DNA barcoding for squids of the family Gonatidae (Cephalopoda: Teuthida) from the boreal North Pacific

References

• Allcock AL, Barratt I, Eléaume M, Linse K, Norman MD, Smith PJ, Steinke D, et al. (2010). Cryptic speciation and the circumpolarity debate: A case study on endemic Southern Ocean octopuses using the COI barcode of life. Deep Sea Res Part II: Top Stud Oceanogr 58:242–9
   Web of Science ®Google Scholar
• Anderson FE. (2000). Phylogeny and historical biogeography of the loliginid squids (Mollusca: Cephalopoda) based on mitochondrial DNA sequence data. Mol Phylogenet Evol 15:191–214
   PubMed Web of Science ®Google Scholar
• Barco A, Houart R, Bonomolo G, Crocetta F, Oliverio M. (2013). Molecular data reveal cryptic lineages within the northeastern Atlantic and Mediterranean small mussel drills of the Ocinebrina edwardsii complex (Mollusca: Gastropoda: Muricidae). Zool J Linn Soc 169:389–407
   Web of Science ®Google Scholar
• Barr NB, Cook A, Elder P, Molongoski J, Prasher D, Robinson DG. (2009). Application of a DNA barcode using the 16S rRNA gene to diagnose pest Arion species in the USA. J Molluscan Stud 75:187–91
   Web of Science ®Google Scholar
• Becker S, Hanner R, Steinke D. (2011). Five years of FISH-BOL: Brief status report. Mitochondrial DNA 22:3–9
   PubMed Web of Science ®Google Scholar
• Brower AVZ. (2006). Problems with DNA barcodes for species delimitation: ‘Ten species’ of Astraptes fulgerator reassessed (Lepidoptera: Hesperiidae). Syst Biodiver 4:127–32
   Web of Science ®Google Scholar
• Bublitz C. (1981). Systematics of the cephalopod family Gonatidae from the south eastern Bering Sea. [Master’s Thesis]. Fairbanks: University of Alaska. 177 p
   Google Scholar
• Cámara S, Carmona L, Cella K, Ekimova I, Martynov A, Cervera JL. (2014). Tergipes tergipes (Förskal. 1775) (Gastropoda: Nudibranchia) is an amphiatlantic species. J Molluscan Stud 80:642–6
   Web of Science ®Google Scholar
• Chen J, Li Q, Kong LF, Yu H. (2011). How DNA barcodes complement taxonomy and explore species diversity: The case study of a poorly understood marine fauna. PLoS One 6:e21326
   PubMed Web of Science ®Google Scholar
• Chuchukalo VI. (2006). Feeding and Forage relationships of Nektonand Nektobenthos in the Far Eastern seas. Vladivostok, TINRO-Centre. 484pp. (In Russian)
   Google Scholar
• Clare EL, Lim BK, Engstrom MD, Eger JL, Hebert PDN. (2007). DNA barcoding of Neotropical bats: Species identification and discovery within Guyana. Mol Ecol Notes 7:184–90
   Web of Science ®Google Scholar
• Dai L, Zheng X, Kong L, Li Q. (2012). DNA barcoding analysis of Coleoidea (Mollusca: Cephalopoda) from Chinese waters. Mol Ecol Resour 12:437–47
   PubMed Web of Science ®Google Scholar
• Collins RA, Cruickshank RH. (2012). The seven deadly sins of DNA barcoding. Mol Ecol Resour 13:969–75
   PubMed Web of Science ®Google Scholar
• Collins RA, Armstrong KF, Meier R. (2012). Barcoding and border biosecurity: Identifying cyprinid fishes in the aquarium trade. PLoS One 7:e28381
   PubMed Web of Science ®Google Scholar
• Dasmahapatra KK, Elias M, Hill RI, Hoffman JI, Mallet J. (2010). Mitochondrial DNA barcoding detects some species that are real, and some that are not. Mol Ecol Resour 10:264–73
   PubMed Web of Science ®Google Scholar
• De Salle R. (2006). Species discovery versus species identification in DNA barcoding efforts: Response to Rubinoff. Conserv Biol 20:1545–7
   PubMed Web of Science ®Google Scholar
