1
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Palacios-Barreto P, Mar-Silva AF, Bayona-Vasquez NJ, Adams DH, Díaz-Jaimes P. Characterization of the complete mitochondrial genome of the brazilian cownose ray Rhinoptera brasiliensis (Myliobatiformes, Rhinopteridae) in the western Atlantic and its phylogenetic implications. Mol Biol Rep 2023; 50:4083-4095. [PMID: 36877343 DOI: 10.1007/s11033-023-08272-0] [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: 10/03/2022] [Accepted: 01/11/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND The Brazilian cownose ray, Rhinoptera brasiliensis has undergone a global population reduction and is currently classified by IUCN as Vulnerable. This species is sometimes confused with Rhinoptera bonasus, the only external diagnostic characteristic to distinguish between both species is the number of rows of tooth plates. Both cownose rays overlap geographically from Rio de Janeiro to the western North Atlantic. This calls for a more comprehensive phylogenetic assessment using mitochondria DNA genomes to better understand the relationships and delimitation of these two species. METHODS AND RESULTS The mitochondrial genome sequences of R. brasiliensis was obtained by next-generation sequencing. The length of the mitochondrial genome was 17,759 bp containing 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a non-coding control region (D-loop). Each PCG was initiated by an authoritative ATG codon, except for COX1 initiated by a GTG codon. Most of the PCGs were terminated by a complete codon (TAA/TAG), while an incomplete termination codon (TA/T) was found in five out of the 13 PCGs. The phylogenetic analysis showed that R. brasiliensis was closely related to R. steindachneri whereas the reported mitogenome as R. steindachneri (GenBank accession number KM364982), differs from multiple mitocondrial DNA sequences of R. steindachneri and is nearly identical to that of R. javanica. CONCLUSION The new mitogenome determined in this study provides new insight into the phylogenetic relationships in Rhinoptera, while providing new molecular data that can be applied to population genetic studies.
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Affiliation(s)
- Paola Palacios-Barreto
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C.P. 04510, Coyoacán, Ciudad de México, México.,Fundación colombiana para la investigación y conservación de Tiburones y Rayas, SQUALUS, Cali, Colombia
| | - Adán Fernando Mar-Silva
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C.P. 04510, Coyoacán, Ciudad de México, México
| | - Natalia J Bayona-Vasquez
- Division of Natural Science and Mathematics, Oxford College, Emory University, 30054, Oxford, GA, USA
| | - Douglas H Adams
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute, Indian River Field Laboratory, 32901, Melbourne, FL, USA
| | - Píndaro Díaz-Jaimes
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México.
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2
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Whitney JL, Coleman RR, Deakos MH. The complete mitochondrial genome of the Reef Manta Ray, Mobula alfredi, from Hawaii. Mitochondrial DNA B Resour 2023; 8:197-203. [PMID: 36755876 PMCID: PMC9901431 DOI: 10.1080/23802359.2023.2167475] [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] [Indexed: 02/05/2023] Open
Abstract
We provide the complete mitochondrial genome of the reef manta ray, Mobula alfredi, using an ezRAD approach. The total length of the mitogenome was 18,166 bp and contained 13 protein-coding genes, 22 transfer RNAs genes, two ribosomal RNA genes, and one non-coding control region. The gene organization and length are similar to other Mobula species. This reference mitogenome that includes the control region is expected to be a valuable resource for molecular-based species identification, population genomics, and phylogeography.
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Affiliation(s)
- Jonathan L. Whitney
- Pacific Islands Fisheries Science Center, National Oceanic and Atmospheric Administration, Honolulu, HI, USA,CONTACT Jonathan L. Whitney Pacific Islands Fisheries Science Center, National Oceanic and Atmospheric Administration, Honolulu, HI, USA
| | - Richard R. Coleman
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA,Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - Mark H. Deakos
- Hawaiʻi Association for Marine Education and Research, Lahaina, HI, USA
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3
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Tracing Patterns and Biodiversity Aspects of the Overlooked Skates and Rays (Subclass Elasmobranchii, Superorder Batoidea) in Greece. DIVERSITY 2023. [DOI: 10.3390/d15010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Species belonging to the superorder Batoidea have been poorly assessed due to the lack of information on their life history aspects and their limited economic value. This work presents an overview of skates and rays inhabiting the marine Greek waters and reports biodiversity issues requiring resolution for conservation purposes. Overall, 30 species from nine families and 16 genera have been documented within the past 22 years, based on the available literature and technical reports from research surveys of the Hellenic Centre for Marine Research (HCMR). However, 28 species are currently confirmed, since the presence of two rajids has not been sufficiently demonstrated and hence is considered as doubtful. Recent changes in nomenclature allowed us to replace old with new names in four species on the Greek list; patterns in the frequency of occurrence were observed and species were assigned into five categories; and diversity and misidentification issues were reported by family. Although Greek waters are oligotrophic and not considered a biodiversity hot spot for elasmobranchs, a high number of batoid species is documented in the area; therefore, the need to reinforce knowledge on biological aspects of skates and rays, define their status and identify their main threats is essential.
