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Published November 3, 2022 | Version v1
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Phylogeny Reconciles Classification in Antarctic Plunderfishes

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Parker, Elyse, Near, Thomas J. (2022): Phylogeny Reconciles Classification in Antarctic Plunderfishes. Ichthyology & Herpetology 110 (4): 662-674, DOI: 10.1643/i2021126, URL: http://dx.doi.org/10.1643/i2021126

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urn:lsid:plazi.org:pub:FFECCA3EFFCAFFD6FFD9FFED5959331B
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http://publication.plazi.org/id/FFECCA3EFFCAFFD6FFD9FFED5959331B

Has part
Taxonomic treatment: 10.5281/zenodo.7852574 (DOI)
Taxonomic treatment: http://treatment.plazi.org/id/03D5B246FFC9FFD5FF57FB995C3836E1 (URL)
Taxonomic treatment: 10.5281/zenodo.7858579 (DOI)
Taxonomic treatment: http://treatment.plazi.org/id/03D5B246FFC9FFD3FC82F9CC58B33178 (URL)
Taxonomic treatment: 10.5281/zenodo.7852576 (DOI)
Taxonomic treatment: http://treatment.plazi.org/id/03D5B246FFCFFFD0FF57FD6758F334F3 (URL)
Figure: 10.5281/zenodo.7846953 (DOI)
Figure: 10.5281/zenodo.7846955 (DOI)
Figure: 10.5281/zenodo.7846957 (DOI)
Figure: 10.5281/zenodo.7846959 (DOI)
Dataset: http://table.plazi.org/id/DF0353D8FFCDFFD1FF57F98358E63587 (URL)
Dataset: http://table.plazi.org/id/DF0353D8FFC2FFDEFFBEFF5F581B33FA (URL)
Is source of
Dataset: http://www.gbif.org/dataset/48f48695-9b0c-4ed8-b573-96aeff1c0b84 (URL)

References

  • Alda, F., V. A. Tagliacollo, M. J. Bernt, B. T. Waltz, W. B. Ludt, B. C. Faircloth, M. E. Alfaro, J. S. Albert, and P. Chakrabarty. 2018. Resolving deep nodes in an ancient radiation of Neotropical fishes in the presence of conflicting signals from incomplete lineage sorting. Systematic Biology 68:573-593.
  • Andriashev, A. P. 1965. A general review of the Antarctic fish fauna, p. 491-550. In: Biogeography and Ecology in Antarctica. J. v. Mieghem and P. v. Oye (eds.). Junk, The Hague.
  • Andriashev, A. P. 1967. Review of the plunder fishes of genus Pogonophryne Reagan (Harpagiferidae) with descriptions of five new species from the East Antarctic and South Orkney Islands, Pisces, Harpagiferidae. Explorations of the Fauna of the Seas IV. (XII). Biological Results of the Soviet Antarctic Expedition (1955-1958). Zoological Journal of the Academy of Sciences, U.S.S.R. 3:389-412.
  • Balushkin, A. V. 1992. Classification, phylogenetic relationships, and origins of the families of the suborder Notothenioidei (Perciformes). Journal of Ichthyology 32: 90-110.
  • Balushkin, A. V. 2000. Morphology, classification, and evolution of notothenioid fishes of the Southern Ocean (Notothenioidei, Perciformes). Journal of Ichthyology 40: S74-S109.
  • Bargelloni, L., S. Marcato, L. Zane, and T. Patarnello. 2000. Mitochondrial phylogeny of notothenioids: a molecular approach to Antarctic fish evolution and biogeography. Systematic Biology 49:114-129.
  • Bargelloni, L., P. A. Ritchie, T. Patarnello, B. Battaglia, D. M. Lambert, and A. Meyer. 1994. Molecular evolution at subzero temperatures: mitochondrial and nuclear phylogenies of fishes from Antarctica (suborder Notothenioidei), and the evolution of antifreeze glycopeptides. Molecular Biology and Evolution 11:854-863.
