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Blackburn DC, Boyer DM, Gray JA, Winchester J, Bates JM, Baumgart SL, Braker E, Coldren D, Conway KW, Rabosky AD, de la Sancha N, Dillman CB, Dunnum JL, Early CM, Frable BW, Gage MW, Hanken J, Maisano JA, Marks BD, Maslenikov KP, McCormack JE, Nagesan RS, Pandelis GG, Prestridge HL, Rabosky DL, Randall ZS, Robbins MB, Scheinberg LA, Spencer CL, Summers AP, Tapanila L, Thompson CW, Tornabene L, Watkins-Colwell GJ, Welton LJ, Stanley EL. Increasing the impact of vertebrate scientific collections through 3D imaging: The openVertebrate (oVert) Thematic Collections Network. Bioscience 2024; 74:169-186. [PMID: 38560620 PMCID: PMC10977868 DOI: 10.1093/biosci/biad120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/08/2023] [Indexed: 04/04/2024] Open
Abstract
The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimens available and the impact of these data on a broad audience of scientists, students, teachers, artists, and more. High-fidelity digital 3D models allow people from multiple communities to simultaneously access and use scientific specimens. Based on our multiyear, multi-institution project, we identify significant technological and social hurdles that remain for fully realizing the potential impact of digital 3D specimens.
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Affiliation(s)
- David C Blackburn
- Florida Museum of Natural History (FLMNH), University of Florida, Gainesville, Florida, United States
- Blackburn served as the lead principal investigator for the oVert Thematic Collections Network
| | - Doug M Boyer
- Duke University, Durham, North Carolina, United States
| | - Jaimi A Gray
- Florida Museum of Natural History (FLMNH), University of Florida, Gainesville, Florida, United States
- Blackburn served as the lead principal investigator for the oVert Thematic Collections Network
| | | | - John M Bates
- Field Museum of Natural History, Chicago, Illinois, United States
| | - Stephanie L Baumgart
- University of Chicago and University of Florida, Gainesville, Florida, United States
| | - Emily Braker
- University of Colorado, Boulder, Colorado, United States
| | - Daryl Coldren
- Field Museum of Natural History, Chicago, Illinois, United States
| | - Kevin W Conway
- Texas A&M University, College Station, Texas, United States
| | | | - Noé de la Sancha
- Chicago State University DePaul University, Chicago, Illinois, United States
| | | | - Jonathan L Dunnum
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States
| | - Catherine M Early
- FLMNH Science Museum of Minnesota, St. Paul, Minnesota, United States
| | - Benjamin W Frable
- Scripps Institute of Oceanography, University of California, San Diego, San Diego, California, United States
| | - Matt W Gage
- Harvard University, Cambridge, Massachusetts, United States
| | - James Hanken
- Harvard University, Cambridge, Massachusetts, United States
| | | | - Ben D Marks
- Field Museum of Natural History, Chicago, Illinois, United States
| | | | | | | | | | | | | | - Zachary S Randall
- Florida Museum of Natural History (FLMNH), University of Florida, Gainesville, Florida, United States
- Blackburn served as the lead principal investigator for the oVert Thematic Collections Network
| | | | | | - Carol L Spencer
- University of California, Berkeley, in Berkeley, California, United States
| | - Adam P Summers
- University of Washington, Seattle, Washington, United States
| | - Leif Tapanila
- Idaho State University, Pocatello, Idaho, United States
| | | | - Luke Tornabene
- University of Washington, Seattle, Washington, United States
| | | | - Luke J Welton
- University of Kansas, Lawrence, Kansas, United States
| | | | - Edward L Stanley
- Florida Museum of Natural History (FLMNH), University of Florida, Gainesville, Florida, United States
- Blackburn served as the lead principal investigator for the oVert Thematic Collections Network
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2