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4
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Hoban ML, Whitney J, Collins AG, Meyer C, Murphy KR, Reft AJ, Bemis KE. Skimming for barcodes: rapid production of mitochondrial genome and nuclear ribosomal repeat reference markers through shallow shotgun sequencing. PeerJ 2022; 10:e13790. [PMID: 35959477 PMCID: PMC9359134 DOI: 10.7717/peerj.13790] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/05/2022] [Indexed: 01/17/2023] Open
Abstract
DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments. The emergence of metabarcoding approaches such as environmental DNA (eDNA) has necessitated multiple marker techniques combined with barcode reference databases backed by voucher specimens. Reference barcodes have traditionally been generated by Sanger sequencing, however sequencing multiple markers is costly for large numbers of specimens, requires multiple separate PCR reactions, and limits resulting sequences to targeted regions. High-throughput sequencing techniques such as genome skimming enable assembly of complete mitogenomes, which contain the most commonly used barcoding loci (e.g., COI, 12S, 16S), as well as nuclear ribosomal repeat regions (e.g., ITS1&2, 18S). We evaluated the feasibility of genome skimming to generate barcode references databases for marine fishes by assembling complete mitogenomes and nuclear ribosomal repeats. We tested genome skimming across a taxonomically diverse selection of 12 marine fish species from the collections of the National Museum of Natural History, Smithsonian Institution. We generated two sequencing libraries per species to test the impact of shearing method (enzymatic or mechanical), extraction method (kit-based or automated), and input DNA concentration. We produced complete mitogenomes for all non-chondrichthyans (11/12 species) and assembled nuclear ribosomal repeats (18S-ITS1-5.8S-ITS2-28S) for all taxa. The quality and completeness of mitogenome assemblies was not impacted by shearing method, extraction method or input DNA concentration. Our results reaffirm that genome skimming is an efficient and (at scale) cost-effective method to generate all mitochondrial and common nuclear DNA barcoding loci for multiple species simultaneously, which has great potential to scale for future projects and facilitate completing barcode reference databases for marine fishes.
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Affiliation(s)
- Mykle L. Hoban
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, Hawai‘i, United States of America
| | - Jonathan Whitney
- Pacific Islands Fisheries Science Center, National Oceanic and Atmospheric Administration, Honolulu, Hawai‘i, United States of America
| | - Allen G. Collins
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Christopher Meyer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Katherine R. Murphy
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Abigail J. Reft
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Katherine E. Bemis
- NOAA National Systematics Laboratory, Natural Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
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5
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Farmer NA, Garrison LP, Horn C, Miller M, Gowan T, Kenney RD, Vukovich M, Willmott JR, Pate J, Harry Webb D, Mullican TJ, Stewart JD, Bassos-Hull K, Jones C, Adams D, Pelletier NA, Waldron J, Kajiura S. The distribution of manta rays in the western North Atlantic Ocean off the eastern United States. Sci Rep 2022; 12:6544. [PMID: 35449381 PMCID: PMC9023537 DOI: 10.1038/s41598-022-10482-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/19/2022] [Indexed: 01/22/2023] Open
Abstract
In 2018, the giant manta ray was listed as threatened under the U.S. Endangered Species Act. We integrated decades of sightings and survey effort data from multiple sources in a comprehensive species distribution modeling (SDM) framework to evaluate the distribution of giant manta rays off the eastern United States, including the Gulf of Mexico. Manta rays were most commonly detected at productive nearshore and shelf-edge upwelling zones at surface thermal frontal boundaries within a temperature range of approximately 20–30 °C. SDMs predicted highest nearshore occurrence off northeastern Florida during April, with the distribution extending northward along the shelf-edge as temperatures warm, leading to higher occurrences north of Cape Hatteras, North Carolina from June to October, and then south of Savannah, Georgia from November to March as temperatures cool. In the Gulf of Mexico, the highest nearshore occurrence was predicted around the Mississippi River delta from April to June and again from October to November. SDM predictions will allow resource managers to more effectively protect manta rays from fisheries bycatch, boat strikes, oil and gas activities, contaminants and pollutants, and other threats.
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Affiliation(s)
- Nicholas A Farmer
- NOAA/National Marine Fisheries Service, Southeast Regional Office, 263 13th Ave S., St. Petersburg, FL, 33701, USA.
| | - Lance P Garrison
- NOAA/National Marine Fisheries Service, Southeast Fisheries Science Center, 75 Virginia Beach Dr., Miami, FL, 33149, USA
| | - Calusa Horn
- NOAA/National Marine Fisheries Service, Southeast Regional Office, 263 13th Ave S., St. Petersburg, FL, 33701, USA
| | - Margaret Miller
- NOAA/National Marine Fisheries Service, Office of Protected Resources, 1315 East-West Highway, Silver Spring, MD, 20910, USA
| | - Timothy Gowan
- Florida Fish and Wildlife Research Institute, 100 8th Ave SE, St. Petersburg, FL, 33701, USA
| | - Robert D Kenney
- Graduate School of Oceanography, University of Rhode Island, Bay Campus Box 40, 215 South Ferry Rd., Narragansett, RI, 02882, USA
| | - Michelle Vukovich
- Normandeau Associates Inc., 4581 NW 6th Street, Suite H, Gainesville, FL, 32609, USA
| | | | - Jessica Pate
- Marine Megafauna Foundation, 7750 Okeechobee Blvd, Ste 4-3038, West Palm Beach, FL, 33411, USA
| | - D Harry Webb
- Georgia Aquarium, 225 Baker St. NW, Atlanta, GA, 30313, USA
| | | | - Joshua D Stewart
- The Manta Trust, Catemwood House, Corscombe, Dorchester, Dorset, DT2 0NT, UK.,NOAA/National Marine Fisheries Service, Southwest Fisheries Science Center, La Jolla Shores Drive, La Jolla, CA, 92037, USA
| | - Kim Bassos-Hull
- Sharks and Rays Conservation Research Program, Mote Marine Laboratory, 1600 Ken Thompson Pkwy, Sarasota, FL, 34236, USA
| | - Christian Jones
- NOAA/National Marine Fisheries Service, Southeast Fisheries Science Center, 3209 Frederic Street, Pascagoula, MS, 39567-4112, USA
| | - Delaney Adams
- Western Washington University, 516 High Street, Bellingham, WA, 98225, USA
| | - Nicole A Pelletier
- The Manta Trust, Catemwood House, Corscombe, Dorchester, Dorset, DT2 0NT, UK
| | - Jordan Waldron
- Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
| | - Stephen Kajiura
- Florida Atlantic University, 777 Glades Road, Boca Raton, FL, 33431, USA
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6
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Love MS, Bizzarro JJ, Cornthwaite AM, Frable BW, Maslenikov KP. Checklist of marine and estuarine fishes from the AlaskaYukon Border, Beaufort Sea, to Cabo San Lucas, Mexico. Zootaxa 2021; 5053:1-285. [PMID: 34810850 DOI: 10.11646/zootaxa.5053.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Indexed: 11/04/2022]
Abstract
This paper is a checklist of the fishes that have been documented, through both published and unpublished sources, in marine and estuarine waters, and out 200 miles, from the United States-Canadian border on the Beaufort Sea to Cabo San Lucas, Mexico. A minimum of 241 families and 1,644 species are known within this range, including both native and nonnative species. For each of these species, we include maximum size, geographic and depth ranges, whether it is native or nonnative, as well as a brief mention of any taxonomic issues.