  • Bloch, M. E., and J. G. Schneider. 1801. Systema ichthyologiae iconibus cx illustratum. Sumtibus auctoris impressum et Bibliopolio Sanderiano commissum, Berolini.
  • Chen, L., A. L. DeVries, and C.-H. C. Cheng. 1997. Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish. Proceedings of the National Academy of Sciences of the United States of America 94:3811-3816.
  • Chifman, J., and L. Kubatko. 2014. Quartet inference from SNP data under the coalescent model. Bioinformatics 30: 3317-3324.
  • Clarke, A., and I. A. Johnston. 1996. Evolution and adaptive radiation of Antarctic fishes. Trends in Ecology & Evolution 11:212-218.
  • Colombo, M., M. Damerau, R. Hanel, W. Salzburger, and M. Matschiner. 2015. Diversity and disparity through time in the adaptive radiation of Antarctic notothenioid fishes. Journal of Evolutionary Biology 28:376-394.
  • Constable, A. J., W. K. de la Mare, D. J. Agnew, I. Everson, and D. Miller. 2000. Managing fisheries to conserve the Antarctic marine ecosystem: practical implementation of the Convention on the Conservation of Antarctic Marine Living Resources (CCAMLR). ICES Journal of Marine Science 57:778-791.
  • Daane, J. M., A. Dornburg, P. Smits, D. J. MacGuigan, M. B. Hawkins, T. J. Near, H. W. Detrich III, and M. P. Harris. 2019. Historical contingency shapes adaptive radiation in Antarctic fishes. Nature Ecology & Evolution 3:1102-1109.
  • Derome, N., W.-J. Chen, A. Dettai, C. Bonillo, and G. Lecointre. 2002. Phylogeny of Antarctic dragonfishes (Bathydraconidae, Notothenioidei, Teleostei) and related families based on their anatomy and two mitochondrial genes. Molecular Phylogenetics and Evolution 24:139-152.
  • Dettai, A., M. Berkani, A. C. Lautredou, A. Couloux, G. Lecointre, C. Ozouf-Costaz, and C. Gallut. 2012. Tracking the elusive monophyly of nototheniid fishes (Teleostei) with multiple mitochondrial and nuclear markers. Marine Genomics 8:49-58.
  • Dollo, L. 1904. Poissons. Expedition antarctique Belge. Resultats du voyage du S. Y. Belgica en 1897-1898-1899 sous le commandement de A. de Gerlache de Gomery. J.-E. Buschmann, Antwerp.
  • Dornburg, A., S. Federman, A. D. Lamb, C. D. Jones, and T. J. Near. 2017. Cradles and museums of Antarctic teleost biodiversity. Nature Ecology & Evolution 1:1379-1384.
  • Duhamel, G., N. Gasco, and P. Davaine. 2005. Poissons des iles Kerguelen et Crozet. Guide regional de l'ocean Austral. Patrimoines Naturels 63:1-419.
  • Eakin, R. R. 1981. Osteology and relationships of the fishes of the Antarctic family Harpagiferidae (Pisces, Notothenioidei), p. 81-147. In: Antarctic Research Series, vol. 31, Biology of the Antarctic Seas IX. L. S. Kornicker (ed.). American Geophysical Union, Washington, D.C.
  • Eakin, R. R. 1990. Artedidraconidae, p. 332-356. In: Fishes of the Southern Ocean. O. Gon and P. C. Heemstra (eds.). J. L. B. Smith Institute of Ichthyology, Grahamstown, South Africa.
  • Eakin, R. R., J. T. Eastman, and C. D. Jones. 2001. Mental barbel variation in Pogonophryne scotti Regan (Pisces: Perciformes: Artedidraconidae). Antarctic Science 13:363- 370.
  • Eakin, R. R., J. T. Eastman, and M. Vacchi. 2006. Sexual dimorphism and mental barbel structure in the South Georgia plunderfish Artedidraco mirus (Perciformes: Notothenioidei: Artedidraconidae). Polar Biology 30:45-52.