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Victor BC, Frable BW, Ludt WB. Halichoeres sanchezi n. sp., a new wrasse from the Revillagigedo Archipelago of Mexico, tropical eastern Pacific Ocean (Teleostei: Labridae). PeerJ 2024; 12:e16828. [PMID: 38436023 PMCID: PMC10908266 DOI: 10.7717/peerj.16828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/04/2024] [Indexed: 03/05/2024] Open
Abstract
A new labrid fish species, Halichoeres sanchezi n. sp., is described from eight specimens collected in the Revillagigedo Archipelago in the tropical eastern Pacific Ocean, off the coast of Mexico. The new species belongs to the Halichoeres melanotis species complex that is found throughout the region, differing by 2.4% in the mtDNA cytochrome c oxidase I sequence from its nearest relative, H. melanotis from Panama, and 2.9% from Halichoeres salmofasciatus from Cocos Island, off Costa Rica. The complex is distinguished from others in the region by having a black spot on the opercular flap and a prominent black area on the caudal fin of males. The juveniles and initial phase of the new species closely resemble those of H. salmofasciatus and Halichoeres malpelo from Malpelo Island of Colombia, differing in having an oblong black spot with a yellow dorsal margin on the mid-dorsal fin of initial-phase adults as well as on juveniles. In contrast, the terminal-phase male color pattern is distinct from other relatives, being vermilion to orangish brown with dark scale outlines, a white patch on the upper abdomen, and a prominent black band covering the posterior caudal peduncle and base of the caudal fin. The new species adds to the list of endemic fish species for the isolated archipelago and is an interesting case of island endemism in the region. The discovery was made during the joint 2022 collecting expedition to the archipelago, which featured a pioneering collaborative approach to an inventory of an island ichthyofauna, specifically including expert underwater photographers systematically documenting specimens in situ, before hand-collection, and then photographed fresh, tissue-sampled, and subsequently vouchered in museum collections.
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Affiliation(s)
- Benjamin C. Victor
- Guy Harvey Research Institute, Nova Southeastern University, Dania Beach, Florida, United States
- Marine Biology, Ocean Science Foundation, Irvine, California, United States
| | - Benjamin W. Frable
- Marine Vertebrate Collection, Scripps Institution of Oceanography, La Jolla, California, United States
| | - William B. Ludt
- Ichthyology, Natural History Museum of Los Angeles County, Los Angeles, California, United States
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Milan J, Fidel T, Hongjamrassilp W, Frable BW, Skelton ZR, Hastings PA. Heterochrony and the evolution of the longjaw mudsucker (Gobiidae, Teleostei). J Fish Biol 2024; 104:155-162. [PMID: 37721159 DOI: 10.1111/jfb.15568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 07/13/2023] [Accepted: 09/15/2023] [Indexed: 09/19/2023]
Abstract
Although longjaw mudsucker (Gillichthys mirabilis, Gobiidae) has been studied extensively for its ability to occupy low-oxygen environments, few studies have addressed the evolution of its exceptionally elongated jaws that extend posteriorly beyond the gill opening in large adults. In this study, the ontogeny of the maxillae of G. mirabilis, Gillichthys seta, and the out-group species Eucyclogobius newberryi was studied within the heterochrony framework using digitized landmarks and caliper measurements. The results show that the maxilla of both species of Gillichthys evolved via acceleration (increased growth rate) and that of G. mirabilis via hypermorphosis (continued growth to a larger body size); two forms of peramorphosis. This is in contrast to earlier studies that concluded that G. seta is paedomorphic. We were unable to confirm an earlier hypothesis of sexual dimorphism in the jaw length of G. mirabilis. The evolution of the elongated jaws and associated large buccopharyngeal membrane in G. mirabilis is hypothesized to increase the surface area for gas exchange during aerial respiration and may also serve to amplify the aggressive gaping display as observed in other fishes.