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Affiliation(s)
- Milton S Love
- Marine Science Institute, University of California, Santa Barbara, CA 93106.
| | - Joseph J Bizzarro
- Cooperative Institute for Marine Ecosystems and Climate, University of California, Santa Cruz, 110 McAllister Way, Santa Cruz, CA 95060. .
| | - A Maria Cornthwaite
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada .
| | - Benjamin W Frable
- Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0244, USA. .
| | - Katherine P Maslenikov
- University of Washington Fish Collection, School of Aquatic and Fishery Sciences and Burke Museum of Natural History and Culture, 1122 NE Boat St., Seattle, WA 98105.
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7
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Hosegood J, Humble E, Ogden R, de Bruyn M, Creer S, Stevens GMW, Abudaya M, Bassos-Hull K, Bonfil R, Fernando D, Foote AD, Hipperson H, Jabado RW, Kaden J, Moazzam M, Peel LR, Pollett S, Ponzo A, Poortvliet M, Salah J, Senn H, Stewart JD, Wintner S, Carvalho G. Phylogenomics and species delimitation for effective conservation of manta and devil rays. Mol Ecol 2020; 29:4783-4796. [PMID: 33164287 DOI: 10.1111/mec.15683] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023]
Abstract
Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.
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Affiliation(s)
- Jane Hosegood
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Emily Humble
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK.,TRACE Wildlife Forensics Network, Edinburgh, UK
| | - Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
| | - Guy M W Stevens
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | | | - Kim Bassos-Hull
- Mote Marine Laboratory, The Center for Shark Research, Sarasota, FL, USA
| | | | - Daniel Fernando
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.,Blue Resources Trust, Colombo, Sri Lanka
| | - Andrew D Foote
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, Trondheim, Norway
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - Jennifer Kaden
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | | | - Lauren R Peel
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.,The Australian Institute of Marine Science, Crawley, WA, Australia.,Save Our Seas Foundation - D'Arros Research Centre, Geneva, Switzerland
| | - Stephen Pollett
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Alessandro Ponzo
- Large Marine Vertebrates Research Institute Philippines, Jagna, Philippines
| | | | - Jehad Salah
- Ministry of Agriculture Directorate General of Fisheries, Gaza City, Palestine
| | - Helen Senn
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Joshua D Stewart
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Sabine Wintner
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa.,School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
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8
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Serena F, Abella AJ, Bargnesi F, Barone M, Colloca F, Ferretti F, Fiorentino F, Jenrette J, Moro S. Species diversity, taxonomy and distribution of Chondrichthyes in the Mediterranean and Black Sea. THE EUROPEAN ZOOLOGICAL JOURNAL 2020. [DOI: 10.1080/24750263.2020.1805518] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- F. Serena
- Institute for Marine Biological Resources and Biotechnology, National Research Council (CNR-IRBIM), Mazara Del Vallo (TR), Italy
| | | | - F. Bargnesi
- Department of Life and Environmental Sciences (Disva), Marche Polytechnic University, Ancona, Italy
- Cattolica Aquarium, Cattolica (RN), Italy
| | - M. Barone
- Fisheries Resources Consultant, Food and Agriculture Organization, Rome, Italy
| | - F. Colloca
- Stazione Zoologica Anton Dohrn-Italian National Institute for Marine Biology, Ecology and Biotechnology, Naples, Italy
| | - F. Ferretti
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg (VA), USA
| | - F. Fiorentino
- Institute for Marine Biological Resources and Biotechnology, National Research Council (CNR-IRBIM), Mazara Del Vallo (TR), Italy
| | - J. Jenrette
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg (VA), USA
| | - S. Moro
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
- Department of Statistical Sciences, Sapienza University of Rome, Rome, Italy
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9
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Wannell GJ, Griffiths AM, Spinou A, Batista R, Mendonça MB, Wosiacki WB, Fraser B, Wintner S, Papadopoulos AI, Krey G, Gubili C. A new minibarcode assay to facilitate species identification from processed, degraded or historic ray (batoidea) samples. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01158-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Swenson JD, Klomp J, Fisher RA, Crow KD. How the Devil Ray Got Its Horns: The Evolution and Development of Cephalic Lobes in Myliobatid Stingrays (Batoidea: Myliobatidae). Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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11
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Fish FE, Kolpas A, Crossett A, Dudas MA, Moored KW, Bart-Smith H. Kinematics of swimming of the manta ray: three-dimensional analysis of open-water maneuverability. ACTA ACUST UNITED AC 2018; 221:jeb.166041. [PMID: 29487154 DOI: 10.1242/jeb.166041] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 02/13/2018] [Indexed: 01/25/2023]
Abstract
For aquatic animals, turning maneuvers represent a locomotor activity that may not be confined to a single coordinate plane, making analysis difficult, particularly in the field. To measure turning performance in a three-dimensional space for the manta ray (Mobula birostris), a large open-water swimmer, scaled stereo video recordings were collected. Movements of the cephalic lobes, eye and tail base were tracked to obtain three-dimensional coordinates. A mathematical analysis was performed on the coordinate data to calculate the turning rate and curvature (1/turning radius) as a function of time by numerically estimating the derivative of manta trajectories through three-dimensional space. Principal component analysis was used to project the three-dimensional trajectory onto the two-dimensional turn. Smoothing splines were applied to these turns. These are flexible models that minimize a cost function with a parameter controlling the balance between data fidelity and regularity of the derivative. Data for 30 sequences of rays performing slow, steady turns showed the highest 20% of values for the turning rate and smallest 20% of turn radii were 42.65±16.66 deg s-1 and 2.05±1.26 m, respectively. Such turning maneuvers fall within the range of performance exhibited by swimmers with rigid bodies.
