New insights into the systematics of North Atlantic Gaidropsarus (Gadiformes, Gadidae): flagging synonymies and hidden diversity

References

• Ávila M, Nunes D, Machado L, Barreiros JP. 2014. Notes on the feeding habits of Gaidropsarus guttatus (Collett, 1890) from Faial Island, Azores, NE Atlantic, PT. Cybium 38:77–80.
   Google Scholar
• Bakke I, Johansen S. 2002. Characterization of mitochondrial ribosomal RNA genes in gadiformes: sequence variations, secondary structural features, and phylogenetic implications. Molecular Phylogenetics and Evolution 25:87–100. doi: 10.1016/S1055-7903(02)00220-8
   Google Scholar
• Bakke I, Johansen SD. 2005. Molecular phylogenetics of Gadidae and related Gadiformes based on mitochondrial DNA sequences. Marine Biotechnology 7:61–69. doi: 10.1007/s10126-004-3131-0
   Google Scholar
• Balushkin AV. 2009. On the first occurrence of the rockling Gaidropsarus pakhorukovi Shcherbachev (Gairdropsarini, Lotidae, Gadidae) and on species diagnostics of G. pakhorukovi and G. parini Svetovidov. Journal of Ichthyology 49:723–729. doi: 10.1134/S0032945209090033
   Google Scholar
• Bañón R, Arronte JC, Vázquez-Dorado S, del Rio JL, de Carlos A. 2013. DNA barcoding of the genus Lepidion (Gadiformes: Moridae) with recognition of Lepidion eques as a junior synonym of Lepidion lepidion. Molecular Ecology Resources 13:189–199. doi: 10.1111/1755-0998.12045
   Google Scholar
• Bañón R, del Rio JL, Piñeiro C, Casas M. 2002. Occurrence of tropical affinity fish in Galician waters, north-west Spain. Journal of the Marine Biological Association of the United Kingdom 82:877–880. doi:10.1017/S0025315402006288
   Google Scholar
• Bañón R, Villegas-Ríos D, Serrano A, Mucientes G, Arronte JC. 2010. Marine fishes from Galicia (NW Spain): an updated checklist. Zootaxa 2667:1–27.
   Google Scholar
• Barlow GW. 1961. Causes and significance of morphological variation in fishes. Systematic Biology 10:105–117.
   Google Scholar
• Barros-García D, Bañón R, Arronte J-C, de Carlos A. 2016. New data reinforcing the taxonomic status of Lepidion eques as synonym of Lepidion lepidion (Teleostei, Gadiformes). Biochemical Systematics and Ecology 68:6–10. doi: 10.1016/j.bse.2016.06.017
   Google Scholar
• Carneiro M, Martins R, Landi M, Costa F. 2014. Updated checklist of marine fishes (Chordata: Craniata) from Portugal and the proposed extension of the Portuguese continental shelf. European Journal of Taxonomy 73:1–73.
   Google Scholar
• Cohen DM, Inada T, Iwamoto T, Scialabba N. 1990. FAO species catalogue. Gadiform fishes of the world (Order Gadiformes). An annotated and illustrated catalogue of cods, hakes, grenadiers and other gadiform fishes known to date. FAO Fisheries Synopsis 125:1–442.
   Google Scholar
• Cohen DM, Russo JL. 1979. Variation in the four beard rockling, Enchelyopus cimbrius, a North Atlantic gadid fish, with comments on the genera of rocklings. United States National Marine Fisheries Service Fishery Bulletin 77:91–104.
   Google Scholar
• Collett R. 1890. Diagnoses de poissons nouveaux provenant des campagnes de “L’Hirondelle.” V. Descriptions de deux espèces nouvelles de genre Onus Risso. Bulletin de la Société Zoologique de France 15:105–109.
   Google Scholar
• Collett R. 1905. On some fishes from the sea off the Azores. Zoologischer Anzeiger 28:723–730.
   Google Scholar
• Collins RA, Cruickshank RH. 2013. The seven deadly sins of DNA barcoding. Molecular Ecology Resources 13:969–975.