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Affiliation(s)
- Jimjohn Milan
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Tyler Fidel
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Watcharapong Hongjamrassilp
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Benjamin W Frable
- Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Zachary R Skelton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Ocean Associates Inc. under contract to Fisheries Resources Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, California, USA
| | - Philip A Hastings
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
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Portner EJ, Mowatt-Larssen T, Carretero ACL, Contreras EA, Woodworth-Jefcoats PA, Frable BW, Choy CA. Harnessing a mesopelagic predator as a biological sampler reveals taxonomic and vertical resource partitioning among three poorly known deep-sea fishes. Sci Rep 2023; 13:16078. [PMID: 37752192 PMCID: PMC10522621 DOI: 10.1038/s41598-023-41298-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/24/2023] [Indexed: 09/28/2023] Open
Abstract
Pelagic predators are effective biological samplers of midtrophic taxa and are especially useful in deep-sea habitats where relatively mobile taxa frequently avoid observation with conventional methods. We examined specimens sampled from the stomachs of longnose lancetfish, Alepisaurus ferox, to describe the diets and foraging behaviors of three common, but poorly known deep-sea fishes: the hammerjaw (Omosudis lowii, n = 79, 0.3-92 g), juvenile common fangtooth (Anoplogaster cornuta, n = 91, 0.6-22 g), and juvenile Al. ferox (n = 138, 0.3-744 g). Diet overlap among the three species was high, with five shared prey families accounting for 63 ± 11% of the total prey mass per species. However, distinct differences in foraging strategies and prey sizes were evident. Resource partitioning was greatest between An. cornuta that specialized on small (mean = 0.13 ± 0.11 g), shallow-living hyperiid amphipods and O. lowii that specialized on large (mean = 0.97 ± 0.45 g), deep-dwelling hatchetfishes. Juvenile Al. ferox foraged on a high diversity of prey from both shallow and deep habitats. We describe the foraging ecologies of three midtrophic fish competitors and demonstrate the potential for biological samplers to improve our understanding of deep-sea food webs.
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Affiliation(s)
- Elan J Portner
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
| | - Tor Mowatt-Larssen
- Virginia Institute of Marine Science, William & Mary, Gloucester Point, VA, USA
| | | | - Emily A Contreras
- Cooperative Institute for Marine and Atmospheric Research, University of Hawai'i, Honolulu, HI, USA
| | - Phoebe A Woodworth-Jefcoats
- Pacific Islands Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Honolulu, HI, USA
| | - Benjamin W Frable
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - C Anela Choy
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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5
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Minich JJ, Härer A, Vechinski J, Frable BW, Skelton ZR, Kunselman E, Shane MA, Perry DS, Gonzalez A, McDonald D, Knight R, Michael TP, Allen EE. Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species. Nat Commun 2022; 13:6978. [PMID: 36396943 PMCID: PMC9671965 DOI: 10.1038/s41467-022-34557-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022] Open
Abstract
Fish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence fish microbiota. To identify factors that explain microbial diversity patterns in a geographical subset of marine fish, we analyzed the microbiota (gill tissue, skin mucus, midgut digesta and hindgut digesta) from 101 species of Southern California marine fishes, spanning 22 orders, 55 families and 83 genera, representing ~25% of local marine fish diversity. We compare alpha, beta and gamma diversity while establishing a method to estimate microbial biomass associated with these host surfaces. We show that body site is the strongest driver of microbial diversity while microbial biomass and diversity is lowest in the gill of larger, pelagic fishes. Patterns of phylosymbiosis are observed across the gill, skin and hindgut. In a quantitative synthesis of vertebrate hindguts (569 species), we also show that mammals have the highest gamma diversity when controlling for host species number while fishes have the highest percent of unique microbial taxa. The composite dataset will be useful to vertebrate microbiota researchers and fish biologists interested in microbial ecology, with applications in aquaculture and fisheries management.
