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Maduna SN, Vivian-Smith A, Jónsdóttir ÓDB, Imsland AK, Klütsch CF, Nyman T, Eiken HG, Hagen SB. Mitogenomics of the suborder Cottoidei (Teleostei: Perciformes): Improved assemblies, mitogenome features, phylogeny, and ecological implications. Genomics 2022; 114:110297. [DOI: 10.1016/j.ygeno.2022.110297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 01/05/2022] [Accepted: 02/01/2022] [Indexed: 11/04/2022]
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Gerringer ME, Dias AS, von Hagel AA, Orr JW, Summers AP, Farina S. Habitat influences skeletal morphology and density in the snailfishes (family Liparidae). Front Zool 2021; 18:16. [PMID: 33863343 PMCID: PMC8052763 DOI: 10.1186/s12983-021-00399-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/14/2021] [Indexed: 12/23/2022] Open
Abstract
We tested the hypothesis that deep-sea fishes have poorly mineralized bone relative to shallower-dwelling species using data from a single family that spans a large depth range. The family Liparidae (snailfishes, Cottiformes) has representatives across the entire habitable depth range for bony fishes (0 m-> 8000 m), making them an ideal model for studying depth-related trends in a confined phylogeny. We used micro-computed tomography (micro-CT) scanning to test three aspects of skeletal reduction in snailfishes (50 species) across a full range of habitat depths: 1) reduction of structural dimensions, 2) loss of skeletal elements, and 3) reduction in bone density. Using depth data from the literature, we found that with increasing depth, the length of the dentary, neurocranium, and suborbital bones decreases. The ventral suction disk decreases width with increasing maximum habitat depth and is lost entirely in some deeper-living taxa, though not all. Although visual declines in bone density in deeper-living taxa were evident across full skeletons, individual densities of the lower jaw, vertebra, suction disk, hypural plate, and otoliths did not significantly decline with any depth metric. However, pelagic and polar taxa tended to show lower density bones compared to other species in the family. We propose that skeletal reductions allow snailfishes to maintain neutral buoyancy at great depths in the water column, while supporting efficient feeding and locomotion strategies. These findings suggest that changes in skeletal structure are non-linear and are driven not only by hydrostatic pressure, but by other environmental factors and by evolutionary ancestry, calling the existing paradigm into question.
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Affiliation(s)
- M E Gerringer
- State University of New York at Geneseo, Geneseo, NY, 14454, USA.
| | - A S Dias
- Whitman College, Walla Walla, WA, 99362, USA
| | | | - J W Orr
- Alaska Fisheries Science Center, RACE Division, NOAA Fisheries, Seattle, WA, 98115, USA
| | - A P Summers
- Friday Harbor Labs, Biology and SAFS, University of Washington, Friday Harbor, WA, 98250, USA
| | - S Farina
- Howard University, Washington, DC, 20059, USA
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Orr JW, Pitruk DL, Manning R, Stevenson DE, Gardner JR, Spies I. A New Species of Snailfish (Cottiformes: Liparidae) Closely Related to Careproctus melanurus of the Eastern North Pacific. COPEIA 2020. [DOI: 10.1643/ci2020008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- James W. Orr
- NOAA, National Marine Fisheries Service, Alaska Fisheries Science Center, Resource Assessment and Conservation Engineering Division, 7600 Sand Point Way NE, Seattle, Washington 98115; (JWO) ; and (DES)
| | - Dmitry L. Pitruk
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, ul. Palchevskogo 17, Vladivostok 690041, Russia;
| | - Rachel Manning
- School of Aquatic and Fishery Sciences, and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington 98195; (RM) ; and (JRG)
| | - Duane E. Stevenson
- NOAA, National Marine Fisheries Service, Alaska Fisheries Science Center, Resource Assessment and Conservation Engineering Division, 7600 Sand Point Way NE, Seattle, Washington 98115; (JWO) ; and (DES)
| | - Jennifer R. Gardner
- School of Aquatic and Fishery Sciences, and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington 98195; (RM) ; and (JRG)
| | - Ingrid Spies
- NOAA, National Marine Fisheries Service, Alaska Fisheries Science Center, Resource Ecology and Fisheries Management Division, 7600 Sand Point Way NE, Seattle, Washington 98115;
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Levin LA, Rouse GW. Giant protists (xenophyophores) function as fish nurseries. Ecology 2020; 101:e02933. [PMID: 31742677 PMCID: PMC7341444 DOI: 10.1002/ecy.2933] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/30/2019] [Accepted: 10/18/2019] [Indexed: 12/02/2022]
Affiliation(s)
- Lisa A. Levin
- Scripps Institution of OceanographyUniversity of California, San DiegoLa JollaCalifornia92093USA
| | - Greg W. Rouse
- Scripps Institution of OceanographyUniversity of California, San DiegoLa JollaCalifornia92093USA
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5