   Google Scholar
• Costa FO, Landi M, Martins R, Costa MH, Costa ME, Carneiro M, et al. 2012. A ranking system for reference libraries of DNA barcodes: application to marine fish species from Portugal. PLoS One 7:e35858. 9 pages. doi: 10.1371/journal.pone.0035858
   Google Scholar
• Danovaro R, Company JB, Corinaldesi C, D’Onghia G, Galil B, Gambi C, et al. 2010. Deep-sea biodiversity in the Mediterranean Sea: the known, the unknown, and the unknowable. PLoS One 5:e11832. 25 pages. doi: 10.1371/journal.pone.0011832
   Google Scholar
• De Buen F. 1934. Notas sobre los Gaidropsaridae (Peces). Un nuevo género (Onogadus) y una nueva especie (Gaidropsarus barbatus). Boletín de la Sociedad Española de Historia Natural 34:499–504.
   Google Scholar
• Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113. 19 pages. doi: 10.1186/1471-2105-5-113
   Google Scholar
• Endo H. 2002. Phylogeny of the order Gadiformes (Teleostei, Paracanthopterygii). Memoirs of the Graduate School of Fisheries Sciences, Hokkaido University 49:75–149.
   Google Scholar
• Fahay MP. 2007. Early Stages of Fishes in the Western North Atlantic Ocean (Davis Strait, Southern Greenland and Flemish Cap to Cape Hatteras). Volume 1, Acipenseriformes through Syngnathiformes. Dartmouth, NS, Canada: Northwest Atlantic Fisheries Organization. 931 pages.
   Google Scholar
• Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791. doi: 10.1111/j.1558-5646.1985.tb00420.x
   Google Scholar
• Francisco SM, Robalo JI, Stefanni S, Levy A, Almada VC. 2014. Gaidropsarus (Gadidae, Teleostei) of the North Atlantic Ocean: a brief phylogenetic review. Journal of Fish Biology 85:473–487. doi: 10.1111/jfb.12437
   Google Scholar
• Froese R, Pauly D. 2016. FishBase. World Wide Web electronic publication. Available via www.fishbase.org, Version October 2016.
   Google Scholar
• Garcia S. 2015. Gaidropsarus granti. The IUCN Red List of Threatened Species 2015:e.T198589A18984376.
   Google Scholar
• Hebert PDN, Cywinska A, Ball SL, de Waard JR. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society B 270:313–321. doi: 10.1098/rspb.2002.2218
   Google Scholar
• Hebert PDN, Gregory TR. 2005. The promise of DNA barcoding for taxonomy. Systematic Biology 54:852–859. doi: 10.1080/10635150500354886
   Google Scholar
• Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM. 2004. Identification of birds through DNA barcodes. PLoS Biology 2:1657–1663. doi: 10.1371/journal.pbio.0020312
   Google Scholar
• Howes GJ. 1991. Biogeography of gadoid fishes. Journal of Biogeography 18:595–622. doi: 10.2307/2845542
   Google Scholar
• Hubert N, Hanner R. 2015. DNA barcoding, species delineation and taxonomy: a historical perspective. DNA Barcodes 2015 3:44–58.
   Google Scholar
• Hyde JR, Underkoffler KE, Sundberg MA. 2014. DNA barcoding provides support for a cryptic species complex within the globally distributed and fishery important opah (Lampris guttatus). Molecular Ecology Resources 14:1239–1247. doi: 10.1111/1755-0998.12268
   Google Scholar
• Iglésias SP, Frotté L, Sellos DY. 2016. Gobius salamansa, a new species of goby (Gobiidae) from the Cape Verde Islands supported by a unique chepalic lateral line system and DNA barcoding. Ichthyological Research 63:356–369. doi: 10.1007/s10228-015-0505-4
   Google Scholar
• Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN. 2007. Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes 7:544–548. doi: 10.1111/j.1471-8286.2007.01748.x
   Google Scholar
• Iwamoto T, Cohen DM. 2016. Gaidropsaridae. In: Carpenter KE, De Angelis N, editors. The Living Marine Resources of the Eastern Central Atlantic. Volume 3. Bony Fishes. Part 1 (Elopiformes to Scorpaeniformes). Rome: FAO, p 2015–2022.
   Google Scholar
• Kekkonen M, Hebert PDN. 2014. DNA barcode-based delineation of putative species: efficient start for taxonomic workflows. Molecular Ecology Resources 14:706–715. doi: 10.1111/1755-0998.12233
   Google Scholar
• Knebelsberger T, Landi M, Neumann H, Kloppmann M, Sell AF, Campbell PD, et al. 2014. A reliable DNA barcode reference library for the identification of the North European shelf fish fauna. Molecular Ecology Resources 14:1060–1071.
