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The mitochondrial genome of the red icefish (Channichthys rugosus) casts doubt on its species status. Polar Biol 2022; 45:1541-1552. [DOI: 10.1007/s00300-022-03083-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/30/2022] [Accepted: 08/31/2022] [Indexed: 11/27/2022]
Abstract
AbstractAntarctic notothenioid fishes are recognised as one of the rare examples of adaptive radiation in the marine system. Withstanding the freezing temperatures of Antarctic waters, these fishes have diversified into over 100 species within no more than 10–20 million years. However, the exact species richness of the radiation remains contested. In the genus Channichthys, between one and nine species are recognised by different authors. To resolve the number of Channichthys species, genetic information would be highly valuable; however, so far, only sequences of a single species, C. rhinoceratus, are available. Here, we present the nearly complete sequence of the mitochondrial genome of C. rugosus, obtained from a formalin-fixed museum specimen sampled in 1974. This sequence differs from the mitochondrial genome of C. rhinoceratus in no more than 27 positions, suggesting that the two species may be synonymous.
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DNA barcoding provides insights into Fish Diversity and Molecular Taxonomy of the Amundsen Sea. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01273-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Genome survey and microsatellite motif identification of Pogonophryne albipinna. Biosci Rep 2021; 41:229204. [PMID: 34223611 PMCID: PMC8292760 DOI: 10.1042/bsr20210824] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/25/2022] Open
Abstract
The genus Pogonophryne is a speciose group that includes 28 species inhabiting the coastal or deep waters of the Antarctic Southern Ocean. The genus has been divided into five species groups, among which the P. albipinna group is the most deep-living group and is characterized by a lack of spots on the top of the head. Here, we carried out genome survey sequencing of P. albipinna using the Illumina HiSeq platform to estimate the genomic characteristics and identify genome-wide microsatellite motifs. The genome size was predicted to be ∼883.8 Mb by K-mer analysis (K = 25), and the heterozygosity and repeat ratio were 0.289 and 39.03%, respectively. The genome sequences were assembled into 571624 contigs, covering a total length of ∼819.3 Mb with an N50 of 2867 bp. A total of 2217422 simple sequence repeat (SSR) motifs were identified from the assembly data, and the number of repeats decreased as the length and number of repeats increased. These data will provide a useful foundation for the development of new molecular markers for the P. albipinna group as well as for further whole-genome sequencing of P. albipinna.
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Parker E, Dornburg A, Struthers CD, Jones CD, Near TJ. Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation. Syst Biol 2021; 71:58-77. [PMID: 34247239 DOI: 10.1093/sysbio/syab057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 07/06/2021] [Accepted: 06/30/2021] [Indexed: 11/14/2022] Open
Abstract
Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are evaluated together, is becoming increasingly apparent. Here, we integrate phylogenetic, population genetic, and coalescent analyses of genome-wide sequence data with investigation of variation in multiple morphological traits to delimit species within the Antarctic barbeled plunderfishes (Artedidraconidae: Pogonophryne). Pogonophryne currently comprises 29 valid species, most of which are distinguished solely by variation in ornamentation of the mental barbel that projects from the lower jaw, a structure previously shown to vary widely within a single species. However, our genomic and phenotypic analyses result in a dramatic reduction in the number of distinct species recognized within the clade, providing evidence to support the recognition of no more than six species. We propose to synonymize 24 of the currently recognized species with five species of Pogonophryne. We find genomic and phenotypic evidence for a new species of Pogonophryne from specimens collected in the Ross Sea. Our findings represent a rare example in which application of molecular data provides evidence of taxonomic oversplitting on the basis of morphology, clearly demonstrating the utility of an integrative species delimitation framework.