  • Eakin, R. R., E. Riginella, and M. La Mesa. 2015. A new species of Artedidraco (Pisces: Artedidraconidae) from the Weddell Sea, Antarctica. Polar Biology 38:1597-1603.
  • Eastman, J. T. 1993. Antarctic Fish Biology: Evolution in a Unique Environment. Academic Press, San Diego.
  • Eastman, J. T. 2000. Antarctic notothenioid fishes as subjects for research in evolutionary biology. Antarctic Science 12: 276-287.
  • Eastman, J. T., and R. R. Eakin. 1999. Fishes of the genus Artedidraco (Pisces, Artedidraconidae) from the Ross Sea, Antarctica, with the description of a new species and a colour morph. Antarctic Science 11:13-22.
  • Eastman, J. T., and R. R. Eakin. 2001. Mental barbel and meristic variation in the Antarctic notothenioid fish Dolloidraco longedorsalis (Perciformes: Artedidraconidae) from the Ross Sea. Polar Biology 24:729-734.
  • Eastman, J. T., and R. R. Eakin. 2021. Checklist of the species of notothenioid fishes. Antarctic Science 33:273- 280.
  • Eaton, D. A. R. 2014. PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. Bioinformatics 30:1844- 1849.
  • Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792-1797.
  • Galili, T. 2015. dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering. Bioinformatics 31:3718-3720.
  • Gill, T. 1861. Synopsis of the harpagiferoids. Proceedings of the Academy of Natural Sciences of Philadelphia 13:510- 512.
  • Grant, P. R. 1986. Ecology and Evolution of Darwin's Finches. Princeton University Press, Princeton, New Jersey.
  • Hastings, P. A. 1993. Relationships of fishes of the perciform suborder Notothenioidei, p. 99-107. In: A History and Atlas of the Fishes of the Antarctic Ocean. R. G. Miller (ed.). Foresta Institute for Ocean and Mountain Studies, Carson City, Nevada.
  • Hoang, D. T., O. Chernomor, A. Von Haeseler, B. Q. Minh, and L. S. Vinh. 2018. UFBoot2: improving the ultrafast bootstrap approximation. Molecular Biology and Evolution 35:518-522.
  • Huang, H., and L. L. Knowles. 2016. Unforeseen consequences of excluding missing data from next-generation sequences: simulation study of RAD sequences. Systematic Biology 65:357-365.
  • Hureau, J.-C. 1985. Artedidraconidae, p. 245-251. In: FAO Species Identification Sheets for Fishery Purposes. Southern Ocean (Fishing Areas 48, 58, and 88) (CCAMLR Convention Area), volume 2. W. Fisher and J.-C. Hureau (eds.). FAO, Rome.
  • Hureau, J.-C. 1986. Relations phylogenetiques au sein des Notothenioidei. Oceanis 12:367-376.
  • Hureau, J.-C. 1990. Harpagiferidae, p. 357-363. In: Fishes of the Southern Ocean. O. Gon and P. C. Heemstra (eds.). J. L. B. Smith Institute of Ichthyology, Grahamstown, South Africa.
  • Iwami, T. 1985. Osteology and relationships of the family Channichthyidae. Memoirs of the National Institute of Polar Research, Tokyo 36:1-69.
  • Kalyaanamoorthy, S., B. Q. Minh, T. K. F. Wong, A. von Haeseler, and L. S. Jermiin. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods 14:587-589.
  • Kolde, R. 2018. Pretty heatmaps. R package version 1.0.10. https://CRAN.R-project.org/package¼pheatmap
  • La Mesa, M., and M. Vacchi. 2005. On the second record of the Antarctic plunderfish Artedidraco glareobarbatus (Artedidraconidae) from the Ross Sea. Polar Biology 29:40-43.