   Google Scholar
• Knebelsberger T, Thiel R. 2014. Identification of gobies (Teleostei: Perciformes: Gobiidae) from the North and Baltic Seas combining morphological analysis and DNA barcoding. Zoological Journal of the Linnean Society 172:831–845. doi: 10.1111/zoj.12189
   Google Scholar
• Landi M, Dimech M, Arculeo M, Biondo G, Martins R, Carneiro M, et al. 2014. DNA barcoding for species assignment: the case of Mediterranean marine fishes. PLoS One 9:e106135. 9 pages. doi: 10.1371/journal.pone.0106135
   Google Scholar
• Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452. doi: 10.1093/bioinformatics/btp187
   Google Scholar
• Marckle DF. 1982. Identification of larval and juvenile Canadian Atlantic gadoids with comments on the systematics of gadid subfamilies. Canadian Journal of Zoology 60:3420–3438. doi: 10.1139/z82-432
   Google Scholar
• Massutí E, Gordon JDM, Moranta ZJ, Swan SC, Stefanescu C, Merrett NR. 2004. Mediterranean and Atlantic deep-sea fish assemblages: differences in biomass composition and size-related structure. Scientia Marina 68(Suppl 3):101–115. doi: 10.3989/scimar.2004.68s3101
   Google Scholar
• Maul GE. 1952. Monografia dos peixes do Museu Municipal do Funchal. Família Gadidae e Bregmacerotidae. Boletim do Museu Municipal do Funchal 6:1–51.
   Google Scholar
• McCusker MR, Denti D, Van Guelpen L, Kenchington E, Bentzen P. 2013. Barcoding Atlantic Canada’s commonly encountered marine fishes. Molecular Ecology Resources 13:177–188. doi: 10.1111/1755-0998.12043
   Google Scholar
• Meier R, Shiyang K, Vaidya G, Ng PKL. 2006. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology 55:715–728. doi: 10.1080/10635150600969864
   Google Scholar
• Messing J. 1983. New M13 vectors for cloning. Methods in Enzymology 101:20–78. doi: 10.1016/0076-6879(83)01005-8
   Google Scholar
• Miller SE. 2007. DNA barcoding and the renaissance of taxonomy. Proceedings of the National Academy of Sciences 104:4775–4776. doi: 10.1073/pnas.0700466104
   Google Scholar
• Moritz C, Cicero C. 2004. DNA barcoding: promise and pitfalls. PLoS Biology 2:1529–1531. doi: 10.1371/journal.pbio.0020354
   Google Scholar
• Morton B, Britton JC. 2000. Origins of the Azorean intertidal biota: the significance of introduced species, survivors of chance events. Life and Marine Sciences, Supplement 2(Part A):29–51.
   Google Scholar
• Mura M, Cau A. 2003. Sulla presenza di Gaidropsarus granti (Regan, 1903) (Osteichthyes, Gadidae) nel Mediterraneo Centro-Occidentale. Biologia Marina Mediterranea 10:866–869.
   Google Scholar
• Nei M, Kumar S. 2000. Molecular Evolution and Phylogenetics. New York: Oxford University Press.
   Google Scholar
• Nelson JS, Grande TC, Wilson MVH. 2016. Fishes of the World, 5th edition. Hoboken, NJ: John Wiley and Sons.
   Google Scholar
• Orsi Relini L, Relini G. 2014. Gaidropsarus granti from a Ligurian seamount: a Mediterranean native species? Marine Ecology 35:35–40. doi:10.1111/maec.12122
   Google Scholar
• Pais A, Merella P, Follesa MC, Garippa G, Golani D. 2008. New data on Gaidropsarus granti (Regan, 1903) (Gadiformes: Lotidae) from the Mediterranean Sea, with emphasis on its parasites. Scientia Marina 72:461–468.
   Google Scholar
• Puckridge M, Andreakis N, Appleyard SA, Ward RD. 2013. Cryptic diversity in flathead fishes (Scorpaeniformes: Platycephalidae) across the Indo-West Pacific uncovered by DNA barcoding. Molecular Ecology Resources 13:32–42. doi: 10.1111/1755-0998.12022
   Google Scholar
• Ratnasingham S, Hebert PDN. 2007. BOLD: the Barcode of Life Data System (http://www.barcodinglife.org). Molecular Ecology Notes 7:355–364. doi: 10.1111/j.1471-8286.2007.01678.x
   Google Scholar
• Ratnasingham S, Hebert PDN. 2013. A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS One 8(7):e66213. 16 pages. doi: 10.1371/journal.pone.0066213
   Google Scholar
• Regan CT. 1903. XXXI. – On a collection of fishes from the Azores. Journal of Natural History, Series 7 12:344–348. doi: 10.1080/00222930308678864
   Google Scholar
• Roa-Varón A, Ortí G. 2009. Phylogenetic relationships among families of Gadiformes (Teleostei, Paracanthopterygii) based on nuclear and mitochondrial data. Molecular Phylogenetics and Evolution 52:688–704. doi: 10.1016/j.ympev.2009.03.020
   Google Scholar
• Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406–425.