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Affiliation(s)
- Frank E Fish
- Department of Biology, West Chester University, West Chester, PA 19383, USA
| | - Allison Kolpas
- Department of Mathematics, West Chester University, West Chester, PA 19383, USA
| | - Andrew Crossett
- Department of Mathematics, West Chester University, West Chester, PA 19383, USA
| | | | - Keith W Moored
- Department of Mechanical Engineering and Mechanics, Lehigh University, Bethlehem, PA 18015, USA
| | - Hilary Bart-Smith
- Department of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, VA 22904, USA
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12
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Duffy CAJ, Tindale SC. First observation of the courtship behaviour of the giant devil ray Mobula mobular (Myliobatiformes: Mobulidae). NEW ZEALAND JOURNAL OF ZOOLOGY 2018. [DOI: 10.1080/03014223.2017.1410850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Clinton A. J. Duffy
- Department of Conservation, Auckland, New Zealand
- Auckland War Memorial Museum, Auckland, New Zealand
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13
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Santillán-Lugo B, Llera-Herrera R, Corro-Espinosa D, Oñate-González EC, Rodríguez-Domínguez G, Saavedra-Sotelo NC. Complete mitochondrial genome of the Devil Ray, Mobula thurstoni (Lloyd, 1908) (Myliobatiformes: Myliobatidae). Mitochondrial DNA B Resour 2017; 2:868-870. [PMID: 33474015 PMCID: PMC7800197 DOI: 10.1080/23802359.2017.1407689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The Devil Ray (Mobula thurstoni) is a species with global distribution and is an important species in conservation terms, here we present its complete mitochondrial genome assembled with Illumina sequencing data. The circular genome was 17,610 bp in length, and consists of 13 protein-coding, two ribosomal RNAs (rRNAs), and 22 transfer RNA (tRNA) genes. Base composition is 30.7% A, 29.1% T, 26.5% C, and 13.7% G, and 40.2% GC content. Protein-coding genes present two start codon (ATG and GUG) and seven stop codon (UAA, AUA, UUU, UUA, AAU, CCU, and UAG). The control region possesses the highest A + T (66.6%) content among all mitochondrial regions. These data would contribute to the evolutionary studies of this genus, where there has been recent reclassification.
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Affiliation(s)
| | - Raúl Llera-Herrera
- Unidad en Acuicultura y Manejo Ambiental, CONACyT-Centro de Investigación en Alimentación y Desarrollo A. C., Mazatlán, Mexico
| | - David Corro-Espinosa
- Centro Regional de investigaciones Pesqueras de Mazatlán, Instituto Nacional de Pesca, Mazatlán, Mexico
| | - Erick C. Oñate-González
- Instituto de Ciencias del Mar y Limnología, Unidad Academica Mazatlan, Universidad Nacional Autónoma de México, Mazatlán, Mexico
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14
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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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15
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White WT, Corrigan S, Yang L, Henderson AC, Bazinet AL, Swofford DL, Naylor GJP. Phylogeny of the manta and devilrays (Chondrichthyes: mobulidae), with an updated taxonomic arrangement for the family. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx018] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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16
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Kornilios P. Polytomies, signal and noise: revisiting the mitochondrial phylogeny and phylogeography of the Eurasian blindsnake species complex (Typhlopidae, Squamata). ZOOL SCR 2017. [DOI: 10.1111/zsc.12243] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Panagiotis Kornilios
- Section of Animal Biology; Department of Biology; School of Natural Sciences; University of Patras; GR-26500 Patras Greece
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17
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Lawson JM, Fordham SV, O'Malley MP, Davidson LNK, Walls RHL, Heupel MR, Stevens G, Fernando D, Budziak A, Simpfendorfer CA, Ender I, Francis MP, Notarbartolo di Sciara G, Dulvy NK. Sympathy for the devil: a conservation strategy for devil and manta rays. PeerJ 2017; 5:e3027. [PMID: 28316882 PMCID: PMC5354073 DOI: 10.7717/peerj.3027] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 01/25/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND International trade for luxury products, medicines, and tonics poses a threat to both terrestrial and marine wildlife. The demand for and consumption of gill plates (known as Peng Yu Sai, "Fish Gill of Mobulid Ray") from devil and manta rays (subfamily Mobulinae, collectively referred to as mobulids) poses a significant threat to these marine fishes because of their extremely low productivity. The demand for these gill plates has driven an international trade supplied by largely unmonitored and unregulated catches from target and incidental fisheries around the world. Scientific research, conservation campaigns, and legal protections for devil rays have lagged behind those for manta rays despite similar threats across all mobulids. METHODS To investigate the difference in attention given to devil rays and manta rays, we examined trends in the scientific literature and updated species distribution maps for all mobulids. Using available information on target and incidental fisheries, and gathering information on fishing and trade regulations (at international, national, and territorial levels), we examined how threats and protective measures overlap with species distribution. We then used a species conservation planning approach to develop the Global Devil and Manta Ray Conservation Strategy, specifying a vision, goals, objectives, and actions to advance the knowledge and protection of both devil and manta rays. RESULTS AND DISCUSSION Our literature review revealed that there had been nearly 2.5-times more "manta"-titled publications, than "mobula" or "devil ray"-titled publications over the past 4.5 years (January 2012-June 2016). The majority of these recent publications were reports on occurrence of mobulid species. These publications contributed to updated Area of Occupancy and Extent of Occurrence maps which showed expanded distributions for most mobulid species and overlap between the two genera. While several international protections have recently expanded to include all mobulids, there remains a greater number of national, state, and territory-level protections for manta rays compared to devil rays. We hypothesize that there are fewer scientific publications and regulatory protections for devil rays due primarily to perceptions of charisma that favour manta rays. We suggest that the well-established species conservation framework used here offers an objective solution to close this gap. To advance the goals of the conservation strategy we highlight opportunities for parity in protection and suggest solutions to help reduce target and bycatch fisheries.
