
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10
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Mitochondrial genome to aid species delimitation and effective conservation of the Sharpnose Guitarfish (Glaucostegus granulatus). Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100648] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Gomes-dos-Santos A, Arrondo NV, Machado AM, Veríssimo A, Pérez M, Román E, Castro LFC, Froufe E. The complete mitochondrial genome of the deep-water cartilaginous fish Hydrolagus affinis (de Brito Capello, 1868) (Holocephali: Chimaeridae). Mitochondrial DNA B Resour 2020. [DOI: 10.1080/23802359.2020.1749154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- André Gomes-dos-Santos
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Nair Vilas Arrondo
- AQUACOV, Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, Vigo, Spain
- UVIGO, PhD Program “Marine Science, Technology and Management” (Do *MAR), Faculty of Biology, University of Vigo, Vigo, Spain
| | - André M. Machado
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Matosinhos, Portugal
| | - Ana Veríssimo
- CIBIO – Research Centre in Biodiversity and Genetic Resources, Vairão, Portugal
| | - Montse Pérez
- AQUACOV, Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, Vigo, Spain
| | - Esther Román
- AQUACOV, Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, Vigo, Spain
| | - L. Filipe C. Castro
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR – Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros de Leixões, Matosinhos, Portugal
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Boissin E, Thorrold SR, Braun CD, Zhou Y, Clua EE, Planes S. Contrasting global, regional and local patterns of genetic structure in gray reef shark populations from the Indo-Pacific region. Sci Rep 2019; 9:15816. [PMID: 31676818 PMCID: PMC6825237 DOI: 10.1038/s41598-019-52221-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/10/2019] [Indexed: 11/21/2022] Open
Abstract
Human activities have resulted in the loss of over 90% of sharks in most ocean basins and one in four species of elasmobranch are now listed at risk of extinction by the IUCN. How this collapse will affect the ability of populations to recover in the face of continued exploitation and global climate change remains unknown. Indeed, important ecological and biological information are lacking for most shark species, particularly estimates of genetic diversity and population structure over a range of spatial scales. Using 15 microsatellite markers, we investigated genetic diversity and population structure in gray reef sharks over their Indo-Pacific range (407 specimens from 9 localities). Clear genetic differentiation was observed between the Indian and the Pacific Ocean specimens (FST = 0.145***). Further differentiation within the Pacific included a West and East cleavage as well as North-Central and South-Central Pacific clusters. No genetic differentiation was detected within archipelagos. These results highlight the legacy of past climate changes and the effects of large ocean expanses and circulation patterns on contrasting levels of connectivity at global, regional and local scales. Our results indicate a need for regional conservation units for gray reef sharks and pinpoint the isolation and vulnerability of their French Polynesian population.
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Affiliation(s)
- E Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France. .,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia.
| | - S R Thorrold
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - C D Braun
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA.,Massachusetts Institute of Technology-Woods Hole Oceanographic Institution Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge, MA, 02139, USA.,School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Y Zhou
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | - E E Clua
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | - S Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
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