   Google Scholar
• Savolainen V, Cowan RS, Vogler AP, Roderick PGK, Lane R. 2005. Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society B 360:1805–1811. doi: 10.1098/rstb.2005.1730
   Google Scholar
• Srivathsan A, Meier R. 2012. On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature. Cladistics 28:190–194. doi: 10.1111/j.1096-0031.2011.00370.x
   Google Scholar
• Stöver BC, Müller KF. 2010. TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 11:7. 9 pages. doi: 10.1186/1471-2105-11-7
   Google Scholar
• Svetovidov AN. 1948. Gaidropsarus. In: Pavlovskii EN, Shtakel’berg AA, editors. Fauna of U.S.S.R.: Fishes, Gadiformes vol. IX, no. 4. Moscow: Zoological Institute of the Academy of Sciences of the USSR, p 79–91. (Original in Russian, English translation Walters WJ, Walters VW, 1962, Israel Program for Scientific Translations, Jerusalem.)
   Google Scholar
• Svetovidov AN. 1986a. Review of three-bearded rocklings of the genus Gaidropsarus Rafinesque, 1810 (Gadidae) with description of a new species. Journal of Ichthyology 62:115–135.
   Google Scholar
• Svetovidov AN. 1986b. Gadidae. In: Whitehead PJP, Bauchot ML, Hureau JC, Nielsen J, Tortonese E, editors. Fishes of the North-Eastern Atlantic and the Mediterranean, Volume 2. Paris: UNESCO, p 680–710.
   Google Scholar
• Tamura K, Stecher G, Peterson D, Filipski A., Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution 30:2725–2729. doi: 10.1093/molbev/mst197
   Google Scholar
• Teletchea F. 2010. After 7 years and 1000 citations: comparative assessment of the DNA barcoding and the DNA taxonomy proposals for taxonomists and non-taxonomists. Mitochondrial DNA 21:206–226. doi: 10.3109/19401736.2010.532212
   Google Scholar
• Teletchea F, Laudet V, Hänni C. 2006. Phylogeny of the Gadidae (sensu Svetovidov, 1948) based on their morphology and two mitochondrial genes. Molecular Phylogenetics and Evolution 38:189–199. doi: 10.1016/j.ympev.2005.09.001
   Google Scholar
• UNEP. 2006. Ecosystems and Biodiversity in Deep-waters and High Seas. UNEP Regional Seas Reports and Studies no. 178. Gland, Switzerland: UNEP/IUCN.
   Google Scholar
• Van der Laan R, Eschmeyer WN, Fricke R. 2014. Family-group names of Recent fishes. Zootaxa 3882:1–230. doi: 10.11646/zootaxa.3882.1.1
   Google Scholar
• Von der Heyden S, Matthee CA. 2008. Towards resolving familial relationships within the Gadiformes, and the resurrection of the Lyconidae. Molecular Phylogenetics and Evolution 48:764–769. doi: 10.1016/j.ympev.2008.01.012
   Google Scholar
• Ward RD, Hanner R, Hebert PDN. 2009. The campaign to DNA barcode all fishes, FISH-BOL. Journal of Fish Biology 74:329–356. doi: 10.1111/j.1095-8649.2008.02080.x
   Google Scholar
• Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society B 360:1847–1857. doi: 10.1098/rstb.2005.1716
   Google Scholar
• Zachariou-Mamalinga H. 1999. The occurrence of the Atlantic fish Gaidropsarus granti in the Mediterranean Sea (South-Eastern Aegean Sea, Dodecanese, Greece, Eastern Mediterranean). Annales Musei Goulandris 10:261–266.
   Google Scholar
• Zemlak TS, Ward RD, Connell AD, Holmes BH, Hebert PDN. 2009. DNA barcoding reveals overlooked marine fishes. Molecular Ecology Resources 9:237–242. doi: 10.1111/j.1755-0998.2009.02649.x
   Google Scholar