587 results on '"Naylor, Gavin J. P."'
Search Results
2. Chimaera compacta, a new species from southern Indian Ocean, and an estimate of phylogenetic relationships within the genus Chimaera (Chondrichthyes: Chimaeridae)
- Author
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Iglésias, Samuel P., Kemper, Jenny M., and Naylor, Gavin J. P.
- Published
- 2022
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3. The appendicular skeleton of the enigmatic shark Leptocharias smithii in comparison with other sharks of the order Carcharhiniformes (Elasmobranchii: Leptochariidae)
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Capretz Batista Da Silva, João Paulo, primary, Medeiros, Jade, additional, Araújo, Marcus Vinícius Gonçalves, additional, Lima, Danilo Pinto, additional, Mianutti, Laura Franco, additional, Mafaldo, Henrique, additional, De Lima, Arthur, additional, and Naylor, Gavin J. P., additional
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- 2024
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4. Towards complete and error-free genome assemblies of all vertebrate species
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Rhie, Arang, McCarthy, Shane A., Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Ko, Byung June, Chaisson, Mark, Gedman, Gregory L., Cantin, Lindsey J., Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, Smith, Michelle, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C., Lama, Tanya M., Grutzner, Frank, Warren, Wesley C., Balakrishnan, Christopher N., Burt, Dave, George, Julia M., Biegler, Matthew T., Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Meyer, Axel, Kautt, Andreas F., Franchini, Paolo, Detrich, III, H. William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin J. P., Pippel, Martin, Malinsky, Milan, Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T., Pesout, Trevor, Houck, Marlys, Misuraca, Ann, Kingan, Sarah B., Hall, Richard, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E., Putnam, Nicholas H., Gut, Ivo, Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Wood, Jonathan, Dagnew, Robel E., Guan, Dengfeng, London, Sarah E., Clayton, David F., Mello, Claudio V., Friedrich, Samantha R., Lovell, Peter V., Osipova, Ekaterina, Al-Ajli, Farooq O., Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S., Makova, Kateryna D., Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P., Kwak, Woori, Clawson, Hiram, Diekhans, Mark, Nassar, Luis, Paten, Benedict, Kraus, Robert H. S., Crawford, Andrew J., Gilbert, M. Thomas P., Zhang, Guojie, Venkatesh, Byrappa, Murphy, Robert W., Koepfli, Klaus-Peter, Shapiro, Beth, Johnson, Warren E., Di Palma, Federica, Marques-Bonet, Tomas, Teeling, Emma C., Warnow, Tandy, Graves, Jennifer Marshall, Ryder, Oliver A., Haussler, David, O’Brien, Stephen J., Korlach, Jonas, Lewin, Harris A., Howe, Kerstin, Myers, Eugene W., Durbin, Richard, Phillippy, Adam M., and Jarvis, Erich D.
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- 2021
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5. Dichichthyidae, a New Family of Deepwater Sharks (Carcharhiniformes) from the Indo–West Pacific, with Description of a New Species
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White, William T., primary, Stewart, Andrew L., additional, O’Neill, Helen L., additional, and Naylor, Gavin J. P., additional
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- 2024
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6. Cover Image
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Byrum, Steven R., primary, Frazier, Bryan S., additional, Grubbs, R. Dean, additional, Naylor, Gavin J. P., additional, and Fraser, Gareth J., additional
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- 2024
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7. Mitogenomic evidence of population differentiation of thorny skate, Amblyraja radiata, in the North Atlantic
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Denton, John S. S., primary, Kneebone, Jeff, additional, Yang, Lei, additional, Lynghammar, Arve, additional, McElroy, David, additional, Corrigan, Shannon, additional, Jakobsdóttir, Klara, additional, Miri, Carolyn, additional, Simpson, Mark, additional, and Naylor, Gavin J. P., additional
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- 2024
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8. How many lineages are there of the stingrays genus Hypanus (Myliobatiformes: Dasyatidae) and why does it matter?
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Petean, Flávia F., primary, Yang, Lei, additional, Corrigan, Shannon, additional, Lima, Sergio M. Q., additional, and Naylor, Gavin J. P., additional
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- 2024
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9. A DNA sequence-based approach to the identification of shark and ray species and its implications for global elasmobranch diversity and parasitology
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Naylor, Gavin J. P., Caira, Janine N., 1957, Jensen, K. (Kirsten), 1971, Rosana, K. A. M., White, William T. (William Toby), 1977, Last, P. R., American Museum of Natural History Library, Naylor, Gavin J. P., Caira, Janine N., 1957, Jensen, K. (Kirsten), 1971, Rosana, K. A. M., White, William T. (William Toby), 1977, and Last, P. R.
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Chondrichthyes ,Classification ,coevolution ,Fishes ,Genetics ,Geographical distribution ,Host-parasite relationships ,Identification ,marine biodiversity ,mitochondrial DNA ,Molecular aspects ,NAD (Coenzyme) ,Nucleotide sequence ,Parasites ,Phylogeny ,Rays (Fishes) ,Sharks ,Variation - Published
- 2012
10. Global genetic diversity and historical demography of the Bull Shark.
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Postaire, Bautisse D., Devloo‐Delva, Floriaan, Brunnschweiler, Juerg M., Charvet, Patricia, Chen, Xiao, Cliff, Geremy, Daly, Ryan, Drymon, J. Marcus, Espinoza, Mario, Fernando, Daniel, Glaus, Kerstin, Grant, Michael I., Hernandez, Sebastian, Hyodo, Susumu, Jabado, Rima W., Jaquemet, Sébastien, Johnson, Grant, Naylor, Gavin J. P., Nevill, John E. G., and Pathirana, Buddhi M.
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DEMOGRAPHY ,GENETIC variation ,PREDATORY aquatic animals ,WHOLE genome sequencing ,SHARKS ,NUCLEOTIDE sequencing ,MOBILE genetic elements - Abstract
Aim: Biogeographic boundaries and genetic structuring have important effects on the inferences and interpretation of effective population size (Ne) temporal variations, a key genetics parameter. We reconstructed the historical demography and divergence history of a vulnerable coastal high‐trophic shark using population genomics and assessed our ability to detect recent bottleneck events. Location: Western and Central Indo‐Pacific (IPA), Western Tropical Atlantic (WTA) and Eastern Tropical Pacific (EPA). Taxon: Carcharhinus leucas (Müller & Henle, 1839). Methods: A DArTcap™ approach was used to sequence 475 samples and assess global genetic structuring. Three demographic models were tested on each population, using an ABC‐RF framework coupled with coalescent simulations, to investigate within‐cluster structure. Divergence times between clusters were computed, testing multiple scenarios, with fastsimcoal. Ne temporal variations were reconstructed with STAIRWAYPLOT. Coalescent simulations were performed to determine the detectability of recent bottleneck under the estimated historical trend for datasets of this size. Results: Three genetic clusters corresponding to the IPA, WTA and EPA regions were identified, agreeing with previous studies. The IPA presented the highest genetic diversity and was consistently identified as the oldest. No significant within‐cluster structuring was detected. Ne increased globally, with an earlier onset in the IPA, during the last glacial period. Coalescent simulations showed that weak and recent bottlenecks could not be detected with our dataset, while old and/or strong bottlenecks would erase the observed ancestral expansion. Main Conclusions: This study further confirms the role of marine biogeographic breaks in shaping the genetic history of large mobile marine predators. Ne historical increases in Ne are potentially linked to extended coastal habitat availability. The limited within‐cluster population structuring suggests that Ne can be monitored over ocean basins. Due to insufficient amount of available genetic data, it cannot be concluded whether overfishing is impacting Bull Shark genetic diversity, calling for whole‐genome sequencing. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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11. The Indo-Pacific Stingray Genus Brevitrygon (Myliobatiformes: Dasyatidae): Clarification of Historical Names and Description of a New Species, B. manjajiae sp. nov., from the Western Indian Ocean
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Last, Peter R., primary, Weigmann, Simon, additional, and Naylor, Gavin J. P., additional
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- 2023
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12. Global genetic diversity and historical demography of the Bull Shark
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Postaire, Bautisse D., primary, Devloo‐Delva, Floriaan, additional, Brunnschweiler, Juerg M., additional, Charvet, Patricia, additional, Chen, Xiao, additional, Cliff, Geremy, additional, Daly, Ryan, additional, Drymon, J. Marcus, additional, Espinoza, Mario, additional, Fernando, Daniel, additional, Glaus, Kerstin, additional, Grant, Michael I., additional, Hernandez, Sebastian, additional, Hyodo, Susumu, additional, Jabado, Rima W., additional, Jaquemet, Sébastien, additional, Johnson, Grant, additional, Naylor, Gavin J. P., additional, Nevill, John E. G., additional, Pathirana, Buddhi M., additional, Pillans, Richard D., additional, Smoothey, Amy F., additional, Tachihara, Katsunori, additional, Tillet, Bree J., additional, Valerio‐Vargas, Jorge A., additional, Lesturgie, Pierre, additional, Magalon, Hélène, additional, Feutry, Pierre, additional, and Mona, Stefano, additional
- Published
- 2023
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13. Demographic inferences after a range expansion can be biased: the test case of the blacktip reef shark (Carcharhinus melanopterus)
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Maisano Delser, Pierpaolo, Corrigan, Shannon, Duckett, Drew, Suwalski, Arnaud, Veuille, Michel, Planes, Serge, Naylor, Gavin J. P., and Mona, Stefano
- Published
- 2019
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14. First complete description of the dark-mouth skate Raja arctowskii Dollo, 1904 from Antarctic waters, assigned to the genus Bathyraja (Elasmobranchii, Rajiformes, Arhynchobatidae)
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Stehmann, Matthias F. W., Weigmann, Simon, and Naylor, Gavin J. P.
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- 2021
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15. Embryonic development in the bonnethead (Sphyrna tiburo), a viviparous hammerhead shark
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Byrum, Steven R., primary, Frazier, Bryan S., additional, Grubbs, R. Dean, additional, Naylor, Gavin J. P., additional, and Fraser, Gareth J., additional
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- 2023
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16. Embryonic development in the bonnethead (Sphyrna tiburo), a viviparous hammerhead shark.
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Byrum, Steven R., Frazier, Bryan S., Grubbs, R. Dean, Naylor, Gavin J. P., and Fraser, Gareth J.