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Affiliation(s)
- Jeremiah J Minich
- The Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
| | - Andreas Härer
- School of Biological Sciences, Department of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, CA, 92093, USA
| | - Joseph Vechinski
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0244, USA
| | - Benjamin W Frable
- Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0244, USA
| | - Zachary R Skelton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Emily Kunselman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0244, USA
| | - Michael A Shane
- Hubbs-SeaWorld Research Institute, 2595 Ingraham Street, San Diego, CA, 92109, USA
| | - Daniela S Perry
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Antonio Gonzalez
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, University of San Diego, California, La Jolla, CA, 92093, USA
- Department of Computer Science, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Todd P Michael
- The Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Eric E Allen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0244, USA
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
- Center for Microbiome Innovation, University of San Diego, California, La Jolla, CA, 92093, USA
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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6
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Kwan GT, Frable BW, Thompson AR, Tresguerres M. Optimizing immunostaining of archival fish samples to enhance museum collection potential. Acta Histochem 2022; 124:151952. [PMID: 36099745 DOI: 10.1016/j.acthis.2022.151952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/31/2022] [Accepted: 09/04/2022] [Indexed: 11/18/2022]
Abstract
Immunohistochemistry (IHC) is a powerful biochemical technique that uses antibodies to specifically label and visualize proteins of interests within biological samples. However, fluid-preserved specimens within natural history collection often use fixatives and protocols that induce high background signal (autofluorescence), which hampers IHC as it produces low signal-to-noise ratio. Here, we explored techniques to reduce autofluorescence using sodium borohydride (SBH), citrate buffer, and their combination on fish tissue preserved with paraformaldehyde, formaldehyde, ethanol, and glutaraldehyde. We found SBH was the most effective quenching technique, and applied this pretreatment to the gill or skin of 10 different archival fishes - including specimens that had been preserved in formaldehyde or ethanol for up to 65 and 37 years, respectively. The enzyme Na+/K+-ATPase (NKA) was successfully immunostained and imaged using confocal fluorescence microscopy, allowing for the identification and characterization of NKA-rich ionocytes essential for fish ionic and acid-base homeostasis. Altogether, our SBH-based method facilitates the use of IHC on archival samples, and unlocks the historical record on fish biological responses to environmental factors (such as climate change) using specimens from natural history collections that were preserved decades to centuries ago.
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Affiliation(s)
- Garfield T Kwan
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, USA; NOAA Fisheries Service, Southwest Fisheries Science Center, La Jolla, CA, USA.
| | - Benjamin W Frable
- Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego, USA
| | - Andrew R Thompson
- NOAA Fisheries Service, Southwest Fisheries Science Center, La Jolla, CA, USA
| | - Martin Tresguerres
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, USA
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7
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Frable BW, Melo BF, Fontenelle JP, Oliveira C, Sidlauskas BL. Biogeographic reconstruction of the migratory Neotropical fish family Prochilodontidae (Teleostei: Characiformes). ZOOL SCR 2022. [DOI: 10.1111/zsc.12531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Benjamin W. Frable
- Marine Vertebrate Collection Scripps Institution of Oceanography University of California San Diego La Jolla California USA
| | - Bruno F. Melo
- Department of Ichthyology American Museum of Natural History New York New York USA
| | - João P. Fontenelle
- Institute of Forestry and Conservation University of Toronto Toronto Ontario Canada
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências Universidade Estadual Paulista Botucatu São Paulo Brazil
| | - Brian L. Sidlauskas
- Department of Fisheries, Wildlife and Conservation Sciences Oregon State University Corvallis Oregon USA
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8
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Tea YK, Allen GR, Goatley CHR, Gill AC, Frable BW. Redescription of Conniella apterygia Allen and its reassignment in the genus Cirrhilabrus Temminck and Schlegel (Teleostei: Labridae), with comments on cirrhilabrin pelvic morphology. Zootaxa 2021; 5061:493-509. [PMID: 34810612 DOI: 10.11646/zootaxa.5061.3.5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Indexed: 11/04/2022]
Abstract
Conniella apterygia is redescribed from re-examination of the holotype, two paratypes, and six additional specimens. The genus is closely allied to Cirrhilabrus, sharing similarities in general morphological and meristic details, but is separated from Cirrhilabrus and most other labrid fishes in lacking pelvic fins and a pelvic girdle. Recent molecular phylogenetic studies have provided strong evidence for the deep nesting of Conniella within Cirrhilabrus, contradicting its generic validity and suggesting that the loss of pelvic elements is autapomorphic. Consequently, the species is redescribed and assigned to the genus Cirrhilabrus, as Cirrhilabrus apterygia new combination. The pelvic morphologies of related cirrhilabrin labrids are discussed, and a new synapomorphy is identified for Paracheilinus.