• De Salle R, Egan MG, Siddall M. (2005). The unholy trinity: Taxonomy, species delimitation and DNA barcoding. Philos Trans R Soc Lond B Biol Sci 360:1905–16
   PubMed Web of Science ®Google Scholar
• Ekimova I, Korshunova T, Schepetov D, Neretina T, Sanamyan N, Martynov A. (2015). Integrative systematics of Northern and Arctic nudibranchs of the genus Dendronotus (Mollusca, Gastropoda) with descriptions of three new species. Zool J Linn Soc 173:841–86
   Web of Science ®Google Scholar
• Felsenstein J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783–91
   PubMed Web of Science ®Google Scholar
• Feng YW, Li Q, Kong LF, Zheng XD. (2011). COI-based DNA barcoding of Arcoida species (Bivalvia: Pteriomorphia) along the coast of China. Mol Ecol Resour 11:435–41
   PubMed Web of Science ®Google Scholar
• Jefferts K. (1983). Zoogeography and systematic of cephalopods of the north eastern Pacific Ocean. [Ph.D Thesis]. Oregon State University. 291 p
   Google Scholar
• Jörger KM, Norenburg JL, Wilson NG, Schrödl M. (2012). Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs. BMC Evol Biol 12:245
   PubMed Web of Science ®Google Scholar
• Goldstein PZ, De Salle R. (2011). Integrating DNA barcode data and taxonomic practice: Determination, discovery and description. BioEssays 33:135–47
   PubMed Web of Science ®Google Scholar
• Hall TA. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Ac Symp Ser 41:95–8
   Google Scholar
• Hebert PDN, Gregory TR. (2005). The promise of DNA barcoding for taxonomy. Syst Biol 54:852–9
   PubMed Web of Science ®Google Scholar
• Hebert P, Cywinska A, Ball S, de Waard J. (2003). Biological identifications through DNA barcodes. Proc Biol Sci 270:313–21
   PubMed Web of Science ®Google Scholar
• Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W. (2004a). Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci USA 101:14812–17
   PubMed Web of Science ®Google Scholar
• Hebert PDN, Stoeckle MY, Zemlack TS, Francis CM. (2004b). Identification of birds through DNA barcodes. PLoS Biol 2:e312
   PubMed Web of Science ®Google Scholar
• Herke SW, Foltz DW. (2002). Phylogeography of two squid (Loligo pealei and L. plei) in the Gulf of Mexico and northwestern Atlantic Ocean. Mar Biol 140:103–15
   Web of Science ®Google Scholar
• Hickerson MJ, Meyer CP, Moritz C. (2006). DNA barcoding will often fail to discover new animal species over broad parameter space. Syst Biol 55:729–39
   PubMed Web of Science ®Google Scholar
• Katugin ON. (2004). Squids of the family Gonatidae from the North Pacific Ocean and their genetic differentiation: Controversial issues in the systematics and phylogeny. Ruthenica 14:73–87 (in Russian with English summary)
   Google Scholar
• Katugin ON, Shevtsov GA, Zuev MA. (2010a). The morphology and biology of Gonatus tinro and Gonatopsis okutanii (Teuthida: Gonatidae) indicate that they are conspecific. ICES J Mar Sci 67:1464–77
   Web of Science ®Google Scholar
• Katugin ON, Yavnov SV, Shevtsov GA. (2010b). Atlas of Cephalopod mollusks of the Far Eastern seas of Russia. Russki Ostrov: Vladivostok 136p
   Google Scholar
• Kimura M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–20
   PubMed Web of Science ®Google Scholar
• Krug PJ, Vendetti JE, Rodriguez AK, Retana JN, Hirano YM, Trowbridge CD. (2013). Integrative species delimitation in photosynthetic sea slugs reveals twenty candidate species in three nominal taxa studied for drug discovery, plastid symbiosis or biological control. Mol Phylogenet Evol 69:1101–19
   PubMed Web of Science ®Google Scholar