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Affiliation(s)
- Julia M Lawson
- Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University , Burnaby , British Columbia , Canada
| | - Sonja V Fordham
- Shark Advocates International, The Ocean Foundation , Washington , D.C. , United States of America
| | - Mary P O'Malley
- WildAid, San Francisco, CA, United States of America; Manta Trust, Dorchester, Dorset, United Kingdom
| | - Lindsay N K Davidson
- Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University , Burnaby , British Columbia , Canada
| | - Rachel H L Walls
- Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University , Burnaby , British Columbia , Canada
| | - Michelle R Heupel
- Australian Institute of Marine Science , Townsville , Queensland , Australia
| | - Guy Stevens
- Manta Trust, Dorchester, Dorset, United Kingdom; Environment Department, University of York, York, United Kingdom
| | - Daniel Fernando
- Manta Trust, Dorchester, Dorset, United Kingdom; Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden; Blue Resources, Colombo, Sri Lanka
| | - Ania Budziak
- Project AWARE Foundation , Rancho Santa Margarita , CA , United States of America
| | - Colin A Simpfendorfer
- Centre for Sustainable Tropical Fisheries and Aquaculture & College of Marine and Environmental Sciences, James Cook University , Townsville , Queensland , Australia
| | - Isabel Ender
- Manta Trust , Dorchester , Dorset , United Kingdom
| | - Malcolm P Francis
- National Institute of Water and Atmospheric Research , Wellington , New Zealand
| | | | - Nicholas K Dulvy
- Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University , Burnaby , British Columbia , Canada
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18
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Liang X, Tian X, Liu W, Wei T, Wang W, Dong Q, Wang B, Meng Y, Zhang R, Gleason ML, Sun G. Comparative analysis of the mitochondrial genomes of Colletotrichum gloeosporioides sensu lato: insights into the evolution of a fungal species complex interacting with diverse plants. BMC Genomics 2017; 18:171. [PMID: 28201983 PMCID: PMC5311727 DOI: 10.1186/s12864-016-3480-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fungal species complex Colletotrichum gloeosporioides sensu lato contains over 20 plant-interacting species. These species exhibit different life styles (e.g., endophytes, foliar and fruit pathogens) and show considerable variation in host and tissue adaptation strategies. Accurate species delimitation in C. gloeosporioides s.l. is very challenging due to nascent lineage boundaries and phenotypic plasticity, which strongly impedes studies of the complex's host-interaction biology. In this study, we first sequenced and compared nine mitogenomes belonging to four C. gloeosporioides s.l. species lineages (C. gloeosporioides, C. fructicola, C. aenigma, and C. siamense s.l.), and evaluated the usefulness of mitogenome sequence in complementing prevailing nuclear markers for species delimitation. RESULTS The C. gloeosporioides s.l. mitogenomes ranged between 52,671 and 58,666 bp in size, and each contained an identical set of genes transcribed in the same direction. Compared with previously reported Colletotrichum mitogenomes, these mitogenomes were uniquely featured by: (1) significantly larger genome size due to richer intron content and longer intergenic region; (2) striking GC content elevation at the intergenic region; and (3) considerable intron content variation among different species lineages. Compared with nuclear DNA markers commonly used in phylogeny, the mitogenome nucleotide diversity was extremely low, yet the mitogenome alignment contained the highest number of parsimony informative sites, which allowed the generation of a high-resolution phylogeny recognizing all taxonomic lineages, including ones belonging to the very nascent C. siamense s.l. complex. The tree topology was highly congruent with the phylogeny based on nuclear marker concatenation except for lineages within C. siamense s.l. Further comparative phylogenetic analysis indicated that lineage-specific rapid divergence of GS and SOD2 markers confounded concatenation-based species relationship inference. CONCLUSIONS This study sheds light on the evolution of C. gloeosporioides s.l. mitogenomes and demonstrates that mitogenome sequence can complement prevailing nuclear markers in improving species delimitation accuracy. The mitogenome sequences reported will be valuable resources for further genetic studies with C. gloeosporioides s.l. and other Colletotrichum species.