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Shen Y, Dai W, Gao Z, Yan G, Gan X, He S. Molecular phylogeny and divergence time estimates using the mitochondrial genome for the hadal snailfish from the Mariana trench. Sci Bull (Beijing) 2017; 62:1106-1108. [PMID: 36659340 DOI: 10.1016/j.scib.2017.07.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 01/21/2023]
Affiliation(s)
- Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Wei Dai
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhaoming Gao
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Guoyong Yan
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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6
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Orr JW. Two New Species of Snailfishes of the GenusCareproctus(Liparidae) from the Aleutian Islands, Alaska. COPEIA 2016. [DOI: 10.1643/ci-15-378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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7
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Manda P, Balhoff JP, Lapp H, Mabee P, Vision TJ. Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 2015. [PMID: 26220875 DOI: 10.1002/dvg.22878] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The abundance of phenotypic diversity among species can enrich our knowledge of development and genetics beyond the limits of variation that can be observed in model organisms. The Phenoscape Knowledgebase (KB) is designed to enable exploration and discovery of phenotypic variation among species. Because phenotypes in the KB are annotated using standard ontologies, evolutionary phenotypes can be compared with phenotypes from genetic perturbations in model organisms. To illustrate the power of this approach, we review the use of the KB to find taxa showing evolutionary variation similar to that of a query gene. Matches are made between the full set of phenotypes described for a gene and an evolutionary profile, the latter of which is defined as the set of phenotypes that are variable among the daughters of any node on the taxonomic tree. Phenoscape's semantic similarity interface allows the user to assess the statistical significance of each match and flags matches that may only result from differences in annotation coverage between genetic and evolutionary studies. Tools such as this will help meet the challenge of relating the growing volume of genetic knowledge in model organisms to the diversity of phenotypes in nature. The Phenoscape KB is available at http://kb.phenoscape.org.
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Affiliation(s)
- Prashanti Manda
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina.,US National Evolutionary Synthesis Center, Durham, North Carolina
| | - James P Balhoff
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina.,US National Evolutionary Synthesis Center, Durham, North Carolina
| | - Hilmar Lapp
- US National Evolutionary Synthesis Center, Durham, North Carolina.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
| | - Paula Mabee
- Department of Biology, University of South Dakota, Vermillion, South Dakota
| | - Todd J Vision
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina.,US National Evolutionary Synthesis Center, Durham, North Carolina
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8
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Phylogeny and taxonomy of sculpins, sandfishes, and snailfishes (Perciformes: Cottoidei) with comments on the phylogenetic significance of their early-life-history specializations. Mol Phylogenet Evol 2014; 79:332-52. [PMID: 25014569 DOI: 10.1016/j.ympev.2014.06.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/27/2014] [Accepted: 06/30/2014] [Indexed: 11/21/2022]
Abstract
Despite recent progress on the higher-level relationships of the Cottoidei and its familial components, phylogenetic conflict and uncertainty remain within the Cottoidea. We analyzed a dataset composed of 4518 molecular (mitochondrial 12S, tRNA-Val, 16S, and cytochrome b and nuclear TMO-4c4, Histone H3, and 28S) and 72 morphological characters for 69 terminals to address cottoid intrarelationships. The resulting well-resolved phylogeny was used to produce a revised taxonomy that is consistent with the available molecular and morphological data and recognizes six families: Agonidae, Cottidae, Jordaniidae, Psychrolutidae, Rhamphocottidae, and Scorpaenichthyidae. The traditional Agonidae was expanded to include traditional hemitripterids and Hemilepidotus. The traditional Cottidae was restricted to Leptocottus, Trachidermus, and the riverine, lacustrine, and Lake Baikal freshwater cottoids. Jordaniidae (Jordania and Paricelinus) was separated from the traditional cottids; Psychrolutidae was expanded from the traditional grouping to include nearly all traditional marine cottids and the single species of bathylutichthyid. Rhamphocottidae was expanded to include the traditional ereuniids, and Scorpaenichthyidae separated Scorpaenichthys from the traditional cottids. The importance of early-life-history characters to the resulting phylogeny and taxonomy were highlighted.