• Kubodera T, Hochberg FG, Young RE, Vecchione M. (2006). Gonatidae Hoyle, 1886. Version 31 May 2006. Available at: http://tolweb.org/Gonatidae/19414/2006.05.31inTheTreeofLifeWebProject, http://tolweb.org/
   Google Scholar
• Lindgren AR. (2010). Molecular inference of phylogenetic relationships among Decapodiformes (Mollusca: Cephalopoda) with special focus on the squid order Oegopsida. Mol Phylogenet Evol 56:77–90
   PubMed Web of Science ®Google Scholar
• Lindgren AR, Katugin ON, Amezquita E, Nishiguchi MK. (2005). Evolutionary relationships among squids of the family Gonatidae (Mollusca: Cephalopoda) inferred from three mitochondrial loci. Mol Phylogenet Evol 36:101–11
   PubMed Web of Science ®Google Scholar
• Lowenstein JH, Burger J, Jeitner CW, Amato G, Kolokotronis SO, Gochfeld M. (2010). DNA barcodes reveal species-specific mercury levels in tuna sushi that pose a health risk to consumers. Biol Lett 6:692–5
   PubMed Web of Science ®Google Scholar
• Ma H, Ma C, Ma L. (2012). Molecular identification of genus Scylla (Decapoda: Portunidae) based on DNA barcoding and polymerase chain reaction. Biochem Syst Ecol 41:41–7
   Web of Science ®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. Syst Biol 55:715–28
   PubMed Web of Science ®Google Scholar
• Meier R. (2008). DNA sequences in taxonomy: Opportunities and challenges. In: Wheeler QD, editor. The new taxonomy. New York: CRC Press. p. 95–127 (Chapter 7)
   Google Scholar
• Nesis KN. (1972). Two species of squids, family Gonatidae, from the North Pacific. Zool Zh (Zool J) 51:1300–7. (In Russian with English summary)
   Google Scholar
• Nesis KN. (1985). Oceanic Cephalopods: Distribution, life forms, evolution. Moscow: Nauka. 287 p (in Russian)
   Google Scholar
• Nesis KN. (1987). Cephalopods of the World. Neptune City: T.F.H Publications. 351 p
   Google Scholar
• Nesis KN. (1989). Teuthofauna of the Okhotsk Sea. Biology of squids Berryteuthis magister and Gonatopsis borealis (Gonatidae). Zool Zh (Zool J) 68:45–56 (in Russian, with English summary)
   Web of Science ®Google Scholar
• Nesis KN. (1997). Gonatid squids in the Subarctic North Pacific: Ecology, biogeography, niche diversity and role in the ecosystem. Adv Mar Biol 32:243–324
   Web of Science ®Google Scholar
• Nesis KN, Nezlin NP. (1993). Intraspecific groupings of gonatid squids. Russ J Aquat Ecol 2:91–102
   Google Scholar
• Okutani T. (1968). Review of Gonatidae (Cephalopoda) from the North Pacific. Venus 27:31–4. (in Japanese)
   Google Scholar
• Okutani T, Kubodera T, Jefferts K. (1988). Diversity, distribution and ecology of gonatid squids in the Subarctic Pacific. A review. Bull Ocean Res Instit 26:159–92
   Google Scholar
• Okutani T, Nemoto T. (1964). Squids as the food of sperm whales in the Bering Sea and Alaskan Gulf. Scientific reports of Whales research Institute, 18:111–122
   Google Scholar
• Pierce GJ, Thorpe RS, Hastie LC, Brierley AS, Guerra A, Boyle PR, Jamieson R, Avila R. (1994). Geographic variation in Loligo forbesi in the Northeast Atlantic Ocean: Analysis of morphometric data and tests of causal hypotheses. Mar Biol 119:541–7
   Web of Science ®Google Scholar
• Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, Hazell S, Kamoun S, et al. (2006). Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst Biol 55:595–609
   PubMed Web of Science ®Google Scholar
• Posada D. (2008). jModelTest: Phylogenetic model averaging. Mol Biol Evol 25:1253–6
   PubMed Web of Science ®Google Scholar