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Affiliation(s)
- Xiaofei Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Xianglin Tian
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Wenkui Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Tingyu Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Wei Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Qiuyue Dong
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Bo Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Yanan Meng
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Rong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Mark L. Gleason
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011 USA
| | - Guangyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
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19
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Cariani A, Messinetti S, Ferrari A, Arculeo M, Bonello JJ, Bonnici L, Cannas R, Carbonara P, Cau A, Charilaou C, El Ouamari N, Fiorentino F, Follesa MC, Garofalo G, Golani D, Guarniero I, Hanner R, Hemida F, Kada O, Lo Brutto S, Mancusi C, Morey G, Schembri PJ, Serena F, Sion L, Stagioni M, Tursi A, Vrgoc N, Steinke D, Tinti F. Improving the Conservation of Mediterranean Chondrichthyans: The ELASMOMED DNA Barcode Reference Library. PLoS One 2017; 12:e0170244. [PMID: 28107413 PMCID: PMC5249125 DOI: 10.1371/journal.pone.0170244] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/30/2016] [Indexed: 11/18/2022] Open
Abstract
Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles. Here we present results generated by the ELASMOMED Consortium, a regional network aiming to sample and DNA-barcode the Mediterranean Chondrichthyans with the ultimate goal to provide a comprehensive DNA barcode reference library. This library will support and improve the molecular taxonomy of this group and the effectiveness of management and conservation measures. We successfully barcoded 882 individuals belonging to 42 species (17 sharks, 24 batoids and one chimaera), including four endemic and several threatened ones. Morphological misidentifications were found across most orders, further confirming the need for a comprehensive DNA barcoding library as a valuable tool for the reliable identification of specimens in support of taxonomist who are reviewing current identification keys. Despite low intraspecific variation among their barcode sequences and reduced samples size, five species showed preliminary evidence of phylogeographic structure. Overall, the ELASMOMED initiative further emphasizes the key role accurate DNA barcoding libraries play in establishing reliable diagnostic species specific features in otherwise taxonomically problematic groups for biodiversity management and conservation actions.
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Affiliation(s)
- Alessia Cariani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Silvia Messinetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Alice Ferrari
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Marco Arculeo
- Department STEBICEF, University of Palermo, Palermo, Italy
| | | | | | - Rita Cannas
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | | | - Alessandro Cau
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Charis Charilaou
- Department of Fisheries and Marine Research, Ministry of Agriculture, Rural Development and Environment, Nicosia, Republic of Cyprus
| | - Najib El Ouamari
- Centre Régional de Institut National Recherche Halieutique, Nador, Morocco
| | - Fabio Fiorentino
- Institute for Coastal Marine Environment (IAMC) National Research Council (CNR), Mazara del Vallo, Italy
| | | | - Germana Garofalo
- Institute for Coastal Marine Environment (IAMC) National Research Council (CNR), Mazara del Vallo, Italy
| | - Daniel Golani
- Department of Evolution, Systematics and Ecology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ilaria Guarniero
- Department DIMEVET, University of Bologna, Ozzano dell'Emilia, Italy
| | - Robert Hanner
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Farid Hemida
- Ecole Nationale Superieure des Sciences de la Mer et d'Amenagement du Littoral, Campus Universitaire de Dely Ibrahim, Alger, Algeria
| | - Omar Kada
- Centre Régional de Institut National Recherche Halieutique, Nador, Morocco
| | | | - Cecilia Mancusi
- Regional Agency for Environmental Protection-Toscana (ARPAT), Livorno, Italy
| | | | | | - Fabrizio Serena
- Regional Agency for Environmental Protection-Toscana (ARPAT), Livorno, Italy
| | - Letizia Sion
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Marco Stagioni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
| | - Angelo Tursi
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Nedo Vrgoc
- Institute of Oceanography and Fisheries, Split, Croatia
| | - Dirk Steinke
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Fausto Tinti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Ravenna, Italy
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20
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Zeng Y, Wu Z, Zhang C, Meng Z, Jiang Z, Zhang J. DNA barcoding of Mobulid Ray Gill Rakers for Implementing CITES on Elasmobranch in China. Sci Rep 2016; 6:37567. [PMID: 27876850 PMCID: PMC5120345 DOI: 10.1038/srep37567] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 11/01/2016] [Indexed: 11/08/2022] Open
Abstract
The Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) has been counted on for conserving threatened marine fish since it regulates the commercial international trade of these species. Implementation of the international treaty for Mantas included on CITES Appendix II is challenging due to insufficient information on species identification and markets management. To fill the gap in such aspects, we identified five species of Mobulid rays (Mobula spps. and Manta spp) by using COI and NADH2 mtDNA markers in dried ray gill rakers from Chinese markets, namely, Mobula japonica (representing 54.8% of the sample set), M. tarapacana (14.4%), M. kuhlii (13.3%), M. thurstoni (6.4%), along with Manta birostris (11.2%; CITES Appendix II). The utilization and conservation statuses of these species were discussed. Based on combination of DNA barcodes and key morphological characters, we developed a three-step process for identifying the gill rakers of Mobulid rays which has been adopted by frontline enforcement in China. We hope that our work can serve as a foundation and basis to reinforce objectives of international treaties, regulation of consumer-driven markets, regional cooperation, and national fishery management on endangered elasmobranchs in China as well as related countries.