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CHONDRICHTHYES ,ANIMAL diversity ,EMBRYOLOGY ,HAMMERHEAD sharks ,SHARKS ,EVOLUTIONARY developmental biology - Abstract
Background: The hammerhead sharks (family Sphyrnidae) are an immediately recognizable group of sharks due to their unique head shape. Though there has long been an interest in hammerhead development, there are currently no explicit staging tables published for any members of the group. The bonnethead Sphyrna tiburo is the smallest member of Sphyrnidae and is abundant in estuarine and nearshore waters in the Gulf of Mexico and Western North Atlantic Ocean. Due to their relative abundance, close proximity to shore, and brief gestation period, it has been possible to collect and document multiple embryonic specimens at progressive stages of development. Results: We present the first comprehensive embryonic staging series for the Bonnethead, a viviparous hammerhead shark. Our stage series covers a period of development from stages that match the vertebrate phylotypic period, from Stage 23, through stages of morphological divergence to complete development at birth—Stage 35). Notably, we use a variety of techniques to document crucial stages that lead to their extreme craniofacial diversity, resulting in the formation of one of the most distinctive characters of any shark species, the cephalofoil or hammer‐like head. Conclusion: Documenting the development of hard‐to‐access vertebrates, like this viviparous shark species, offers important information about how new and diverse morphologies arise that otherwise may remain poorly studied. This work will serve as a platform for future comparative developmental research both within sharks and across the phylogeny of vertebrates, underpinning the extreme potential of craniofacial development and morphological diversity in vertebrate animals. Key Findings: A staging series for one of the smallest hammerhead species.Observing the developmental timing and growth of fins and cephalofoil in hammerheads.This work will serve as a platform for future comparative developmental research both with hammerhead sharks and across chondrichthyan fishes. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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17. Identifying isolated shark teeth of the genus Carcharhinus to species : relevance for tracking phyletic change through the fossil record
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Naylor, Gavin J. P., Marcus, Leslie Floyd, 1930-2002, American Museum of Natural History Library, Naylor, Gavin J. P., and Marcus, Leslie Floyd, 1930-2002
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Anatomy ,Carcharhinus ,Classification ,Fishes ,Sharks ,Teeth - Published
- 1994
18. From rivers to ocean basins: The role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator
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Devloo‐delva, Floriaan, Burridge, Christopher P., Kyne, Peter M., Brunnschweiler, Juerg M., Chapman, Demian D., Charvet, Patricia, Chen, Xiao, Cliff, Geremy, Daly, Ryan, Drymon, J. Marcus, Espinoza, Mario, Fernando, Daniel, Barcia, Laura Garcia, Glaus, Kerstin, González‐garza, Blanca I., Grant, Michael I., Gunasekera, Rasanthi M., Hernandez, Sebastian, Hyodo, Susumu, Jabado, Rima W., Jaquemet, Sébastien, Johnson, Grant, Ketchum, James T., Magalon, Hélène, Marthick, James R., Mollen, Frederik H., Mona, Stefano, Naylor, Gavin J. P., Nevill, John E. G., Phillips, Nicole M., Pillans, Richard D., Postaire, Bautisse D., Smoothey, Amy F., Tachihara, Katsunori, Tillet, Bree J., Valerio‐vargas, Jorge A., Feutry, Pierre, Devloo‐delva, Floriaan, Burridge, Christopher P., Kyne, Peter M., Brunnschweiler, Juerg M., Chapman, Demian D., Charvet, Patricia, Chen, Xiao, Cliff, Geremy, Daly, Ryan, Drymon, J. Marcus, Espinoza, Mario, Fernando, Daniel, Barcia, Laura Garcia, Glaus, Kerstin, González‐garza, Blanca I., Grant, Michael I., Gunasekera, Rasanthi M., Hernandez, Sebastian, Hyodo, Susumu, Jabado, Rima W., Jaquemet, Sébastien, Johnson, Grant, Ketchum, James T., Magalon, Hélène, Marthick, James R., Mollen, Frederik H., Mona, Stefano, Naylor, Gavin J. P., Nevill, John E. G., Phillips, Nicole M., Pillans, Richard D., Postaire, Bautisse D., Smoothey, Amy F., Tachihara, Katsunori, Tillet, Bree J., Valerio‐vargas, Jorge A., and Feutry, Pierre
- Abstract
The Bull Shark (Carcharhinus leucas) faces varying levels of exploitation around the world due to its coastal distribution. Information regarding population connectivity is crucial to evaluate its conservation status and local fishing impacts. In this study, we sampled 922 putative Bull Sharks from 19 locations in the first global assessment of population structure of this cosmopolitan species. Using a recently developed DNA-capture approach (DArTcap), samples were genotyped for 3400 nuclear markers. Additionally, full mitochondrial genomes of 384 Indo-Pacific samples were sequenced. Reproductive isolation was found between and across ocean basins (eastern Pacific, western Atlantic, eastern Atlantic, Indo-West Pacific) with distinct island populations in Japan and Fiji. Bull Sharks appear to maintain gene flow using shallow coastal waters as dispersal corridors, whereas large oceanic distances and historical land-bridges act as barriers. Females tend to return to the same area for reproduction, making them more susceptible to local threats and an important focus for management actions. Given these behaviors, the exploitation of Bull Sharks from insular populations, such as Japan and Fiji, may instigate local decline that cannot readily be replenished by immigration, which can in turn affect ecosystem dynamics and functions. These data also supported the development of a genetic panel to ascertain the population of origin, which will be useful in monitoring the trade of fisheries products and assessing population-level impacts of this harvest.
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- 2023
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19. Genetic and phenotypic diversity in the wedgefish Rhynchobatus australiae , a threatened ray of high value in the shark fin trade
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Giles, Jenny L., Riginos, Cynthia, Naylor, Gavin J. P., and Ovenden, Jennifer R.
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- 2016
20. A bizarre Eocene dasyatoid batomorph (Elasmobranchii, Myliobatiformes) from the Bolca Lagerstätte (Italy) reveals a new, extinct body plan for stingrays
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Marramà, Giuseppe, Carnevale, Giorgio, Giusberti, Luca, Naylor, Gavin J. P., and Kriwet, Jürgen
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- 2019
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21. Mosaic of plesiomorphic and derived characters in an Eocene myliobatiform batomorph (Chondrichthyes, Elasmobranchii) from Italy defines a new, basal body plan in pelagic stingrays
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Marramà, Giuseppe, Carnevale, Giorgio, Naylor, Gavin J. P., and Kriwet, Jürgen
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- 2019
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22. Systematics and Phylogenetic Interrelationships of the Enigmatic Late Jurassic Shark Protospinax annectans Woodward, 1918 with Comments on the Shark–Ray Sister Group Relationship
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Jambura, Patrick L., primary, Villalobos-Segura, Eduardo, additional, Türtscher, Julia, additional, Begat, Arnaud, additional, Staggl, Manuel Andreas, additional, Stumpf, Sebastian, additional, Kindlimann, René, additional, Klug, Stefanie, additional, Lacombat, Frederic, additional, Pohl, Burkhard, additional, Maisey, John G., additional, Naylor, Gavin J. P., additional, and Kriwet, Jürgen, additional
- Published
- 2023
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23. From rivers to ocean basins: The role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator
- Author
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Devloo‐Delva, Floriaan, primary, Burridge, Christopher P., additional, Kyne, Peter M., additional, Brunnschweiler, Juerg M., additional, Chapman, Demian D., additional, Charvet, Patricia, additional, Chen, Xiao, additional, Cliff, Geremy, additional, Daly, Ryan, additional, Drymon, J. Marcus, additional, Espinoza, Mario, additional, Fernando, Daniel, additional, Barcia, Laura Garcia, additional, Glaus, Kerstin, additional, González‐Garza, Blanca I., additional, Grant, Michael I., additional, Gunasekera, Rasanthi M., additional, Hernandez, Sebastian, additional, Hyodo, Susumu, additional, Jabado, Rima W., additional, Jaquemet, Sébastien, additional, Johnson, Grant, additional, Ketchum, James T., additional, Magalon, Hélène, additional, Marthick, James R., additional, Mollen, Frederik H., additional, Mona, Stefano, additional, Naylor, Gavin J. P., additional, Nevill, John E. G., additional, Phillips, Nicole M., additional, Pillans, Richard D., additional, Postaire, Bautisse D., additional, Smoothey, Amy F., additional, Tachihara, Katsunori, additional, Tillet, Bree J., additional, Valerio‐Vargas, Jorge A., additional, and Feutry, Pierre, additional
- Published
- 2023
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24. DNA capture reveals transoceanic gene flow in endangered river sharks
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Li, Chenhong, Corrigan, Shannon, Yang, Lei, Straube, Nicolas, Harris, Mark, Hofreiter, Michael, White, William T., and Naylor, Gavin J. P.
- Published
- 2015
25. Can We Identify Genes with Increased Phylogenetic Reliability?
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Doyle, Vinson P., Young, Randee E., Naylor, Gavin J. P., and Brown, Jeremy M.
- Published
- 2015
26. Revision of the Western Indian Ocean Angel Sharks, Genus Squatina (Squatiniformes, Squatinidae), with Description of a New Species and Redescription of the African Angel Shark Squatina africana Regan, 1908.
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Weigmann, Simon, Vaz, Diego F. B., Akhilesh, K. V., Leeney, Ruth H., and Naylor, Gavin J. P.
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SHARKS ,BIRTH size ,ENDANGERED species ,OCEAN ,SPECIES ,FISH morphology ,SKELETON - Abstract
Simple Summary: Angel sharks (genus Squatina) are small- to medium-sized sharks with flattened bodies, that live on the seafloor. Until now, 23 valid species of angel sharks have been identified around the world, of which over half are thought to be facing a moderate to severe risk of extinction. Several juvenile angel sharks were collected by researchers working on the Mascarene Plateau, an elevated area of seabed in the Indian Ocean, in 1988 and 1989. They appeared different in coloration and in body shape and structure to a species known from East Africa and Madagascar, the African angel shark. Additional angel sharks were caught off the western coast of India in 2016 and in the central western Indian Ocean in 2017, including adult individuals. Information on body measurements and skeleton structure were collected, and genetic analyses were also conducted on these sharks and on museum specimens previously identified as African angel sharks. The results indicated that the specimens collected from the Mascarene Plateau and off southwestern India were a species that is new to science. It is genetically and morphologically distinct from the African angel shark; is smaller when born and when fully grown; and lives in a distinctly different area. The newly described species has been named Lea's angel shark. Sampling efforts on the Saya de Malha Bank (part of the Mascarene Plateau, western Indian Ocean) unveiled three unusual small juvenile angel shark specimens, that were a much paler color than the only known western Indian Ocean species, Squatina africana Regan, 1908. However, it took many years before further specimens, including adults of both sexes, and tissue samples were collected. The present manuscript contains a redescription of S. africana based on the holotype and additional material, as well as the formal description of the new species of Squatina. All specimens of the new species, hereafter referred to as Squatina leae sp. nov., were collected in the western Indian Ocean off southwestern India and on the Mascarene Plateau at depths of 100–500 m. The new species differs from S. africana in a number of characteristics including its coloration when fresh, smaller size at birth, size at maturity, and adult size, genetic composition, and distribution. Taxonomic characteristics include differences in the morphology of the pectoral skeleton and posterior nasal flap, denticle arrangement and morphology, vertebral counts, trunk width, pectoral–pelvic space, and clasper size. A key to the species of Squatina in the Indian Ocean is provided. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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27. Species in Disguise: A New Species of Hornshark from Northern Australia (Heterodontiformes: Heterodontidae).