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Morgan JAT, Macbeth M, Broderick D, Whatmore P, Street R, Welch DJ, Ovenden JR. Hybridisation, paternal leakage and mitochondrial DNA linearization in three anomalous fish (Scombridae). Mitochondrion 2013; 13:852-61. [PMID: 23774068 DOI: 10.1016/j.mito.2013.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/04/2013] [Accepted: 06/07/2013] [Indexed: 11/16/2022]
Abstract
Using mitochondrial DNA for species identification and population studies assumes that the genome is maternally inherited, circular, located in the cytoplasm and lacks recombination. This study explores the mitochondrial genomes of three anomalous mackerel. Complete mitochondrial genome sequencing plus nuclear microsatellite genotyping of these fish identified them as Scomberomorus munroi (spotted mackerel). Unlike normal S. munroi, these three fish also contained different linear, mitochondrial genomes of Scomberomorus semifasciatus (grey mackerel). The results are best explained by hybridisation, paternal leakage and mitochondrial DNA linearization. This unusual observation may provide an explanation for mtDNA outliers in animal population studies.
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Affiliation(s)
- Jess A T Morgan
- Molecular Fisheries Laboratory, University of Queensland, PO Box 6097, St Lucia, Queensland 4072, Australia; Queensland Alliance for Agriculture and Food Innovation, University of Queensland, 306 Carmody Rd, St Lucia, Queensland 4072, Australia.
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Abstract
The FISH-BOL campaign was initiated in 2005, and currently has barcoded for the cytochrome c oxidase subunit I (COI) gene about 8,000 of the 31,000 fish species currently recognised. This includes the great majority of the world's most important commercial species. Results thus far show that about 98% and 93% of marine and freshwater species, respectively, are barcode distinguishable. One important issue that needs to be more fully addressed in FISH-BOL concerns the initial misidentification of a small number of barcode reference specimens. This is unsurprising considering the large number of fish species, some of which are morphologically very similar and others as yet unrecognised, but constant vigilance and ongoing attention by the FISH-BOL community is required to eliminate such errors. Once the reference library has been established, barcoding enables the identification of unknown fishes at any life history stage or from their fragmentary remains. The many uses of the FISH-BOL barcode library include detecting consumer fraud, aiding fisheries management, improving ecological analyses including food web syntheses, and assisting with taxonomic revisions.
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Affiliation(s)
- Robert D Ward
- Wealth from Oceans Flagship, CSIRO Marine and Atmospheric Research, Tasmania, Australia.
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Baharum SN, Nurdalila AA. Application of 16s rDNA and cytochrome b ribosomal markers in studies of lineage and fish populations structure of aquatic species. Mol Biol Rep 2011; 39:5225-32. [PMID: 22167328 DOI: 10.1007/s11033-011-1320-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 12/03/2011] [Indexed: 12/13/2022]
Abstract
The most economically important form of aquaculture is fish farming, which is an industry that accounts for an ever increasing share of world fishery production. Molecular markers can be used to enhance the productivity of the aquaculture and fish industries to meet the increasing demand. Molecular markers can be identified via a DNA test regardless of the developmental stage, age or environmental challenges experienced by the organism. The application of 16s and cytochrome b markers has enabled rapid progress in investigations of genetic variability and inbreeding, parentage assignments, species and strain identification and the construction of high resolution genetic linkage maps for aquaculture fisheries. In this review, the advantages of principles and potential power tools of 16s and cytochrome b markers are discussed. Main findings in term of trend, aspects and debates on the reviewed issue made from the model of aquatic species for the benefit of aquaculture genomics and aquaculture genetics research are discussed. The concepts in this review are illustrated with various research examples and results that relate theory to reality and provide a strong review of the current status of these biotechnology topics.
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Affiliation(s)
- Syarul Nataqain Baharum
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia.