  • La Mesa, M., J. T. Eastman, and M. Vacchi. 2004. The role of notothenioid fish in the food web of the Ross Sea shelf waters: a review. Polar Biology 27:321-338.
  • Lecointre, G., C. Gallut, C. Bonillo, A. Couloux, C. Ozouf-Costaz, and A. Dettai. 2011. The Antarctic fish genus Artedidraco is paraphyletic (Teleostei, Notothenioidei, Artedidraconidae). Polar Biology 34:1135-1145.
  • Lombarte, A., I. Olaso, and A. Bozzano. 2003. Ecomorphological trends in the Artedidraconidae (Pisces: Perciformes: Notothenioidei) of the Weddell Sea. Antarctic Science 15: 211-218.
  • Lonnberg, E. 1905. The fishes of the Sweedish South Polar Expedition. Wissenschaftliche Ergebnisse der Schwedischen Sudpolar-Expedition 1901-1903 5:1-69.
  • Mastretta-Yanes, A., N. Arrigo, N. Alvarez, T. H. Jorgensen, D. Pinero, and B. C. Emerson. 2015. Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference. Molecular Ecology Resources 15:28-41.
  • Matschiner, M., R. Hanel, and W. Salzburger. 2011. On the origin and trigger of the notothenioid adaptive radiation. PLoS ONE 6:e18911.
  • McCartney-Melstad, E., M. Gidis, and H. B. Shaffer. 2019. An empirical pipeline for choosing the optimal clustering threshold in RADseq studies. Molecular Ecology Resources 19:1195-1204.
  • McCormack, J. E., M. G. Harvey, B. C. Faircloth, N. G. Crawford, T. C. Glenn, and R. T. Brumfield. 2013. A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing. PLoS ONE 8:e54848.
  • Minh, B. Q., M. A. T. Nguyen, and A. von Haeseler. 2013. Ultrafast approximation for phylogenetic bootstrap. Molecular Biology and Evolution 30:1188-1195.
  • Near, T. J., and C.-H. C. Cheng. 2008. Phylogenetics of notothenioid fishes (Teleostei: Acanthomorpha): inferences from mitochondrial and nuclear gene sequences. Molecular Phylogenetics and Evolution 47:832-840.
  • Near, T. J., A. Dornburg, K. L. Kuhn, J. T. Eastman, J. N. Pennington, T. Patarnello, L. Zane, D. A. Fernandez, and C. D. Jones. 2012. Ancient climate change, antifreeze, and the evolutionary diversification of Antarctic fishes. Proceedings of the National Academy of Sciences of the United States of America 109:3434-3439.
  • Near, T. J., D. J. MacGuigan, E. Parker, C. D. Struthers, C. D. Jones, and A. Dornburg. 2018. Phylogenetic analysis of Antarctic notothenioids illuminates the utility of RADseq for resolving Cenozoic adaptive radiations. Molecular Phylogenetics and Evolution 129:268-279.
  • Near, T. J., J. J. Pesavento, and C.-H. C. Cheng. 2004. Phylogenetic investigations of Antarctic notothenioid fishes (Perciformes: Notothenioidei) using complete gene sequences of the mitochondrial encoded 16S rRNA. Molecular Phylogenetics and Evolution 32:881-891.
  • Nelson, J. S. 1994. Fishes of the World. Third edition. Wiley, New York.
  • Neyelov, A. V., and V. P. Prirodina. 2006. Description of Harpagifer permitini sp. nova (Harpagiferidae) from the sublittoral zone of South Georgia and redescription of the littoral H. georgianus Nybelin. Journal of Ichthyology 46:1- 12.
  • Nguyen, L. T., H. A. Schmidt, A. von Haeseler, and B. Q. Minh. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Molecular Biology and Evolution 32:268-274.
  • Norman, J. R. 1938. Coast fishes. Part III. The Antarctic zone. Discovery Reports 18:1-104.