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White, William T., Mollen, Frederik H., O'Neill, Helen L., Yang, Lei, and Naylor, Gavin J. P.
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PECTORAL fins ,SPECIES ,ZEBRAS - Abstract
A new species of hornshark is described from northwestern Australia based on six whole specimens and a single egg case. Heterodontus marshallae n. sp. was previously considered to be conspecific with H. zebra from the Western Pacific. The new species differs from H. zebra in the sequence of its NADH2 gene, several morphological characters, egg case morphology and key coloration features. Despite the coloration being similar between H. marshallae n. sp. and H. zebra, i.e., pale background with 22 dark brown bands and saddles, they differ consistently in two key aspects. Firstly, the snout of H. marshallae n. sp. has a dark semicircular bar, usually bifurcated for most of its length vs. a pointed, triangular shaped dark marking in H. zebra. Secondly, H. zebra has a dark bar originating below the posterior gill slits and extending onto anterior pectoral fin, which is absent in H. marshallae n. sp. The Heterodontus marshallae n. sp. is endemic to northwestern Australia and occurs in deeper waters (125–229 m) than H. zebra (0–143 m). [ABSTRACT FROM AUTHOR]
- Published
- 2023
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28. Can Partial Warp Scores Be Used as Cladistic Characters?
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Naylor, Gavin J. P., Marcus, Leslie F., editor, Corti, Marco, editor, Loy, Anna, editor, Naylor, Gavin J. P., editor, and Slice, Dennis E., editor
- Published
- 1996
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29. Placoid scales in bioluminescent sharks: Scaling their evolution using morphology and elemental composition
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Lourtie, Alexia, primary, Duchatelet, Laurent, additional, Straube, Nicolas, additional, Puozzo, Nathan, additional, Grace, Mark A., additional, Naylor, Gavin J. P., additional, and Delroisse, Jérôme, additional
- Published
- 2022
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30. A Comparison of Methods for Assessing the Structural Similarity of Proteins
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Adams, Dean C., Naylor, Gavin J. P., Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, and Guerra, Concettina, editor
- Published
- 2003
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31. Centrophorus uyato
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White, William T., Guallart, Javier, Ebert, David A., Naylor, Gavin J. P., Mo, Ana Veríssi, Cotton, Charles F., Harris, Mark, Serena, Fabrizio, and Iglésias, Samuel P.
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Centrophorus ,Animalia ,Squaliformes ,Centrophorus uyato ,Biodiversity ,Centrophoridae ,Chordata ,Taxonomy ,Elasmobranchii - Abstract
Centrophorus uyato (Rafinesque, 1810) Little Gulper Shark Synonymy. Dalatias nocturnus Rafinesque, 1810: 11, pl. 14, fig. 3 (Type locality: Sicily, Italy)— Cuvier, 1818: 455; Cuvier, 1829: 392; Cuvier, 1837: 246; Swainson, 1838: 129, 160; Swainson, 1839: 313; Duméril, 1865: 436; Jordan & Evermann, 1917: 77; Bigelow & Schroeder, 1948: 500. Spinax uyatus — Bonaparte, 1834: 49, fig. 2 (Italy); Bonaparte, 1846: 16 (Mediterranean); Böhlke, 1984: 158. Acanthias uyatus — Müller & Henle, 1839: 85 (Mediterranean); Gray, 1851: vii, 71 (Mediterranean); Steindachner, 1864: 27; Duméril, 1865: 439 (Algerian coast, Mediterranean); Barbosa du Bocage & de Brito Capello, 1866: 7, 21; Günther, 1870: 419 (Mediterranean); Canestrini, 1872: 40; Steindachner, 1875: 466; Moreau, 1881: 346 (Mediterranean); Réguis, 1882: 72; Rochebrune, 1883: 47 (Senegal and Gambia); Hilgendorf, 1884: 518; Duncan, 1891: 35 (Mediterranean); Moreau, 1892: 39; Seeley, 1895: 35 (Mediterranean); Parona, 1898: 38 (Ligurian Sea); Duncker, 1914: 291; de Buen, 1916: 303, figs (Mediterranean coast of Morocco); Landolt, 1947: 353. Centrophorus granulosus — Müller & Henle, 1839: 89, pl. 33 (Sicily, Italy); Barbosa du Bocage & de Brito Capello, 1864: 261 (Portugal); Vinciguerra, 1883: 18 (482) (Gulf of Genoa); Goode & Bean, 1896: 12, pl. 3, fig. 11 (W Atlantic, Mediterranean and adjacent areas); Boutan, 1926: 1 (Algeria); Dieuzeide, 1928a: 15, figs (Algeria); Dieuzeide, 1928b: 1314 (Algeria?); Andr & Canal, 1929: 511 (Algeria); Arcidiacono, 1931: 609 (Gulf of Squillace, Italy); Gruvel, 1931: 74 (State of Syria [Syria, Lebanon, Israel]); Ranzi, 1932: 240 (Naples, Italy); Belloc, 1934: 146, fig. (Western Sahara, Morocco, Canary Islands and Madeira); Ranzi, 1934: 343, 370 (Naples, Italy); Fowler, 1936: 73 (Mediterranean); Fowler, 1941 (in part): 231 (Mediterranean, inc. Italy); Šoljan, 1948: 66, figs (Adriatic Sea); Bigelow et al., 1955: 6 (Gulf of Mexico); Kirinčić & Lepetić, 1955: 24 (southern Adriatic Sea); Tortonese, 1956: 176, figs 94-95 (Italy); Cadenat, 1959: 748, fig. 1b (West Africa); Maurin, 1968: 82 (Morocco to Algeria); Maurin & Bonnet, 1970: 147 (Canary Islands to Cape Verde); Karrer, 1975: 64 (Namibia); Karlovac, 1976: 601, fig. 4 (Adriatic Sea); Guitart, 1979: 67, fig. 46 (Cuba); Bouchet et al., 1982: 577 (Tunisia); Zupanovic & El-Buni, 1982: 111 (Libya); Uyeno et al., 1983: 62, figs (Suriname); Compagno, 1984a: 37, figs (Atlantic and Indo-West Pacific); Gilat & Gelman, 1984: 263 (Levant Sea, Israel); McEachran & Branstetter, 1984: 130, fig. (NE Atlantic and Mediterranean); Muñoz-Chapuli, 1984: 9 (NE Atlantic);? Quéro, 1984: 43, fig.; Capapé, 1985: 97, fig. 1–7 (Eastern Atlantic); Jardas, 1985: 50 (Adriatic Sea); Anon, 1986: 93, fig. 22 (Atlantic Ocean); Bass et al., 1986 (in part): 50, fig. 5.1 (Walvis Bay and Mozambique); Golani, 1986: 23, fig. 2 (Levantine Sea, Israel); Muñoz-Chapuli & Ramos, 1989: 65, figs 1a, 3a, 4b and c, 5a, 6a, 7a (NE Atlantic and Mediterranean); Compagno et al., 1991: 54 (Hondeklip Bay to Namibia); Benli et al., 1993: 133, figs 1 and 2 (Sea of Marmara); Pisanty & Golani, 1995: 388 (Levantine Sea, Israel); Lanfranco, 1996: 6, pl. 4 (Malta); Aldebert, 1997: 284 (Gulf of Lion, France); Guallart, 1998: 1, figs (Balearic Sea); Bello, 1999: 69 (Adriatic Sea); Hernández-Hamón & Núñez, 1998: 107 (Pacific Columbia); Ungaro et al., 1999: 180 (Albania); Capapé et al., 2000: 129 (Languedoc coast, France); Bertrand et al., 2000: 5 (Gibraltar to Aegean Sea, Mediterranean); Golani & Pisanty, 2000: 71 (Levantine Sea, Israel); Baino et al., 2001: 234 (Alboran Island to Aegean Sea, Mediterranean); Guallart & Vicent, 2001: 135, fig. 4 (Balearic Sea, Spain); Bilecenoglu et al., 2002: 16 (Turkey); Schembri et al., 2003: 76, fig. 3c (Malta); McLaughlin & Morrissey, 2004: 481, fig. 3 (Cayman Trench, Jamaica); Moreno García, 2004: 214 (in part, not figs) (Mediterranean Sea); Sion et al., 2004: 155 (Ionian Sea, Greece); Golani, 2005: 11 (Levantine Sea, Israel); Lteif, 2015: 16, figs 9a, 14, (Lebanon); Serena, 2005: 27, figs, pl. I, 8 (Mediterranean Sea); Serét, 2005: 21 (Libya); Bessho, 2006: 28, figs 27–30, 33–35 (Japan, Namibia); Golani et al., 2006: 38, fig. (eastern Mediterranean); Hadjichristophorou, 2006: 163 (Cyprus); Megalofonou & Chatzispyrou, 2006: 67, fig. 4 (Crete, Greece); Mejía-Falla et al., 2007: 116 (Colombia); Psomadakis et al., 2009: 200 (Gulf of Naples, Italy); D’Onghia et al., 2010: 401 (Ionian Sea, Greece); Lipej & Dulĉić, 2010: 10 (Adriatic Sea); Damalas & Vassilopoulou, 2011: 145 (Aegean Sea, Greece); Colloca & Lelli, 2012: 12 (Lebanon); Costa et al., 2012: 7 (Portugal); Guijarro et al., 2012: 89 (Balearic Islands, Spain); Güven et al., 2012: 278 (Antalya Bay, Turkey); Iglésias, 2013: 38, pl. 16 (France and Cape Verde); Carneiro et al., 2014: 13 (Portugal); Farrugio & Soldo, 2014: 33 (Sicily, Italy and Tunisia); Veríssimo et al., 2014: 6 (Gulf of Mexico); Goren & Galil, 2015: 510 (Levant Sea, Israel); Barría et al., 2015a: 226 (Catalan Sea, Spain and Gulf of Lions, France); Barría et al., 2015b: 114 (Catalan Sea, Spain and Gulf of Lions, France); Carpenter & De Angelis, 2016: 1170, figs (Eastern Atlantic); Ramírez-Amaro et al., 2016: 639 (western Mediterranean); Cariani et al., 2017: 5 (Mediterranean);? Haroun et al., 2017: 84 (Egypt); Gajić, 2019: 101, fig. 14 (Croatia, Montenegro and Albania); Bariche & Fricke, 2020: 17, fig. 12 (Lebanon). ? Acanthias nigrescens Nardo, 1860: 70, 96 (Type locality: Venice, Italy). Entoxychirus uyatus — Gill, 1862: 498; Whitley, 1934: 199 (Australia). Acanthias ujatus — Döderlein, 1878: 30 (Sicily, Italy); Döderlein, 1881: 92 (Italy). Centrophorus uyatus — Goode & Bean, 1896: 508; Garman, 1906: 204; Garman, 1913: 9, 196. Squalus uyatus — Garman, 1899: 28. Squalus uyato — Garman, 1906: 204. Centrophorus bragancae Regan, 1906: 438 (Type locality: Cezimbra, Portugal)— Regan, 1908: 53 (coast of Portugal); Strand, 1908: 83. Centrophorus