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12
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Teimori A, Abd Jalil Jawad L, Al-Kharusi LH, Al-Mamry JM, Reichenbacher B. Late Pleistocene to Holocene diversification and historical zoogeography of the Arabian killifish (<i>Aphanius dispar</i>) inferred from otolith morphology. SCIENTIA MARINA 2011; 0. [DOI: 10.3989/scimar.03635.26c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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13
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Teletchea F. After 7 years and 1000 citations: Comparative assessment of the DNA barcoding and the DNA taxonomy proposals for taxonomists and non-taxonomists. ACTA ACUST UNITED AC 2010; 21:206-26. [DOI: 10.3109/19401736.2010.532212] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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14
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Baldwin ZH, Orr JW. A New Species of the Snailfish Genus Paraliparis (Scorpaeniformes: Liparidae) from the Eastern Bering Sea. COPEIA 2010. [DOI: 10.1643/ci-09-228] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Lannoo MJ, Eastman JT, Orr JW. Nervous and Sensory Systems in Sub-Arctic and Antarctic Snailfishes of the Genus Paraliparis (Teleostei: Scorpaeniformes: Liparidae). COPEIA 2009. [DOI: 10.1643/cg-08-157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Raupach MJ, Mayer C, Malyutina M, Wägele JW. Multiple origins of deep-sea Asellota (Crustacea: Isopoda) from shallow waters revealed by molecular data. Proc Biol Sci 2009; 276:799-808. [PMID: 19033145 PMCID: PMC2664356 DOI: 10.1098/rspb.2008.1063] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Asellota are a highly variable group of Isopoda with many species in freshwater and marine shallow-water environments. However, in the deep sea, they show their most impressive radiation with a broad range of astonishing morphological adaptations and bizarre body forms. Nevertheless, the evolution and phylogeny of the deep-sea Asellota are poorly known because of difficulties in scoring morphological characters. In this study, the molecular phylogeny of the Asellota is evaluated for 15 marine shallow-water species and 101 deep-sea species, using complete 18S and partial 28S rDNA gene sequences. Our molecular data support the monophyly of most deep-sea families and give evidence for a multiple colonization of the deep sea by at least four major lineages of asellote isopods. According to our molecular data, one of these lineages indicates an impressive radiation in the deep sea. Furthermore, the present study rejects the monophyly of the family Janiridae, a group of plesiomorphic shallow-water Asellota, and several shallow-water and deep-sea genera (Acanthaspidia, Ianthopsis, Haploniscus, Echinozone, Eurycope, Munnopsurus and Syneurycope).
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Affiliation(s)
- Michael J Raupach
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany.
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Jamieson AJ, Fujii T, Solan M, Matsumoto AK, Bagley PM, Priede IG. Liparid and macrourid fishes of the hadal zone: in situ observations of activity and feeding behaviour. Proc Biol Sci 2009; 276:1037-45. [PMID: 19129104 DOI: 10.1098/rspb.2008.1670] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Using baited camera landers, the first images of living fishes were recorded in the hadal zone (6000-11000 m) in the Pacific Ocean. The widespread abyssal macrourid Coryphaenoides yaquinae was observed at a new depth record of approximately 7000 m in the Japan Trench. Two endemic species of liparid were observed at similar depths: Pseudoliparis amblystomopsis in the Japan Trench and Notoliparis kermadecensis in the Kermadec Trench. From these observations, we have documented swimming and feeding behaviour of these species and derived the first estimates of hadal fish abundance. The liparids intercepted bait within 100-200 min but were observed to preferentially feed on scavenging amphipods. Notoliparis kermadecensis act as top predators in the hadal food web, exhibiting up to nine suction-feeding events per minute. Both species showed distinctive swimming gaits: P. amblystomopsis (mean length 22.5 cm) displayed a mean tail-beat frequency of 0.47 Hz and mean caudal:pectoral frequency ratio of 0.76, whereas N. kermadecensis (mean length 31.5 cm) displayed respective values of 1.04 and 2.08 Hz. Despite living at extreme depths, these endemic liparids exhibit similar activity levels compared with shallow-water liparids.
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Affiliation(s)
- A J Jamieson
- Oceanlab, University of Aberdeen, Main Street, Newburgh, Aberdeenshire AB41 6AA, UK.
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