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Affiliation(s)
- Yi-Kai Tea
- School of Life and Environmental Sciences, University of Sydney, New South Wales 2006, Australia. 2Ichthyology, Australian Museum Research Institute, 1 William Street, Sydney, New South Wales 2010, Australia..
| | - Gerald R Allen
- Department of Aquatic Zoology, Western Australian Museum, Locked Bag 49, Welshpool DC, Perth, Western Australia 6986, Australia. .
| | - Christopher H R Goatley
- Ichthyology, Australian Museum Research Institute, 1 William Street, Sydney, New South Wales 2010, Australia. Function, Evolution and Anatomy Research (FEAR) Lab, School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia. .
| | - Anthony C Gill
- School of Life and Environmental Sciences, University of Sydney, New South Wales 2006, Australia. 2Ichthyology, Australian Museum Research Institute, 1 William Street, Sydney, New South Wales 2010, Australia..
| | - Benjamin W Frable
- Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0244, USA. .
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Prokofiev AM, Frable BW. A New Species of Photonectes from the Pacific Ocean off Oahu, Hawaii with a Revised Identification Key for the Genus (Teleostei: Stomiidae: Melanostomiinae). Ichthyology & Herpetology 2021. [DOI: 10.1643/i2020148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Artem M. Prokofiev
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii prospect 33, Moscow 119071, Russia (address for correspondence); and P. P. Shirshov Institute of Oceanology, Russian Academy of Sciences, Nakhimovsky prospect
| | - Benjamin W. Frable
- Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093-0244; . Send reprint requests to this address
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11
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Gold Z, Curd EE, Goodwin KD, Choi ES, Frable BW, Thompson AR, Walker HJ, Burton RS, Kacev D, Martz LD, Barber PH. Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem. Mol Ecol Resour 2021; 21:2546-2564. [PMID: 34235858 DOI: 10.1111/1755-0998.13450] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/25/2021] [Accepted: 06/03/2021] [Indexed: 01/08/2023]
Abstract
DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross-validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus-specific validation efforts.
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Affiliation(s)
- Zachary Gold
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Emily E Curd
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Kelly D Goodwin
- Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Stationed at Southwest Fisheries Science Center, La Jolla, California, USA
| | - Emma S Choi
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Benjamin W Frable
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Andrew R Thompson
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, La Jolla, California, USA
| | - Harold J Walker
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Ronald S Burton
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Dovi Kacev
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Lucas D Martz
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Paul H Barber
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
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Frable BW, Mccrea MH, Love MS, Craig MT. A new maximum size for the family Nomeidae and the third record of a longfin cigarfish, Cubiceps paradoxus (Stromateoidei: Nomeidae) from California, USA. J Fish Biol 2020; 97:1573-1575. [PMID: 32876944 DOI: 10.1111/jfb.14516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
We report the largest specimen from the stromateoid family Nomeidae. The specimen, measuring 1283 mm total length unpreserved, was caught on hook and line from shore in Port Hueneme, California, USA in June 2019. Despite scavenging damage, the specimen was identified as a longfin cigarfish, Cubiceps paradoxus, using morphological characters and molecular techniques. This is the third record of C. paradoxus from California. We also provide an account of a previously unreported C. paradoxus collected off the US-Mexico Border in 1999 that was examined but not preserved.