uyato — Fowler, 1936: 72, fig. 21 (Mediterranean and eastern Atlantic); Tortonese, 1938: 310 (Mediterranean); Poll 1951: 64, figs 33–34 (Angola and Namibia); Bigelow et al., 1953: 227, fig. 4 (Gulf of Mexico; Nice, Mediterranean Sea); Aksiray, 1954?: 233 (Turkish Seas); Bigelow et al., 1955: 5, 9; Springer & Bullis, 1956: 42 (Gulf of Mexico); Bigelow & Schroeder, 1957: 54, 66, 69, 72, 79–84, fig. 8e (Gulf of Mexico); Springer & Garrick, 1964: 81, 91; Krefft & Tortonese, 1973: 39 (NE Atlantic and Mediterranean); Bass et al., 1976: 31, figs 22, 24E, 24F, pl. 7 (southern Mozambique); Bridger, 1978: 26 (west of Ireland and Britain); Compagno, 1981: 8 [sharks] (Eastern Central Atlantic); Castro, 1983: 54, figs (Gulf of Mexico); Allu et al., 1984: 125 (Namibia); Compagno, 1984a: 45, figs (Atlantic, Indo-West Pacific); Compagno, 1984b: 9 [sharks] (Western Indian Ocean); McEachran & Branstetter, 1984: 132, fig. (NE Atlantic and Mediterranean); Lloris, 1986: 96, fig 24 (Namibia); Turón et al., 1986: 63 (Namibia); Fischer et al., 1987: 823 (Mediterranean); Compagno, 1988b: 603 (Comoro Islands); Compagno et al., 1989: 24, fig. (Hondeklip Bay, South Africa to Namibia);? Clark & Kristof, 1990: 277, fig. 9 (Caribbean); Springer, 1990: 11 (Gulf of Mexico, Mediterranean, and Natal, South Africa); Applegate et al., 1993: 35 (Atlantic Mexican waters); Gomon et al., 1994: 92, 94, figs 30, 31 (southern Australia); Last & Stevens, 1994: 60, figs, pl. 4 (fig. 8.5) (southern Australia); Meriç, 1995: 192 (Sea of Marmara, Turkey); Perry et al., 1995: 139 (Gulf of Mexico); Reiner, 1996: 22, fig. (Cape Verde); Bonfil, 1997: 105 (Veracruz, Mexico); Joseph, 1999: [unpaginated] (Sri Lanka); Cervigón & Alcalá, 1999 (Venezuela); Clarke, 2000: 377 (Rockall Trough, NE Atlantic); Baino et al., 2001: 234 (Alboran Island to Aegean Sea, Mediterranean); Graham et al., 2001: 551 (south-eastern Australia); Yearsley et al., 2001: 35, 360 (southern Australia); Bilecenoglu et al., 2002: 17 (Turkey); Daley et al., 2002: 53 (southern Australia); Ali & Saad, 2003: 58, fig. (Syria); Schembri et al., 2003: 77, fig. 3d (Malta); Serena, 2005: 28, figs, pl. I, 9 (Mediterranean Sea, NE Atlantic, Western Indian, Gulf of Mexico and Taiwan); Meriç et al., 2007: 31 (Turkey); White, 2008: 87, figs (southern Australia); Scacco et al., 2010: 39, fig. 3f (Mediterranean Sea); Castro, 2011: 81, figs 16a-e (north-western Atlantic); Davenport et al.: 2011: 557 (north-western Atlantic, USA); White et al., 2013: 36, fig. 2, 15, 16 (Atlantic); Veríssimo et al., 2014: 6, fig. 5 (Gulf of Mexico); Hipes, 2015: 1, fig. 11 (Gulf of Mexico, USA); Wienerroither et al., 2015: 834, fig. 2 (northern Norway); Farrag, et al., 2016: 481, fig. 2a (Egypt); Driggers et al., 2017: 52 (Gulf of Mexico); Haroun et al., 2017: 84 (Egypt); Lteif et al., 2017: 1491 (Lebanon); Biscoito et al., 2018: 471, fig. 7 (Madeira, Portugal); Carneiro et al., 2019: 36 (Portugal); Ehemann et al., 2019: 4 (Venezuela); Fernando et al., 2019: 231, figs 5e, 18d-f (Mutur, Sri Lanka); Follesa et al., 2019: 85 (Mediterranean); Psomadakis et al., 2019: 162, figs, pl. X (fig. 70) (Myanmar); Iglésias, 2020: 46, pl. 21 (France and Cape Verde); Ebert & Dando, 2021: 217, figs (NE Atlantic and Mediterranean); Kousteni et al., 2021: 1, figs 2 and 3 (Cypriot waters). Centrophorus machiquensis Maul, 1955: 5, figs 13–16 (Type locality: Madeira)— Krefft & Tortonese, 1973: 39 (Madeira); Ali & Saad, 2003: 57, fig. (Syria); Biscoito et al., 2018: 470, fig. 6 (Madeira, Portugal); Almeida & Biscoito, 2019: 99 (Canary Islands and Madeira); Carneiro et al., 2019: 36 (Portugal). Centrophorus ujato — Tortonese, 1956: 178, fig. 96 (Genova, Italy); Bini, 1967: 97, fig. (Italy); Sara, 1968: 1, figs 1–3 (west of Sicily); FAO, 1971: no pagination (Mediterranean Sea). Centrophorus spp. (granulosus group)— Forster et al, 1970 (in part): 388 (Western Indian Ocean). Centrophorus (forme) uyato-machiquensis — Cadenat & Blache, 1981: 58, figs. 36, 37 and 40 (NE Atlantic). Centrophorus spp. — Peyronel et al., 1984: 643 (Bay of Ajaccio, Corsica, France). Centrophorus cf. harrissoni (Undescribed gulper shark #2)— Kiraly et al., 2003: 2 (Puerto Rico, US Virgin Islands, Virginia, North Carolina and Florida Straits to Dry Tortugas). Centrophorus bragance — Hernández-Hamón & Núñez, 1998: 108 (as questionable synonym of C. granulosus). Centrophorus sp. (uyato ?)— Morón et al., 1998: 144 (Beruwela, Sri Lanka). Centrophorus sp. cf. uyato — Saad, et al., 2004: 430 (Syria). ? Centrophorus sp. (non uyato)— Serét, 2005: 21 (Libya). Centrophorus zeehaani White, Ebert & Compagno, 2008: 1, figs 8-10 (Type locality: South Australia)— Last & Stevens, 2009: 68, pl. 9.7, figs (southern Australia); Pethybridge et al., 2010: 1369 (Tasmania and Great Australian Bight, Australia); Pethybridge et al., 2011: 2743 (Tasmania and Victoria, Australia); Graham & Daley, 2011: 583 (southern Australia); Daley et al., 2012: 708 (southern Australia); White et al., 2013: 41 (southern Australia); Daley et al., 2015:127 (southern Australia); Wienerroither et al., 2015: 834, fig. 2 (northern Norway); Bineesh et al., 2016: 461 (Kollam, India). Centrophorus cf. uyato — McLaughlin & Morrissey, 2005: 1185, figs 2, 3 (Cayman Trench, Jamaica); Veríssimo et al., 2014: 7 (Gulf of Mexico); Serena et al., 2020: 502, 509 (Mediterranean); Bellodi et al., 2022: 2 (Mediterranean Sea). Centrophorus zeehani — Daley et al., 2012: fig. 2 (misspelling; southern Australia); Bineesh et al., 2016: 466 (misspelling; Kollam, India). Centrophorus ‘uyato’ — White et al., 2017: 86 (Eastern Atlantic); Almeida & Biscoito, 2019: 100 (Mediterranean Sea, Canary Islands and Madeira). Centrophorus cf. granulosus — Follesa et al., 2019: 85 (Mediterranean); FAO, 2018: unpaginated, fig. (Mediterranean Sea). ? Centrophorus granulosus — Parenti, 2019: 102 (Sicily). Material examined. Neotype: BMNH 2021.10.4.1 (eviscerated; GenBank accession ON167716), female 983 mm TL, between Gorgona and Capraia islands, Ligurian Sea, 43°19.8′ N, 9°56.1′ E, 180 m, 20 Dec. 2012. Other specimens: Australia: AMS I 44310 –001 (paratype of Centrophorus zeehaani; GenBank accession ON167706), adult male 826 mm TL, southwest of Coffin Bay, South Australia, 35°14′ S, 134°29′ E, 360–600 m, 28 July 2005; CSIRO CA 4104, adult male 843 mm TL, east of Gabo Island, Victoria, 37°40′ S, 150°15′ E, 504–508 m, 4 May 1984; CSIRO H 866–02, immature male 456 mm TL, CSIRO H 867–01, female 439 mm TL, east of Jervis Bay, New South Wales, 34°58′ S, 151°09′ E, 490–576 m, 10 Sep. 1986; CSIRO H 2268–02, adult male 800 mm TL, west of Bunbury, Western Australia, 33°03′ S, 114°25′ E, 701 m, 10 Feb. 1989; CSIRO H 6307–01 (skeletal parts), female 1027 mm TL, 12 July 2004, east of Flinders Island, Tasmania, ~ 40° S, ~ 149° E, 350–430 m; CSIRO H 6309–01 (skeletal parts; GenBank accession ON167708), adult male 865 mm TL, CSIRO H 6309–02 (skeletal parts), adult male 876 mm TL, CSIRO H 6309–04 (skeletal parts), adult male 906 mm TL, east of Flinders Island, Tasmania, ~ 40° S, ~ 149° E, 400–450 m, 1 Aug. 2004; CSIRO H 6310–04 (skeletal parts), female 970 mm TL, northeast of Flinders Island, Tasmania, 39°04′ S, 148°39′ E, 500–680 m, 24 Jul. 1986; CSIRO H 6311–01 (skeletal parts), female 655 mm TL, east of St. Helens, Tasmania, 41°27′ S, 148°44′ E, 850–860 m, 5 Jun. 1987; CSIRO H 6500-02, adult male 862 mm TL, east of Flinders Island, Tasmania, 40°15′ S, 148°45′ E, 329–512 m, 21 Aug. 2003; CSIRO H 6503–02 (skeletal parts), female 991 mm TL, CSIRO H 6503–03 (skeletal parts; GenBank accession ON167709), female 1023 mm TL, CSIRO H 6503–04 (skeletal parts; GenBank accession ON167710), female 987 mm TL, CSIRO H 6503–05 (skeletal parts), female 957 mm TL, northeast of Flinders Island, Tasmania, 39°20′ S, 148°45′ E, 370–420 m, 7 Apr. 2003; CSIRO H 6504–02, adult male 854 mm TL, CSIRO H 6504–03, female 817 mm TL, CSIRO H 6504–04, juvenile male 666 mm TL, CSIRO H 6504–05, adult male 861 mm TL, east of Jervis Bay, New South Wales, 35°12′ S, 150°58′ E, 320–500 m, July to Aug. 2003; CSIRO H 6628–01 (paratype of Centrophorus zeehaani), immature male 506 mm TL, CSIRO H 6628–02 (paratype of Centrophorus zeehaani; GenBank accession ON167705), immature male 645 mm TL, CSIRO H 6628–03 (paratype of Centrophorus zeehaani), adult male 875 mm TL, CSIRO H 6628–04 (paratype of Centrophorus zeehaani), adult male 910 mm TL, CSIRO H 6628–05 (holotype of Centrophorus zeehaani), adult male 893 mm TL, CSIRO H 6628–06 (paratype of Centrophorus zeehaani), adult male 852 mm TL, CSIRO H 6628–07 (paratype of Centrophorus zeehaani), adult male 906 mm TL, NMV A 29736 –001 (paratype of Centrophorus zeehaani), adult male 820 mm TL, southwest of Coffin Bay, South Australia, 35°14′ S, 134°29′ E, 360–600 m, 28 July 2005; CSIRO unreg. (DB 02/181), Great Australian Bight, adult male 857 mm TL; CSIRO unreg. (LJVC 880517), female 