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Affiliation(s)
- Yan Zeng
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Endangered Species Scientific Commission, People’s Republic of China, Beijing 100101, China
| | - Zhongze Wu
- CITES Management Authority, People’s Republic of China, Beijing, 100714, China
| | - Chunguang Zhang
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhibin Meng
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Endangered Species Scientific Commission, People’s Republic of China, Beijing 100101, China
| | - Zhigang Jiang
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Endangered Species Scientific Commission, People’s Republic of China, Beijing 100101, China
| | - Jie Zhang
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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21
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Hinojosa-Alvarez S, Walter RP, Diaz-Jaimes P, Galván-Magaña F, Paig-Tran EM. A potential third Manta Ray species near the Yucatán Peninsula? Evidence for a recently diverged and novel genetic Manta group from the Gulf of Mexico. PeerJ 2016; 4:e2586. [PMID: 27833795 PMCID: PMC5101608 DOI: 10.7717/peerj.2586] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 09/20/2016] [Indexed: 11/29/2022] Open
Abstract
We present genetic and morphometric support for a third, distinct, and recently diverged group of Manta ray that appears resident to the Yucatán coastal waters of the Gulf of Mexico. Individuals of the genus Manta from Isla Holbox are markedly different from the other described manta rays in their morphology, habitat preference, and genetic makeup. Herein referred to as the Yucatán Manta Ray, these individuals form two genetically distinct groups: (1) a group of mtDNA haplotypes divergent (0.78%) from the currently recognized Manta birostris and M. alfredi species, and (2) a group possessing mtDNA haplotypes of M. birostris and highly similar haplotypes. The latter suggests the potential for either introgressive hybridization between Yucatán Manta Rays and M. birostris, or the retention of ancestral M. birostris signatures among Yucatán Manta Rays. Divergence of the genetically distinct Yucatán Manta Ray from M. birostris appears quite recent (<100,000 YBP) following fit to an Isolation-with-Migration model, with additional support for asymmetrical gene flow from M. birostris into the Yucatán Manta Ray. Formal naming of the Yucatán Manta Ray cannot yet be assigned until an in-depth taxonomic study and further confirmation of the genetic identity of existing type specimens has been performed.
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Affiliation(s)
- Silvia Hinojosa-Alvarez
- Posgrado en Ciencias del Mar y Limnología/Laboratorio de Genética de Organismos Acuáticos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico; Instituto de Biotecnología, Chamilpa, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Ryan P Walter
- Department of Biological Science, California State University , Fullerton , CA , United States
| | - Pindaro Diaz-Jaimes
- Instituto de Ciencias del Mar y Limnología, Unidad Académica de Ecología y Biodiversidad Acuática, Laboratorio de Genética de Organismos Acuáticos, Universidad Nacional Autónoma de México , Ciudad de México , Mexico
| | - Felipe Galván-Magaña
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas , La Paz , Baja California Sur , México
| | - E Misty Paig-Tran
- Department of Biological Science, California State University , Fullerton , CA , United States
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22
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Growth, productivity, and relative extinction risk of a data-sparse devil ray. Sci Rep 2016; 6:33745. [PMID: 27658342 PMCID: PMC5034314 DOI: 10.1038/srep33745] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 09/01/2016] [Indexed: 11/23/2022] Open
Abstract
Devil rays (Mobula spp.) face intensifying fishing pressure to meet the ongoing international demand for gill plates. The paucity of information on growth, mortality, and fishing effort for devil rays make quantifying population growth rates and extinction risk challenging. Furthermore, unlike manta rays (Manta spp.), devil rays have not been listed on CITES. Here, we use a published size-at-age dataset for the Spinetail Devil Ray (Mobula japanica), to estimate somatic growth rates, age at maturity, maximum age, and natural and fishing mortality. We then estimate a plausible distribution of the maximum intrinsic population growth rate (rmax) and compare it to 95 other chondrichthyans. We find evidence that larger devil ray species have low somatic growth rate, low annual reproductive output, and low maximum population growth rates, suggesting they have low productivity. Fishing rates of a small-scale artisanal Mexican fishery were comparable to our estimate of rmax, and therefore probably unsustainable. Devil ray rmax is very similar to that of manta rays, indicating devil rays can potentially be driven to local extinction at low levels of fishing mortality and that a similar degree of protection for both groups is warranted.
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23
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Stewart JD, Hoyos-Padilla EM, Kumli KR, Rubin RD. Deep-water feeding and behavioral plasticity in Manta birostris revealed by archival tags and submersible observations. ZOOLOGY 2016; 119:406-413. [PMID: 27461910 DOI: 10.1016/j.zool.2016.05.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/07/2016] [Accepted: 05/24/2016] [Indexed: 11/29/2022]
Abstract
Foraging drives many fundamental aspects of ecology, and an understanding of foraging behavior aids in the conservation of threatened species by identifying critical habitats and spatial patterns relevant to management. The world's largest ray, the oceanic manta (Manta birostris) is poorly studied and threatened globally by targeted fisheries and incidental capture. Very little information is available on the natural history, ecology and behavior of the species, complicating management efforts. This study provides the first data on the diving behavior of the species based on data returned from six tagged individuals, and an opportunistic observation from a submersible of a manta foraging at depth. Pop-off archival satellite tags deployed on mantas at the Revillagigedo Archipelago, Mexico recorded seasonal shifts in diving behavior, likely related to changes in the location and availability of zooplankton prey. Across seasons, mantas spent a large proportion of their time centered around the upper limit of the thermocline, where zooplankton often aggregate. Tag data reveal a gradual activity shift from surface waters to 100-150m across the tagging period, possibly indicating a change in foraging behavior from targeting surface-associated zooplankton to vertical migrators. The depth ranges accessed by mantas in this study carry variable bycatch risks from different fishing gear types. Consequently, region-specific data on diving behavior can help inform local management strategies that reduce or mitigate bycatch of this vulnerable species.