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Affiliation(s)
- Benjamin W Frable
- Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Merit H Mccrea
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
| | - Milton S Love
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
| | - Matthew T Craig
- NOAA, National Marine Fisheries Service, Southwest Fisheries Science Center, La Jolla, California, USA
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13
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Affiliation(s)
- Benjamin W. Frable
- Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California;
| | - Yi-Kai Tea
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia; . Send reprint requests to this address
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Tea YK, Frable BW, Gill AC. Erratum to: Cirrhilabrus cyanogularis, a new species of fairy wrasse from the Philippines and Indonesia (Teleostei: Labridae). Zootaxa 2018; 4483:187. [PMID: 30313803 DOI: 10.11646/zootaxa.4483.1.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Indexed: 11/04/2022]
Abstract
Following publication of the original article (Tea et al., 2018), an error was noted in the museum registration number for the holotype of the new species Cirrhilabrus cyanogularis (PNM 15354). This registration number is a duplicate number already in use for the holotype of Cirrhilabrus shutmani (Tea Gill, 2017). The new registration number for the holotype of Cirrhilabrus cyanogularis is now PNM 15360.
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Affiliation(s)
- Yi-Kai Tea
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia..
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Frable BW, Melo BF, Sidlauskas BL, Hoekzema K, Vari RP, Oliveira C. Data on the multilocus molecular phylogenies of the Neotropical fish family Prochilodontidae (Teleostei: Characiformes). Data Brief 2016; 9:128-42. [PMID: 27642619 PMCID: PMC5018087 DOI: 10.1016/j.dib.2016.08.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/01/2016] [Accepted: 08/08/2016] [Indexed: 11/26/2022] Open
Abstract
The data presented herein support the article "Molecular phylogenetics of the Neotropical fish family Prochilodontidae (Teleostei: Characiformes)" (B.F. Melo, B.L. Sidlauskas, B.W. Frable, K. Hoekzema, R.P. Vari, C. Oliveira, 2016) [1], which inferred phylogenetic relationships of the prochilodontids from an alignment of three mitochondrial and three nuclear loci (5279 bp) for all 21 recognized prochilodontid species and 22 related species. Herein, we provide primer sequences, museum voucher information and GenBank accession numbers. Additionally, we more fully describe the maximum-likelihood and Bayesian phylogenetic analyses of the concatenated dataset, detail the Bayesian species tree analysis, and provide the maximum likelihood topologies congruent with prior morphological hypotheses that were compared with the unconstrained tree using Shimodaira-Hasegawa tests.
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Affiliation(s)
- Benjamin W Frable
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA; Marine Vertebrate Collection, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Bruno F Melo
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Brian L Sidlauskas
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Kendra Hoekzema
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Richard P Vari
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
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Melo BF, Sidlauskas BL, Hoekzema K, Frable BW, Vari RP, Oliveira C. Molecular phylogenetics of the Neotropical fish family Prochilodontidae (Teleostei: Characiformes). Mol Phylogenet Evol 2016; 102:189-201. [PMID: 27262428 DOI: 10.1016/j.ympev.2016.05.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/14/2016] [Accepted: 05/29/2016] [Indexed: 11/28/2022]
Abstract
Migratory detritivores of the characiform family Prochilodontidae occur throughout the freshwaters of much of South America. Prochilodontids often form massive populations and many species achieve substantial body sizes; a combination that makes them one of the most commercially important fish groups on the continent. Their economic significance notwithstanding, prochilodontids have never been the subject of a comprehensive molecular phylogenetic analysis. Using three mitochondrial and three nuclear loci spanning all prochilodontid species, we generated a novel phylogenetic hypothesis for the family. Our results strongly support monophyly of the family and the three included genera. A novel, highly supported placement of Ichthyoelephas sister to the clade containing Prochilodus and Semaprochilodus diverges from a previous morphological hypothesis. Most previously hypothesized interspecific relationships are corroborated and some longstanding polytomies within Prochilodus and Semaprochilodus are resolved. The morphologically similar P. brevis, P. lacustris, P. nigricans and P. rubrotaeniatus are embedded within what is herein designated as the P. nigricans group. Species limits and distributions of these species are problematic and the group clearly merits taxonomic revision.
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Affiliation(s)
- Bruno F Melo
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
| | - Brian L Sidlauskas
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Kendra Hoekzema
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Benjamin W Frable
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Richard P Vari
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
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