840 mm TL, unknown location; PMH095-11 (jaws only), female 104 cm TL, Albany, Western Australia. Eastern Atlantic (including Mediterranean): AMNH 78267, female 922 mm TL, AMNH 78269, female 937 mm TL, AMNH 78271, female 1016 mm TL, AMNH 78273, adult male 872 mm TL, AMNH 78277, adult male 895 mm TL, AMNH 78279, adult male 890 mm TL, between Tenerife and Gran Canaria, Canary Islands, Spain, 3 Oct. 1986; AMNH 78280, female 996 mm TL, AMNH 78282, female 1059 mm TL, AMNH 78283, female 1056 mm TL, AMNH 78284, adult male 832 mm TL, AMNH 78285, female 921 mm TL, AMNH 78286, female 1004 mm TL, AMNH 78291, female 1034 mm TL, AMNH 78292, female 980 mm TL, AMNH 78294, adult male 891 mm TL, between Tenerife and Gran Canaria, Canary Islands, Spain, 4 Oct. 1986; BMNH 1862.4.22.29, female 449 mm TL, Madeira, Portugal; BMNH 1864.7.18.1, female 894 mm TL, Madeira, Portugal; BMNH 1904.11.30.9- 10 (2 specimens), female 1036 mm TL, adult male 888 mm TL, west of Faro, Portugal, 662 m depth; BMNH 1904.11.30.11 (paralectotype of Centrophorus bragancae), juvenile male 488 mm TL, off Sesimbra, Portugal, 841 m depth; BMNH 1904.11.30.12 (lectotype of Centrophorus bragancae), female 467.5 mm TL, off Sesimbra, Portugal, 505 m depth; BMNH 2013.9.20.34, female 875 mm TL, BMNH 2013.9.20.35, female 930 mm TL, BMNH 2013.9.20.36, female 935 mm TL, BMNH 2013.9.20.37, female 731 mm TL, BMNH 2013.9.20.38, adult male 843 mm TL, BMNH 2013.9.20.39, adult male 865 mm TL, northeast Atlantic; CSIRO H 7471-01 (GenBank accession ON167715), adult male 853 mm TL, east of Corsica, France, 42°05.8′ N, 9°44.5′ E, 550–565 m, 30 May 2012; CSIRO H 7472-01, juvenile male 440 mm TL, southeast of Corsica, France, 41°47.9′ N, 9°30.5′ E, 466–480 m, 31 May 2012; ERB 1288, male 770 mm TL, Concarneau fish-market, France, 9 Sep. 2000; ERB 0763, male, 850 mm TL, Concarneau, France, 13 May 2009; HUJ 10885, female 760 mm TL, Hadera, Israel, 13 Sep. 1982; HUJ 11339, adult male 796 mm TL, Haifa Bay, Israel, 1 Mar. 1983; HUJ 17029, female 476 mm TL, Haifa, Israel, 16 Mar. 1983; HUMZ 151304, juvenile male 578 mm TL; HUMZ 151306, female 978 mm TL, Namibia; HUJ 21135 (GenBank accession ON167718), female 753 mm TL, Haifa fishing port, Israel, 29 July 2013; MNHN-IC 1905- 0568, juvenile male 454 mm TL, Portugal, 460 m depth, June 1903; MNHN-IC 1969-0269, juvenile male 499 mm TL, southwest of Monrovia, Liberia, 6°08′ N, 10°56′ W, 400 m depth, 27 Apr. 1964; MNHN-IC 0000-1224, female 537 mm TL, Naples, Italy; MNHN-IC 2005-0169, adult male 892 mm TL, west of Ireland, 28 Apr. 2005; NMW 15009, female 889 mm TL, Nice; NMW 63020, adult male 880 mm TL, Nice, France, 1902, Published as part of White, William T., Guallart, Javier, Ebert, David A., Naylor, Gavin J. P., Mo, Ana Veríssi-, Cotton, Charles F., Harris, Mark, Serena, Fabrizio & Iglésias, Samuel P., 2022, Revision of the genus Centrophorus (Squaliformes: Centrophoridae): Part 3 - Redescription of Centrophorus uyato (Rafinesque) with a discussion of its complicated nomenclatural history, pp. 1-51 in Zootaxa 5155 (1) on pages 15-41, DOI: 10.11646/zootaxa.5155.1.1, http://zenodo.org/record/6669082, {"references": ["Rafinesque, C. S. (1810) Caratteri di alcuni nuovi generi e nuove specie di animali e piante della Sicilia, con varie osservazioni sopra i medisimi. Sanfilippo, Palermo, 1, 3 - 69. https: // doi. org / 10.5962 / bhl. title. 104418", "Cuvier, G. (1818) Dictionnaire des sciences naturelles, dans lequel on traite meithodiquement des diffeirens e \u02c6 tres de la nature, consideireis soit en eux-me \u02c6 mes, d'apreIs l'eitat actuel de nos connoissances, soit relativement aI l'utilitei qu'en peuvent retirer la meidecine, l'agriculture, le commerce et les artes. 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(1986) On deep-water sharks caught off the Mediterranean coast of Israel. Israel Journal of Zoology, 34, 23 - 31.", "Munoz-Chapuli, R. & Ramos, F. (1989) Review of the Centrophorus sharks (Elasmobranchii, Squalidae) of the eastern Atlantic. Cybium, 13, 65 - 81.", "Compagno, L. J. V., Ebert, D. A. & Cowley, P. A. (1991) Distribution of offshore demersal cartilaginous fish (class Chondrichthyes) off the west coast of southern Africa, with notes on their systematics. South African Journal of Marine Science, 11, 43 - 139. https: // doi. org / 10.2989 / 025776191784287664", "Benli, H. A., Cihangir, B. & Bizsel, K. C. (1993) A new record for the Sea of Marmara; (Family: Squalidae) Centrophorus granulosus (Bloch & Schneider, 1801). Doda, Turkish Journal Of Zoology, 17, 133 - 135.", "Pisanty, S. & Golani, D. (1995) Vertical distribution of demersal fish on the continental slope of Israel (Eastern Mediterranean). In: Armantrout, N. B. (Ed.), Condition of the world's aquatic habitats. 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(2001) Changes in composition during embryo development of the gulper shark, Centrophorus granulosus (Elasmobranchii, Centrophoridae): an assessment of maternal-embryonic nutritional relationships. Environmental Biology of Fishes, 61, 135 - 150. https: // doi. org / 10.1023 / A: 1011080429625", "Bilecenoglu, M., Taskavak, E., Mater, S. & Kaya, M. (2002). Checklist of the marine fishes of Turkey. Zootaxa, 113 (1), 1 - 194. https: // doi. org / 10.11646 / zootaxa. 113.1.1", "Schembri, T., Fergusson, I. K. & Schembri, P. J. (2003) Revision of the records of shark and ray species from the Maltese Islands (Chordata: Chondrichthyes). The Central Mediterranean Naturalist, 4, 71 - 104.", "McLaughlin, D. M. & Morrissey, J. F. (2004) New records of elasmobranchs from the Cayman Trench, Jamaica. Bulletin of Marine Science, 75, 481 - 485.", "Sion, L., Bozzano, A., D'Onghia, G., Capezzuto, F. & Panza, M. (2004) Chondrichthyes species in deep waters of the Mediterranean Sea. 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- 2022
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32. Placoid scales in bioluminescent sharks: Scaling their evolution using morphology and elemental composition
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UCL - SST/ELI/ELIB - Biodiversity, Lourtie, Alexia, Duchatelet, Laurent, Straube, Nicolas, Puozzo, Nathan, Grace, Mark A., Naylor, Gavin J. P., Delroisse, Jerôme, UCL - SST/ELI/ELIB - Biodiversity, Lourtie, Alexia, Duchatelet, Laurent, Straube, Nicolas, Puozzo, Nathan, Grace, Mark A., Naylor, Gavin J. P., and Delroisse, Jerôme
- Abstract
Elasmobranchs are characterised by the presence of placoid scales on their skin. These scales, structurally homologous to gnathostome teeth, are thought to have various ecological functions related to drag reduction, predator defense or abrasion reduction. Some scales, particularly those present in the ventral area, are also thought to be functionally involved in the transmission of bioluminescent light in deep-sea environments. In the deep parts of the oceans, elasmobranchs are mainly represented by squaliform sharks. This study compares ventral placoid scale morphology and elemental composition of more than thirty deep-sea squaliform species. Scanning Electron Microscopy and Energy Dispersive X-ray spectrometry, associated with morphometric and elemental composition measurements were used to characterise differences among species. A maximum likelihood molecular phylogeny was computed for 43 shark species incuding all known families of Squaliformes. Character mapping was based on this phylogeny to estimate ancestral character states among the squaliform lineages. Our results highlight a conserved and stereotypical elemental composition of the external layer among the examined species. Phosphorus-calcium proportion ratios (Ca/P) slightly vary from 1.8-1.9, and fluorine is typically found in the placoid scale. By contrast, there is striking variation in shape in ventral placoid scales among the investigated families. Character-mapping reconstructions indicated that the shield-shaped placoid scale morphotype is likely to be ancestral among squaliform taxa. The skin surface occupied by scales appears to be reduced in luminous clades which reflects a relationship between scale coverage and the ability to emit light. In luminous species, the placoid scale morphotypes are restricted to pavement, bristle- and spine-shaped except for the only luminescent somniosid, Zameus squamulosus, and the dalatiid Mollisquama mississippiensis. These results, deriving from an unprecedent
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33. Redescription of Scymnodon ichiharai Yano and Tanaka 1984 (Squaliformes: Somniosidae) from the western North Pacific, with comments on the definition of somniosid genera
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White, William T., Vaz, Diego F. B., Ho, Hsuan-Ching, Ebert, David A., de Carvalho, Marcelo R., Corrigan, Shannon, Rochel, Elisabeth, de Carvalho, Murilo, Tanaka, Sho, and Naylor, Gavin J. P.