  • Olaso, I., M. Rauschert, and C. De Broyer. 2000. Trophic ecology of the family Artedidraconidae (Pisces: Osteichthyes) and its impact on the eastern Weddell Sea benthic system. Marine Ecology Progress Series 194:143-158.
  • O'Leary, S. J., J. B. Puritz, S. C. Willis, C. M. Hollenbeck, and D. S. Portnoy. 2018. These aren't the loci you're looking for: principles of effective SNP filtering for molecular ecologists. Molecular Ecology 27:3193-3206.
  • Parker, E., A. Dornburg, C. D. Struthers, C. D. Jones, and T. J. Near. 2021. Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation. Systematic Biology 71:58-77.
  • Peterson, B. K., J. N. Weber, E. H. Kay, H. S. Fisher, and H. E. Hoekstra. 2012. Double digest RADseq: an inexpensive method for ee novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7:e37135.
  • Potter, S. 2018. grImport2: importing 'SVG' graphics. R package version 0.1-4. https://CRAN.R-project.org/ package¼grImport2
  • Prirodina, V. P. 2000. On the systematic position of littoral and deep-water species of the genus Harpagifer (Harpagiferidae, Notothenioidei) from Macquarie Island with a description of two new species. Journal of Ichthyology 40:488-494.
  • Prirodina, V. P. 2002. Redescription of littoral and deep-sea species of the genus Harpagifer (Harpagiferidae, Notothenioidei) off islands of the Indian Ocean Sector of the Southern Ocean with description of a new species. Journal of Ichthyology 42:701-712.
  • Prirodina, V. P. 2004. Harpagifer crozetensis sp. nova (Harpagiferidae, Notothenioidei), a new species from the littoral of the Crozet Islands (Indian Ocean Sector of Antarctica). Journal of Ichthyology 44:395-399.
  • Regan, C. T. 1913. The Antarctic fishes of the Scottish National Antarctic Expedition. Transactions of the Royal Society of Edinburgh 49:229-292.
  • Regan, C. T. 1914. Fishes. British Antarctic Terra Nova Expedition 1910. Natural History Report Zoology 1:1-54.
  • Ritchie, P. A., S. Lavoue, and G. Lecointre. 1997. Molecular phylogenetics and the evolution of Antarctic notothenioid fishes. Comparative Biochemistry and Physiology Part A: Physiology 118:1009-1025.
  • Rokas, A., D. Kruger, and S. B. Carroll. 2005. Animal evolution and the molecular signature of radiations compressed in time. Science 310:1933-1938.
  • Roule, L. 1913. Description d'un genre nouveau et des deux espece nouvelle de poissons antarctique. (Expedition Antarctique Francaise commandee par M.J.B. Charcot). Bulletin du Museum National d'Histoire Naturelle 19:4-7.
  • Rutschmann, S., M. Matschiner, M. Damerau, M. Muschick, M. F. Lehmann, R. Hanel, and W. Salzburger. 2011. Parallel ecological diversification in Antarctic notothenioid fishes as evidence for adpative radiation. Molecular Ecology 20:4707-4721.
  • Ruud, J. T. 1954. Vertebrates without erythrocytes and blood pigment. Nature 173:848-850.
  • Schluter, D. 2000. The Ecology of Adaptive Radiation. Oxford University Press, Oxford.
  • Simpson, G. G. 1953. The Major Features of Evolution. Columbia University Press, New York.
  • Snir, S., and S. Rao. 2012. Quartet MaxCut: a fast algorithm for amalgamating quartet trees. Molecular Phylogenetics and Evolution 62:1-8.
  • Suh, A., L. Smeds, and H. Ellegren. 2015. The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds. PLoS Biology 13:e1002224.
  • Waite, E. R. 1911. British Antarctic Expedition 1907-9 under the command of Sir E. H. Shackleton, C.V.O. Reports on the Scientific Investigations 2:11-16.
  • Zheng, X., D. Levine, J. Shen, S. M. Gogarten, C. Laurie, and B. S. Weir. 2012. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28:3326-3328.