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Affiliation(s)
- Elyse Parker
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, Charlotte, NC 28223, USA
| | - Carl D Struthers
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Christopher D Jones
- Antarctic Ecosystem Research Division, NOAA Southwest Fisheries Science Center, La Jolla, CA 92037, USA
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA.,Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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Biogeography of the Antarctic dragonfishes Acanthodraco dewitti and Psilodraco breviceps with re-description of Acanthodraco dewitti larvae (Notothenioidei: Bathydraconidae). Polar Biol 2020. [DOI: 10.1007/s00300-020-02661-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Christiansen H, Dettai A, Heindler FM, Collins MA, Duhamel G, Hautecoeur M, Steinke D, Volckaert FAM, Van de Putte AP. Diversity of Mesopelagic Fishes in the Southern Ocean - A Phylogeographic Perspective Using DNA Barcoding. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Yoon TH, Kang HE, Lee SR, Lee JB, Baeck GW, Park H, Kim HW. Metabarcoding analysis of the stomach contents of the Antarctic Toothfish ( Dissostichus mawsoni) collected in the Antarctic Ocean. PeerJ 2017; 5:e3977. [PMID: 29134141 PMCID: PMC5680711 DOI: 10.7717/peerj.3977] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/10/2017] [Indexed: 01/23/2023] Open
Abstract
Stomach contents of the Antarctic toothfish, Dissostichus mawsoni, collected from subareas 58.4 and 88.3, were analyzed using next generation sequencing (NGS) technology. After processing the raw reads generated by the MiSeq platform, a total of 131,233 contigs (130 operational taxonomic units [OTUs]) were obtained from 163 individuals in subarea 58.4, and 75,961 contigs (105 OTUs) from 164 fish in subarea 88.3. At 98% sequence identity, species names were assigned to most OTUs in this study, indicating the quality of the DNA barcode database for the Antarctic Ocean was sufficient for molecular analysis, especially for fish species. A total of 19 species was identified from the stomach of D. mawsoni in this study, which included 14 fish species and five mollusks. More than 90% of contigs belonged to fish species, supporting the postulate that the major prey of D. mawsoni are fish. Two fish species, Macrourus whitsoni and Chionobathyscus dewitti, were the most important prey items (a finding similar to that of previous studies). We also obtained genotypes of prey items by NGS analysis, identifying an additional 17 representative haplotypes in this study. Comparison with three previous morphological studies and the NGS-based molecular identification in this study extended our knowledge regarding the prey of D. mawsoni, which previously was not possible. These results suggested that NGS-based diet studies are possible, if several current technical limitations, including the quality of the barcode database or the development of precise molecular quantification techniques to link them with morphological values, are overcome. To achieve this, additional studies should be conducted on various marine organisms.
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Affiliation(s)
- Tae-Ho Yoon
- Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan, Republic of Korea
| | - Hye-Eun Kang
- Department of Marine Biology, Pukyong National University, Busan, Republic of Korea
| | - Soo Rin Lee
- Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan, Republic of Korea
| | - Jae-Bong Lee
- National Institute of Fisheries Science (NIFS), Busan, Republic of Korea
| | - Gun Wook Baeck
- Department of Seafood & Aquaculture Science/Institute of Marine Industry/Marine Bio-Education & Research Center, College of Marine Science, Gyeongsang National University, Tongyeong, Republic of Korea
| | - Hyun Park
- Korea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon, Republic of Korea
| | - Hyun-Woo Kim
- Interdisciplinary Program of Biomedical, Mechanical and Electrical Engineering, Pukyong National University, Busan, Republic of Korea.,Department of Marine Biology, Pukyong National University, Busan, Republic of Korea
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Dornburg A, Eytan RI, Federman S, Pennington JN, Stewart AL, Jones CD, Near TJ. Molecular data support the existence of two species of the Antarctic fish genus Cryodraco (Channichthyidae). Polar Biol 2015. [DOI: 10.1007/s00300-015-1859-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sparks JS, Schelly RC, Smith WL, Davis MP, Tchernov D, Pieribone VA, Gruber DF. The covert world of fish biofluorescence: a phylogenetically widespread and phenotypically variable phenomenon. PLoS One 2014; 9:e83259. [PMID: 24421880 PMCID: PMC3885428 DOI: 10.1371/journal.pone.0083259] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 10/31/2013] [Indexed: 12/30/2022] Open
Abstract
The discovery of fluorescent proteins has revolutionized experimental biology. Whereas the majority of fluorescent proteins have been identified from cnidarians, recently several fluorescent proteins have been isolated across the animal tree of life. Here we show that biofluorescence is not only phylogenetically widespread, but is also phenotypically variable across both cartilaginous and bony fishes, highlighting its evolutionary history and the possibility for discovery of numerous novel fluorescent proteins. Fish biofluorescence is especially common and morphologically variable in cryptically patterned coral-reef lineages. We identified 16 orders, 50 families, 105 genera, and more than 180 species of biofluorescent fishes. We have also reconstructed our current understanding of the phylogenetic distribution of biofluorescence for ray-finned fishes. The presence of yellow long-pass intraocular filters in many biofluorescent fish lineages and the substantive color vision capabilities of coral-reef fishes suggest that they are capable of detecting fluoresced light. We present species-specific emission patterns among closely related species, indicating that biofluorescence potentially functions in intraspecific communication and evidence that fluorescence can be used for camouflage. This research provides insight into the distribution, evolution, and phenotypic variability of biofluorescence in marine lineages and examines the role this variation may play.
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Affiliation(s)
- John S. Sparks
- Department of Ichthyology, American Museum of Natural History, Division of Vertebrate Zoology, New York, New York United States of America
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Robert C. Schelly
- Department of Ichthyology, American Museum of Natural History, Division of Vertebrate Zoology, New York, New York United States of America
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - W. Leo Smith
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Matthew P. Davis
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Dan Tchernov
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Mount Carmel, Haifa, Israel
| | - Vincent A. Pieribone
- Department of Ichthyology, American Museum of Natural History, Division of Vertebrate Zoology, New York, New York United States of America
- Department of Cellular and Molecular Physiology, The John B. Pierce Laboratory, Inc., Yale University, New Haven, Connecticut, United States of America
| | - David F. Gruber
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Department of Natural Sciences, Baruch College, City University of New York, New York, New York, United States of America
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