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- 2015
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34. Taxonomic Identification of Two Poorly Known Lantern Shark Species Based on Mitochondrial DNA From Wet-Collection Paratypes
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Agne, Stefanie, primary, Naylor, Gavin J. P., additional, Preick, Michaela, additional, Yang, Lei, additional, Thiel, Ralf, additional, Weigmann, Simon, additional, Paijmans, Johanna L. A., additional, Barlow, Axel, additional, Hofreiter, Michael, additional, and Straube, Nicolas, additional
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- 2022
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35. The Phylogeny of Rays and Skates (Chondrichthyes: Elasmobranchii) Based on Morphological Characters Revisited
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Villalobos-Segura, Eduardo, primary, Marramà, Giuseppe, additional, Carnevale, Giorgio, additional, Claeson, Kerin M., additional, Underwood, Charlie J., additional, Naylor, Gavin J. P., additional, and Kriwet, Jürgen, additional
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- 2022
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36. Global shark species richness is more constrained by energy than evolutionary history
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Sheahan, Emmaline R, primary, Naylor, Gavin J. P., additional, and McGlinn, Daniel J, additional
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- 2022
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37. What's in a Likelihood? Simple Models of Protein Evolution and the Contribution of Structurally Viable Reconstructions to the Likelihood
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Lakner, Clemens, Holder, Mark T., Goldman, Nick, and Naylor, Gavin J. P.
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- 2011
38. Introduction to Comparisons among Taxa at the Level of Species, Genus and Family
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Naylor, Gavin J. P., Marcus, Leslie F., editor, Corti, Marco, editor, Loy, Anna, editor, Naylor, Gavin J. P., editor, and Slice, Dennis E., editor
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- 1996
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39. Integrated Taxonomy Revealed Genetic Differences in Morphologically Similar and Non-Sympatric Scoliodon macrorhynchos and S. laticaudus
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Lim, Kean Chong, primary, White, William T., additional, Then, Amy Y. H., additional, Naylor, Gavin J. P., additional, Arunrugstichai, Sirachai, additional, and Loh, Kar-Hoe, additional
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- 2022
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40. Choosing the Best Genes for the Job: The Case for Stationary Genes in Genome-Scale Phylogenetics
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Collins, Timothy M., Fedrigo, Olivier, and Naylor, Gavin J. P.
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- 2005
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41. Pseudorhinobatos Marramà & Carnevale & Naylor & Varese & Giusberti & Kriwet 2021
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Marramà, Giuseppe, Carnevale, Giorgio, Naylor, Gavin J. P., Varese, Massimo, Giusberti, Luca, and Kriwet, Jürgen
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Rhinobatidae ,Rhinopristiformes ,Animalia ,Biodiversity ,Chordata ,Taxonomy ,Elasmobranchii ,Pseudorhinobatos - Abstract
GENUS † PSEUDORHINOBATOS Zoobank registration: urn:lsid:zoobank.org:act: 75367FF8-9DCA-406F-B257-8A34595CE1BF Type species: Trygonorhina dezignii Heckel, 1853. Etymology: After the Ancient Greek ψεῦδος (pseudos), false, and Rhinobatos, one of the living rhinobatid genera, therefore remarking their apparent similarity; gender masculine. Diagnosis: A rhinobatid guitarfish characterized by a wedge-shaped pectoral disc, longer (44.8% TL) than wide (38.5% TL); head length (from snout to scapulocoracoid) 29.8% TL; tail length (from pelvicfin origin to the posteriormost tip) 56% TL; pelvic-fin length 17.8% TL; snout to pelvic-fin origin 44.8% TL: well-developed lateral skin folds extending along the lateral margins of tail; rostral cartilage about 65% of neurocranial length; no horn-like processes on nasal capsules; 42 nasal lamellae; nuchal cartilages absent; anteriormost synarcual centrum located near the midlength of the synarcual; 118–138 vertebral centra, of which 18 monospondylous, and 100–120 diplospondylous; about 20 rib pairs; propterygia extending close to the margins of the pectoral disc; first propterygial segment not reaching the level of nasal capsules; propterygial radials extending as far as nasal capsule level; 60–62 pectoral-fin radials, of which 30–32 propterygial, seven to nine mesopterygial, one to two neopterygial, 20–22 metapterygial; about 21 pelvic-fin radials; closely arranged, small dermal denticles forming a continuous and regular covering on the ventral side of the body; denticle crown smooth, rhomboidal or lozenge in shape; thorns completely covering the dorsal side of the body; thorns of globular or arrow shape with prominent ridges; teeth extremely small (up to 750 µm); crown low, not globular; lingual visor slightly convex; regular central lingual uvula with apices rounded and not enlarged; two very incipient, not divergent, lateral lingual uvulae; labial apron absent; transverse keel separating the crown into labial and lingual faces, and forming a wide obtuse angle in lingual view; enameloid surface completely smooth; holaulacorhizid root bilobed, wide, displaced lingually, not broader or higher than the crown; root lobes triangular in shape in basal view, with regular, not undulated margins; lobes separated by a marked and deep furrow exhibiting a single central nutritive foramen; two additional foramina on lingual root face; low collar on upper part of the root stem., Published as part of Marramà, Giuseppe, Carnevale, Giorgio, Naylor, Gavin J. P., Varese, Massimo, Giusberti, Luca & Kriwet, Jürgen, 2021, Anatomy, taxonomy and phylogeny of the Eocene guitarfishes from the Bolca Lagerstätten, Italy, provide new insights into the relationships of the Rhinopristiformes (Elasmobranchii: Batomorphii) in Zoological Journal of the Linnean Society 192, {"references":["Heckel MJ. 1853. Bericht uber die vom Herrn Cavaliere Achille de Zigno hier angelangte. Sammlung fossiler Fische. Sitzungsberichte der Kaiserlichen Akademie der Wissenschaften. Mathematisch-Naturwissenschaftliche Klasse 11: 122 - 138."]}
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42. Comment on “An early Miocene extinction in pelagic sharks”
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Naylor, Gavin J. P., primary, de Lima, Arthur, additional, Castro, José I., additional, Hubbell, Gordon, additional, and de Pinna, Mario C. C., additional
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- 2021
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43. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications
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Formenti, Giulio, Rhie, Arang, Balacco, Jennifer, Haase, Bettina, Mountcastle, Jacquelyn, Fedrigo, Olivier, Brown, Samara, Capodiferro, Marco Rosario, Al-Ajli, Farooq O., Ambrosini, Roberto, Houde, Peter, Koren, Sergey, Oliver, Karen, Smith, Michelle, Skelton, Jason, Betteridge, Emma, Dolucan, Jale, Corton, Craig, Bista, Iliana, Torrance, James, Tracey, Alan, Wood, Jonathan, Uliano-Silva, Marcela, Howe, Kerstin, McCarthy, Shane, Winkler, Sylke, Kwak, Woori, Korlach, Jonas, Fungtammasan, Arkarachai, Fordham, Daniel, Costa, Vania, Mayes, Simon, Chiara, Matteo, Horner, David S., Myers, Eugene, Durbin, Richard, Achilli, Alessandro, Braun, Edward L., Phillippy, Adam M., Jarvis, Erich D., Kirschel, Alexander N. G., Digby, Andrew, Veale, Andrew, Bronikowski, Anne, Murphy, Bob, Robertson, Bruce, Baker, Clare, Mazzoni, Camila, Balakrishnan, Christopher, Lee, Chul, Mead, Daniel, Teeling, Emma, Aiden, Erez Lieberman, Todd, Erica, Eichler, Evan, Naylor, Gavin J. P., Zhang, Guojie, Smith, Jeramiah, Wolf, Jochen, Touchon, Justin, Delmore, Kira, Jakobsen, Kjetill, Komoroske, Lisa, Wilkinson, Mark, Genner, Martin, Pšenička, Martin, Fuxjager, Matthew, Stratton, Mike, Liedvogel, Miriam, Gemmell, Neil, Minias, Piotr, Dunn, Peter O., Sudmant, Peter, Morin, Phil, Ayub, Qasim, Kraus, Robert, Vernes, Sonja, Smith, Steve, Lama, Tanya, Edwards, Taylor, Smith, Tim, Gilbert, Tom, Marques-Bonet, Tomas, Einfeldt, Tony, Venkatesh, Byrappa, Johnson, Warren, Warren, Wes, Bukhman, Yury, Formenti, Giulio [0000-0002-7554-5991], and Apollo - University of Cambridge Repository
- Subjects
Vertebrate ,Research ,Assembly ,Sequencing ,Duplications ,Long reads ,Repeats ,Mitochondrial DNA - Abstract
Background: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. Results: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100–300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. Conclusions: Our results indicate that even in the “simple” case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.