• Puillandre N, Lambert A, Brouillet S, Achaz G. (2012). ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol Ecol 21:1864–77
   PubMed Web of Science ®Google Scholar
• Ronquist F, Huelsenbeck JP. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–4
   PubMed Web of Science ®Google Scholar
• Roper CFE, Jorgensen EM, Katugin ON, Jereb P. (2010). Family Gonatidae Hoyle, 1886. In: Jereb P, Roper CFE, editors. Cephalopods of the world: An annotated and illustrated catalogue of Cephalopod species known to date. (FAO species catalogue for fisheries purposes), no. 4, vol. 2. Myopsid and Oegopsid Squids:200-222
   Google Scholar
• Rubinoff D, Cameron S, Will K. (2006). A genomic perspective on the shortcomings of mitochondrial DNA for ‘barcoding’ identification. J Hered 97:581–94
   PubMed Web of Science ®Google Scholar
• Sarkar IN, Planet PJ, Desalle R. (2008). CAOS software for use in character-based DNA barcoding. Mol Ecol Resour 8:1256–9
   PubMed Web of Science ®Google Scholar
• Saitou N, Nei M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–25
   PubMed Web of Science ®Google Scholar
• Sin YW, Yau C, Chu KH. (2009). Morphological and genetic differentiation of two loliginid squids, Uroteuthis (Photololigo) chinensis and Uroteuthis (Photololigo) edulis (Cephalopoda: Loliginidae) in Asia. J Exp Mar Biol Ecol 369:22–30
   Web of Science ®Google Scholar
• Schindel DE, Miller SE. (2005). DNA barcoding a useful tool for taxonomists. Nature 435:17
   PubMed Web of Science ®Google Scholar
• Srivathsan A, Meier R. (2011). On the inappropriate use of Kimura‐2‐parameter (K2P) divergences in the DNA‐barcoding literature. Cladistics 28:190–4
   Web of Science ®Google Scholar
• Strugnell J, Norman M, Jackson J, Drummond AJ, Cooper A. (2005). Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework. Mol Phyl E 37:426–41
   PubMed Web of Science ®Google Scholar
• Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–9
   PubMed Web of Science ®Google Scholar
• Turanov SV, Kartavtsev YP. (2014). The taxonomic composition and distribution of sand lances from the genus Ammodytes (Perciformes: Ammodytidae) in the North Pacific. Russ J Mar Biol 40:447–54
   Web of Science ®Google Scholar
• Undheim EAB, Norman JA, Thoen HH, Fry BG. (2010). Genetic identification of Southern Ocean octopod samples using mtCOI. C R Biol 333:395–404
   PubMed Web of Science ®Google Scholar
• Zuev MA, Katugin ON, Shevtsov GA, Dakus AV. (2007). Distribution and differentiation of the boreo pacific gonate squid Boreoteuthis borealis (Sasaki, 1923) (Cephalopoda: Gonatidae) in the Okhotsk Sea and north western Pacific Ocean. Proc VNIRO 147:266–283 (in Russian with English summary)
   Google Scholar
• Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. (2005). DNA barcoding Australia’s fish species. Phil Trans R Soc B 360:847–1857
   Web of Science ®Google Scholar
• Wiemers M, Fiedler K. (2007). Does the DNA barcoding gap exist? A case study in blue butterflies (Lepidoptera: lycaenidae). Front Zool 4:8
   PubMed Web of Science ®Google Scholar
• Will KW, Rubinoff D. (2004). Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics 20:47–55
   PubMed Web of Science ®Google Scholar
• Will KW, Mishler BD, Wheeler QD. (2005). The perils of DNA barcoding and the need for integrative taxonomy. Syst Biol 54:844–51
   PubMed Web of Science ®Google Scholar
• Zhang AB, Muster C, Liang HB. (2012). A fuzzy-set-theory-based approach toanalyse species membership in DNA barcoding. Mol Ecol 21:1848–63
   PubMed Web of Science ®Google Scholar