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Affiliation(s)
- Joshua D Stewart
- Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA; The Manta Trust, Catemwood House, Corscombe, Dorchester, Dorset, DT2 0NT, UK.
| | - Edgar Mauricio Hoyos-Padilla
- Pelagios Kakunja A.C., Sinaloa 1540, Las Garzas, 23070, La Paz, Baja California Sur, Mexico; Fins Attached, 19675 Still Glen Drive, Colorado Springs, CO 80908, USA
| | - Katherine R Kumli
- Pacific Manta Research Group, University of California Davis Bodega Marine Laboratory, 2099 Westshore Rd., Bodega Bay, CA 94923, USA
| | - Robert D Rubin
- Pacific Manta Research Group, University of California Davis Bodega Marine Laboratory, 2099 Westshore Rd., Bodega Bay, CA 94923, USA; Santa Rosa Junior College, 1501 Mendocino Ave, Santa Rosa, CA 95401, USA
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24
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Cunha CM, Oliveira LE, Kfoury JR. Comparative anatomy of the extraocular muscles in four Myliobatoidei rays (Batoidea, Myliobatiformes). J Anat 2016; 228:877-86. [PMID: 26853799 PMCID: PMC4831342 DOI: 10.1111/joa.12438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2015] [Indexed: 11/30/2022] Open
Abstract
Extraocular muscles are classically grouped as four rectus and two oblique muscles. However, their description and potential associations with species behavior are limited. The objective was to characterize extraocular muscles in four Myliobatoidei rays from diverse habitats with divergent behaviors. Heads (10 per species) of Dasyatis hypostigma, Gymnura altavela, Mobula thurstoni and Pteroplatytrygon violacea were decalcified and dissected to characterize and describe extraocular muscles. Principal component analysis (PCA) was used to evaluate relationships between muscle length and species; for P. violacea, D. hypostigma and G. altavela, these were qualitatively and quantitatively consistent with the general pattern of extraocular muscles in vertebrates. In contrast, for M. thurstoni, the two oblique muscles were completely fused and there was a seventh extraocular muscle, named m. lateral rectus β (both were apparently novel findings in this species). There were also significant differences in eye disposition in the chondrocranium. The PCA axis 1 (rectus muscles) and PCA axis 2 (oblique muscles) accounted for 98.47% of data variability. Extraocular muscles had significant differences in length and important anatomical differences among sampled species that facilitated grouping species according to their life history. In conclusion, extraocular muscles are not uniform in all vertebrate species, thereby providing another basis for comparative studies.
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Affiliation(s)
- Carlo M Cunha
- Academy of Natural Sciences, Philadelphia, PA, USA
- Capes Foundation, Ministry of Education of Brazil, Brasília, DF, Brazil
| | - Luciano E Oliveira
- Ecology and Environmental Resources Post Graduation Program, Uberlândia Federal University, Uberlândia, MG, Brazil
| | - José R Kfoury
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of São Paulo, SP, São Paulo, Brazil
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25
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Gaitán-Espitia JD, Solano-Iguaran JJ, Tejada-Martinez D, Quintero-Galvis JF. Mitogenomics of electric rays: evolutionary considerations within Torpediniformes (Batoidea; Chondrichthyes). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12417] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Juan Diego Gaitán-Espitia
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- CSIRO Oceans & Atmosphere; GPO Box 1538 Hobart 7001 TAS Australia
| | - Jaiber J. Solano-Iguaran
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- Programa de Magister en Ciencias mención Genética; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
| | - Daniela Tejada-Martinez
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- Programa de Doctorado en Ciencias mención Ecología y Evolución; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
| | - Julian F. Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- Programa de Magister en Ciencias mención Genética; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
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26
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Bustamante C, Barría C, Vargas-Caro C, Ovenden JR, Bennett MB. The phylogenetic position of the giant devil ray Mobula mobular (Bonnaterre, 1788) (Myliobatiformes, Myliobatidae) inferred from the mitochondrial genome. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3540-1. [PMID: 26260171 DOI: 10.3109/19401736.2015.1074208] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The giant devil ray, Mobula mobular, is a member of one of the most distinct groups of cartilaginous fishes, the Mobulidae (manta and devil rays), and is the only mobulid assessed as Endangered due its restricted distribution, high bycatch mortality and suspected population decline. The complete mitochondrial genome is 18 913 base pairs in length and comprises 2 rRNAs, 13 protein-coding genes, 22 tRNAs and 2 non-coding regions. Comparison with the partial mitogenome of M. japanica suggests a sister-cryptic species complex and two different taxonomic units. However, the limited divergence within the species (>99.9% genetic identity) may be the result of a geographically and numerically restricted population of M. mobular within the Mediterranean Sea.
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Affiliation(s)
- Carlos Bustamante
- a School of Biomedical Sciences, The University of Queensland , St Lucia , Queensland , Australia .,b Molecular Fisheries Laboratory, The University of Queensland , St Lucia , Queensland , Australia , and
| | - Claudio Barría
- c Institut de Ciències del Mar (ICM-CSIC) , Barcelona , Spain
| | - Carolina Vargas-Caro
- a School of Biomedical Sciences, The University of Queensland , St Lucia , Queensland , Australia .,b Molecular Fisheries Laboratory, The University of Queensland , St Lucia , Queensland , Australia , and
| | - Jennifer R Ovenden
- b Molecular Fisheries Laboratory, The University of Queensland , St Lucia , Queensland , Australia , and
| | - Michael B Bennett
- a School of Biomedical Sciences, The University of Queensland , St Lucia , Queensland , Australia
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27
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Austin CM, Tan MH, Croft LJ, Meekan MG, Gan HY, Gan HM. The complete mitogenome of the bluespotted ribbontail ray Taeniura lymma (Forsskål, 1775) (Elasmobranchii: Myliobatiformes: Dasyatidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3205-7. [DOI: 10.3109/19401736.2015.1007348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Christopher M. Austin
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia,
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia,
| | - Mun Hua Tan
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia,
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia,
| | - Laurence J. Croft
- Malaysian Genomics Resource Centre Berhad, Boulevard Signature Office, Mid Valley City, Kuala Lumpur, Malaysia, and
| | - Mark G. Meekan
- Australian Institute of Marine Science, UWA Oceans Institute, Crawley, Western Australia, Australia
| | - Huan You Gan
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia,
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia,
| | - Han Ming Gan
- Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, Bandar Sunway, Petaling Jaya, Selangor, Malaysia,
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia,
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