- Published
- 2021
44. Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for lantern shark taxonomy (Chondrichthyes: Etmopteridae)
- Author
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Straube, Nicolas, primary, Preick, Michaela, additional, Naylor, Gavin J. P., additional, and Hofreiter, Michael, additional
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- 2021
- Full Text
- View/download PDF
45. Towards complete and error-free genome assemblies of all vertebrate species
- Author
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National Institutes of Health (US), National Human Genome Research Institute (US), Ministry of Health and Welfare (South Korea), Wellcome Trust, European Molecular Biology Laboratory, Howard Hughes Medical Institute, Rockefeller University, Robert and Rosabel Osborne Endowment, European Commission, National Library of Medicine (US), Korea Institute of Marine Science & Technology, Ministry of Oceans and Fisheries (South Korea), Alfred P. Sloan Foundation, Max Planck Society, Maine Department of Inland Fisheries & Wildlife, National Science Foundation (US), University of Queensland, Science Exchange, Northeastern University (US), Federal Ministry of Education and Research (Germany), EMBO, National Key Research and Development Program (China), Qatar Society of Al-Gannas (Algannas), Katara Cultural Village, Government of Qatar, Monash University Malaysia, Hessen State Ministry of Higher Education, Research and the Arts, Ministry of Science, Research and Art Baden-Württemberg, Agency for Science, Technology and Research A*STAR (Singapore), European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Fundación la Caixa, Generalitat de Catalunya, Irish Research Council, Danish National Research Foundation, Australian Research Council, Rhie, Arang, McCarthy, Shane A., Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C, Lama, Tanya M, Grützner, Frank, Warren, Wesley C., Balakrishnan, Christopher N., Pippel, Martin, Burt, Dave, George, Julia M., Biegler, Matthew T., Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Malinsky, Milan, Meyer, Axel, Kautt, Andreas F., Franchini, Paolo, Detrich III, H. William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin J. P., Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T., Pesout, Trevor, Houck, Marlys L., Misuraca, Ann, Kingan, Sarah B., Hall, Richard, Wood, Jonathan, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E., Putnam, Nicholas H., Gut, Ivo, Dagnew, Robel E., Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Guan, Dengfeng, London, Sarah E., Clayton, David F., Mello, Claudio V., Friedrich, Samantha R., Lovell, Peter V., Osipova, Ekaterina, Al-Ajli, Farooq O., Diekhans, Mark, Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S., Makova, Kateryna D., Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Nassar, Luis, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P., Kwak, Woori, Clawson, Hiram, Paten, Benedict, Kraus, Robert H. S., Crawford, Andrew J., Gilbert, M. Thomas P., Zhang, Guojie, Venkatesh, Byrappa, Murphy, Robert W., Koepfli, Klaus-Peter, Ko, Byung June, Shapiro, Beth, Johnson, Warren E., Di Palma, Federica, Marqués-Bonet, Tomàs, Teeling, Emma C., Warnow, Tandy, Marshall Graves, Jennifer, Ryder, Oliver A., Haussler, David, O’Brien, Stephen J., Chaisson, Mark, Korlach, Jonas, Lewin, Harris A., Howe, Kerstin, Myers, Eugene W., Durbin, Richard, Phillippy, Adam M., Jarvis, Erich D., Gedman, Gregory L., Cantin, Lindsey J., Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, Smith, Michelle, National Institutes of Health (US), National Human Genome Research Institute (US), Ministry of Health and Welfare (South Korea), Wellcome Trust, European Molecular Biology Laboratory, Howard Hughes Medical Institute, Rockefeller University, Robert and Rosabel Osborne Endowment, European Commission, National Library of Medicine (US), Korea Institute of Marine Science & Technology, Ministry of Oceans and Fisheries (South Korea), Alfred P. Sloan Foundation, Max Planck Society, Maine Department of Inland Fisheries & Wildlife, National Science Foundation (US), University of Queensland, Science Exchange, Northeastern University (US), Federal Ministry of Education and Research (Germany), EMBO, National Key Research and Development Program (China), Qatar Society of Al-Gannas (Algannas), Katara Cultural Village, Government of Qatar, Monash University Malaysia, Hessen State Ministry of Higher Education, Research and the Arts, Ministry of Science, Research and Art Baden-Württemberg, Agency for Science, Technology and Research A*STAR (Singapore), European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Fundación la Caixa, Generalitat de Catalunya, Irish Research Council, Danish National Research Foundation, Australian Research Council, Rhie, Arang, McCarthy, Shane A., Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C, Lama, Tanya M, Grützner, Frank, Warren, Wesley C., Balakrishnan, Christopher N., Pippel, Martin, Burt, Dave, George, Julia M., Biegler, Matthew T., Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Malinsky, Milan, Meyer, Axel, Kautt, Andreas F., Franchini, Paolo, Detrich III, H. William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin J. P., Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T., Pesout, Trevor, Houck, Marlys L., Misuraca, Ann, Kingan, Sarah B., Hall, Richard, Wood, Jonathan, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E., Putnam, Nicholas H., Gut, Ivo, Dagnew, Robel E., Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Guan, Dengfeng, London, Sarah E., Clayton, David F., Mello, Claudio V., Friedrich, Samantha R., Lovell, Peter V., Osipova, Ekaterina, Al-Ajli, Farooq O., Diekhans, Mark, Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S., Makova, Kateryna D., Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Nassar, Luis, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P., Kwak, Woori, Clawson, Hiram, Paten, Benedict, Kraus, Robert H. S., Crawford, Andrew J., Gilbert, M. Thomas P., Zhang, Guojie, Venkatesh, Byrappa, Murphy, Robert W., Koepfli, Klaus-Peter, Ko, Byung June, Shapiro, Beth, Johnson, Warren E., Di Palma, Federica, Marqués-Bonet, Tomàs, Teeling, Emma C., Warnow, Tandy, Marshall Graves, Jennifer, Ryder, Oliver A., Haussler, David, O’Brien, Stephen J., Chaisson, Mark, Korlach, Jonas, Lewin, Harris A., Howe, Kerstin, Myers, Eugene W., Durbin, Richard, Phillippy, Adam M., Jarvis, Erich D., Gedman, Gregory L., Cantin, Lindsey J., Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, and Smith, Michelle
- Abstract
High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1,2,3,4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
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- 2021
46. Hemitrygon yemenensis Moore & Last & Naylor 2020, sp. nov
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Moore, Alec B. M., Last, Peter R., and Naylor, Gavin J. P.
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Dasyatidae ,Myliobatiformes ,Animalia ,Biodiversity ,Chordata ,Hemitrygon yemenensis ,Taxonomy ,Elasmobranchii ,Hemitrygon - Abstract
Hemitrygon yemenensis sp. nov. (Figs. 1–5, Table 1) Holotype. NMW 60783, adult male 223 mm DW, Gischin, Yemen, collected 1902. Paratype. NMW 99841, female 206 mm DW, collected with holotype. Diagnosis. A small species of Hemitrygon (attaining at least 22 cm DW) with the following combination of characters: disc width subequal to length; snout elongate, tip narrowly pointed, angle 107–110°, length 2.1–2.3 times interorbital width; preoral length 2.6–2.7 times mouth width; internasal distance 1.8–1.9 in prenasal length; body and tail mostly naked, denticles confined largely to head; single continuous median row (broken in paratype) of 8–18 small to large thorns on disc (two scapular thorns on each side of adult male), 4–13 similar thorns on tail before caudal sting (more thorns on male than female); tail moderately elongate, slender, whip-like beyond sting, width 0.5–1.2 times its depth, postcloacal tail length 1.9–2.2 times precloacal length; ventral cutaneous fold long, very slender, its length 1.9–2.0 in DW, height 0.3–0.4 in tail depth at its midlength; dorsal skin fold elongate, low, much shorter than ventral fold; distance from cloaca to sting 1.5–1.6 in precloacal length; pectoral-fin radials ~115; total vertebral centra 125–126, monospondylous vertebrae (including all synarcual) 38–39. Description. Disc quadrangular, bluntly angular anteriorly and slightly produced; length subequal to width, width 0.99 times length in adult male holotype (0.98 in female paratype); axis of greatest width of disc slightly forward of scapular region, its distance from snout tip 1.83 (1.89) times in distance from tip of snout to pectoral-fin insertion; body moderately robust, thickness 7.1 (7.4) times in disc width, raised slightly above cranium (marginally more so in scapular region); anterior margin of disc concave anteriorly, straight medially, strongly and evenly convex just before pectoral-fin apex; apex broadly rounded; posterior margin weakly convex; free rear tip broadly rounded. Pelvic fins weakly triangular, anterior and posterior margins almost straight, apices narrowly rounded, free rear tip broadly rounded; relatively large, length 24.3% (25.3%) DW; 1.49 (1.66) times width across fin bases. Tail moderately elongate, slender, with a long, very low ventral skin fold and a shorter and lower dorsal fold (modified somewhat through partial desiccation); postcloacal tail 2.22 (1.88) times precloacal length; width at axil of pelvic fin 1.31 (1.63) times its depth; tapering gradually and evenly to sting base (missing in holotype but position evident as a scar; sting broken at base in paratype); narrowly oval in cross-section near origin of ventral skin fold, width 1.03 (1.25) times height at fold origin; tapering evenly in dorsoventral view below sting scar; very slender, whip-like beyond sting scar, becoming progressively more compressed toward tail tip; subquadrangular in cross-section above mid ventral fold, depth 1.36 (1.16) times width; at end of fold suboval, weakly compressed, depth 1.37 (1.07) times width; filamentous towards tail apex. Dorsal skin fold reduced to low, elongate ridge, length 77 (36) times its height, 1.37 (2.03) in snout length, 2.68 (3.99) in length of ventral fold; its height 1.91 (1.04) in height of mid ventral fold; origin near likely position of undamaged sting apex. Ventral skin fold long, very narrow, length 2.03 (1.87) in disc width, 3.82 (3.05) in post cloacal tail; commencing almost below sting origin, origin 1.1% (1.0%) before sting origin; depth at quarter length 0.43 (0.27), at mid length 0.39 (0.30), at three quarter 0.32 (0.29) in adjacent tail height; distance from cloaca to sting origin 1.54 (1.62) in precloacal length; length of tail beyond ventral fold 0.65 (1.00) in fold length, 2.48 (3.04) in tail length. Lateral line on ventral surface distinct. Snout elongate, subtriangular; apex lobe-like, narrowly and bluntly pointed; angle 107 o (110 o); preoral snout length 2.58 (2.66) times mouth width, 2.34 (2.48) times internarial distance, 1.16 (1.23) times distance between first gill slits; direct preorbital snout length 2.05 (2.31) times interorbital length; snout to maximum disc width 1.97 (2.10) in DW; interorbital space broad, almost flat; eyes small, almost lateral, barely protruding in both types, ventral margin partly covered by thin skin fold; orbit not elevated above disc, diameter 1.00 (0.91) in spiracle length, eye diameter 1.58 (1.35) in spiracle length; inter-eye distance 3.81 (3.31) times eye diameter. Spiracles subrectangular to suboval, enlarged, opening dorsolaterally. Nostril elongate, suboval, directed posterolaterally; anterior margin fleshy; anterior nasal fold internal, broad, membranous; weak oronasal groove present; internasal distance 1.78 (1.93) in prenasal length, 2.51 (2.84) times nostril length. Nasal curtain skirt-like, relatively broad, short, width 1.74 (1.70) times length; not bilobed; surface flat, smooth, without longitudinal medial groove, not covered with minute pores; apex partly recessible within lateral margin of oronasal groove; lateral margin concave (possibly distorted through preservation; paratype almost straight), smooth edged; posterior margin not strongly fringed, weakly concave, not following contour of lower jaw, well removed from symphysis of lower jaw when mouth closed. Jaws asymmetric with teeth visible when mouth closed. Upper jaw strongly arched (teeth highly visible), symphysial part of jaw projecting ventrally; lower jaw strongly convex with truncate apex, broad band of symphysial teeth visible when mouth closed; lateral grooves deep (most evident on right side of holotype), almost straight, extending from nostril to well below lower jaw, longer than nasal curtain length. Lower jaw not projecting forward when mouth open, mouth not protrusible; skin on chin very fleshy, corrugate (more so in less dehydrated paratype); jaws of types not prised apart to reveal oral papillae. Teeth of adult male holotype rather large, variable in shape; those in mid lateral part of upper jaw almost plate-like, their crowns more than twice size of those either side; those at symphysis of upper jaw much smaller, upright, crowns with well-developed slender cusps; cusps much shorter in those teeth posterolaterally; crowns on symphysial teeth in lower jaw somewhat globular, slightly large than those at symphysis of upper jaw; those toward angle of lower jaw concealed; teeth not close-set in either jaw, in straight to semi-oblique rows, not obviously arranged quincuncially; rows in upper jaw ~31 (counted from photograph). Teeth of female paratype smaller than adult male, more similar in size and shape, more closely arranged, quincuncial. Gill openings S-shaped; length of first gill slit 1.36 (1.32) times length of fifth gill slit, 3.64 (3.38) times in mouth width; distance between first gill slits 2.02 (2.01) times internasal distance, 0.43 (0.41) times ventral head length; distance between fifth gill slits 1.31 (1.24) times internasal distance, 0.28 (0.25) times ventral head length. Squamation. Disc and tail with well-developed thorns and an otherwise largely naked disc; holotype with small, widely spaced stellate, dermal denticles on raised part of head; denticles sparse elsewhere, scattered few on post sting tail. Mid-dorsal thorn series in holotype in a single continuous, closely spaced row from nuchal region to sting base; 18 thorns on disc (8 on head, 10 on posterior disc), length 2.0– 6.3 mm, width 1.1 to 2.8 mm; 13 thorns on tail before sting scar, length 3.1–7.9 mm, width 2.1–2.8 mm; thorns very well developed, with rectangular bases and long, semi-erect, pungent lanceolate crowns; two similar thorns on each side of scapulocoracoid; thorns on tail much larger and more widely spaced than those on disc. Squamation of paratype less well developed; fewer dermal denticles on head (~ 12 in orbito-spiracular region); median thorn row less well developed, discontinuous, 8 thorns on disc (4 on head, 4 on posterior disc), length 2.8–5.5 mm, width 1.5–2.5 mm; 4 thorns on tail before sting base, length 6.2–7.2 mm, width 2.5– 2.5 mm. Both type specimens lacking an intact sting; distance from sting base to pectoral-fin insertion 49.4% (49.6%) DW; distance from cloaca to sting base 0.54 (0.53) in disc length. Clasper of adult moderately depressed, robust basally, convex distally and tapering to a blunt or narrowly rounded point; post cloacal length 31.0% DW. Total pectoral radials ~115 left side only (~115 right side only); propterygials ~51 (~47), mesopterygials 16–17 (17–18) and metapterygials ~48 left side only (~51 right side only). Total pelvic radials in right side of paratype 1 + ~26. Total vertebral segments (including first synarcual centra) 125 (126); all synarcual and monospondylous centra 38 (39); total diplospondylous centra 87 (87). Colouration. No information on live colour. In preservative (holotype): Uniformly brownish on dorsal surface, lightest around orbit, orbital membrane darker brown; thorns typical paler than surrounding skin, obvious. Ventral surface yellowish brown (blotching likely to be due to preservation and partial desiccation. Paratype: Dorsal surface pale brownish, lighter than holotype (possible artefact of preservation); scapular region, orbit and interorbit palest. Ventral surface almost uniformly white, paler than dorsal surface. Size.— Male holotype mature at 223 mm DW; stage of development of female paratype 206 mm DW unknown. Distribution. Type material reported as collected from Gischin, assumed to be Qishn in eastern Yemen, on the Arabian Sea coast (Fig. 6). Etymology. Epithet derived from the country of collection. Vernacular name: Heins’ stingray, after Marie and Wilhelm Hein who collected the type material shortly before Wilhelm’s death, and who also collected the holotype of the rare shark Carcharhinus leiodon. Remarks. The dasyatid genus Hemitrygon Müller & Henle 1838 presently comprises several small to medium-sized stingray species distributed in shallow marine, estuarine and freshwater environments. The new species H. yemenensis is currently known only from its collection locality (off eastern Yemen in the northwestern Indian Ocean), whereas almost all species of the genus Hemitrygon are largely restricted to the western Pacific (H. bennetti and H. parvonigra also occur in the eastern Indian Ocean) (Last et al., 2016). The extent of this disjunct distribution is unusual for a small-bodied coastal batoid, so additional scrutiny of the provenance of these specimens was required. However, we believe the collection locality of Gischin (Qishn) in Yemen is most likely correct for a number of reasons. Firstly, Wilhelm and Marie Hein undertook a well-documented expedition from Vienna to South Arabia from December 1901 – April 1902, most of which was spent in Gischin, although they stopped in Aden and Mukalla (Fig. 6). In Gischin they researched Mehri, a Modern South Arabian language that is unique to eastern Yemen and southern Oman. Wilhelm Hein is not known to have visited the western Pacific region (i.e. the core distribution of Hemitrygon) during his lifetime, and died in 1903, the year after the expedition to Gischin (Müller 1909, Klein-Franke 2006). Secondly, listings of NMW holdings of reptiles and teleost fish collected by the Heins on the same expedition appear to be consistent with the fauna of southern Arabia (ABMM, unpubl. data). Finally, the only other elasmobranch that the Heins collected in Gischin, the smoothtooth blacktip shark C. leiodon, has been recorded in eastern Yemen and the adjacent waters of southern Oman, despite having a highly limited known distribution (Henderson & Reeve, 2011; Moore et al., 2013), providing further evidence that the collection locality of H. yemenensis is likely correct. Hemitrygon yemenensis sp. nov. most closely resembles H. akajei (Müller & Henle, 1841) from the western North Pacific, H. bennetti (Müller & Henle, 1841) from the Indo-West Pacific and the Bay of Bengal, and H. fluviorum (Ogilby, 1908) from Australian seas, than any other 10 members of the genus treated recently in a guide to rays of the world (Last et al., 2016). These species all have well-developed thorns and tubercles in a median row on the disc and tail, and a short thorn row on each shoulder of adult males. However the disc shape of H. yemenensis is characteristically marked by a longer and more narrowly pointed snout than these species (and any other member of the genus), and the disc’s length is shorter than its width for all species of Hemitrygon other than H. yemenensis. Compared to the most similar species, H. bennetti, it has a shorter tail (cloaca origin to tail tip 163–188% DW in H. yemenensis vs. 209–258% DW in H. bennetti, n=6), longer disc (length 101–102% DW vs. 91–97% DW), head (length 51–52% DW vs. 44–49% DW) and snout (direct length 25–27% DW vs. 22–24% DW), slightly narrower interorbit (width 11.8–12.3% DW vs. 12.7–14.0% DW), larger eye and orbit (eye diameter 4.6–4.7% DW vs. 3.1–3.7% DW); longer proportions around the head of H. yemenensis are reflected by longer prenasal and preoral lengths. Although the elasmobranch fauna of Yemen has been poorly documented, at least fourteen other species of the family Dasyatidae either occur or are likely to occur there (Last et al., 2016). Of these, H. yemenensis is most similar in morphology to Brevitrygon walga (Müller & Henle, 1841), Maculabatis species (e.g. M. ambigua Last, Bogorodsky & Alpermann, 2016), and Pateobatis jenkinsii (Annandale, 1909) (Last et al., 2016) but unlike all of these species has dorsal and ventral folds on the tail. Hemitrygon yemenensis can also be distinguished from these species by a combination of small size of adult males, squamation (notably an absence of a denticle band, and the arrangement of thorns on disc, tail, and shoulder in adult males), and tail morphology (i.e. length, thickness). Although no fresh material was available for this study, colouration of live or freshly caught H. yemenensis may also be an important distinguishing field character and should be documented at the earliest opportunity. It is noteworthy that nearly 120 years have elapsed since the type specimens of H. yemenensis were collected, and the species has not been recorded nor additional material collected since. It remains to be seen if this apparent rarity is simply a reflection of a paucity of sampling effort near the type locality or a change in its conservation status.
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- 2020
- Full Text
- View/download PDF
47. Skeletal anatomy, phylogenetic relationships and paleoecology of the Eocene stingray Arechia Cappetta, 1983 (Batomorphii: Myliobatiformes) from Monte Postale (Bolca Lagerstätte, Italy)
- Author
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Marramà, Giuseppe, Carnevale, Giorgio, Naylor, Gavin J. P., and Jurgen, Kriwet
- Published
- 2020
48. Revision of the Eocene ‘Platyrhina’ species from the Bolca Lagerstätte (Italy) reveals the first possible panray (Batomorphii: Zanobatidae) in the fossil record
- Author
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Marramà, Giuseppe, Carnevale, Giorgio, Claeson, Kerin M., Naylor, Gavin J. P., and Jurgen, Kriwet
- Published
- 2020
49. Chimaera compacta, a new species from southern Indian Ocean, and an estimate of phylogenetic relationships within the genus Chimaera (Chondrichthyes: Chimaeridae)
- Author
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Iglésias, Samuel P., primary, Kemper, Jenny M., additional, and Naylor, Gavin J. P., additional
- Published
- 2021
- Full Text
- View/download PDF
50. Identifying isolated shark teeth of the genus Carcharhinus to species : relevance for tracking phyletic change through the fossil record
- Author
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Naylor, Gavin J. P., Marcus, Leslie Floyd, 1930-2002, American Museum of Natural History Library, Naylor, Gavin J. P., and Marcus, Leslie Floyd, 1930-2002
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Anatomy ,Carcharhinus ,Classification ,Fishes ,Sharks ,Teeth
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