Molecular phylogenetic reconstruction and taxonomic investigation of eelpouts (Cottoidei: Zoarcales) based on Co-1 and Cyt-b mitochondrial genes

References

• Anderson ME. 1994. Systematics and osteology of the Zoarcidae (Teleostei: Perciformes). Ichthyol Bull JLB Smith Inst Ichthyol. 60:1–120.
   Google Scholar
• Anderson ME. 2003. Suborder: Zoarcoidei (Eelpouts and relatives). Grzimek’s Animal Life Encyclopedia. Michigan Farmington Hills: The Gale Group Inc.
   Google Scholar
• Betancur RR, Broughton RE, Wiley EO, Carpenter K, Lopez JA, et al. 2013. The tree of life and a new classification of bony fishes. PLoS Currents: Tree of Life. 5:1–33
   Google Scholar
• Betancur RR, Wiley E, Bailly N, Miya M, Lecointre G, et al. 2014. Phylogenetic Classification of Bony Fishes -Version 3. Available from: (http://www.deepfin.org/Classification_v3.htm).
   Google Scholar
• Broughton RE, Betancur RR, Li C, Arratia G, Ortí G. 2013. Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution. PLoS Currents: Tree of Life. 5:1–34
   Google Scholar
• Chereshnev IA, Radchenko OA, Petrovskaya AV. 2012. Taxonomic structure of the subfamily Xiphisterinae and its position in the systematics of the Pricklebacks (Stichaeidae, Zoarcoidei). Vestn Severo-Vostochnogo Nauch Tsentra DVO RAN. 8:90–99. In Russian).
   Google Scholar
• Chereshnev IA, Radchenko OA, Petrovskaya AV. 2013. Relationships and position of the taxa of the subfamily Xiphisterinae in the system of the suborder Zoarcoidei (Perciformes). Russ J Mar Biol. 39:276–286.
   Web of Science ®Google Scholar
• Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 6:361–375.
   PubMed Web of Science ®Google Scholar
• Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792–1797.
   PubMed Web of Science ®Google Scholar
• Eschmeyer WN, Fong JD. SPECIES BY FAMILY/SUBFAMILY. Available from: (http://researcharchive.calacademy.org/research/ichthyology/catalog/SpeciesByFamily.asp). Electronic version accessed 8 August 2015.
   Google Scholar
• Ghigliotti L, Møller PR, Cheng CH, Christiansen JS, Fevolden SE, Pisano E. 2012. Exploring the diversity of Arctic eelpouts: first cytogenetic data on species of the genus Lycodes (Teleostei, Zoarcidae). Marine Genomics. 8:35–41.
   PubMed Web of Science ®Google Scholar
• Hillis DM, Mable BK, Moritz C. 1996. Application of molecular systematics: The state of the field and a look to the future. In: Hillis DM, Moritz C, Mable B., editors. Molecular Systematics. Sunderland, Massachusetts (01375–0407, USA): Sinauer. Assoc. Inc. 515–543.
   Google Scholar
• Huson DH, Scornavacca C. 2012. Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks. Systematic Biology. 61:1061–1067.
   PubMed Web of Science ®Google Scholar
• Imamura H, Yabe M. 2002. Demise of the Scorpaeniformes (Actinopterygii: Percomorpha): an alternative phylogenetic hypothesis. Bull Fish Sci Hokkaido Univ. 53:107–128.
   Google Scholar
• Inoue JG, Miya M, Tsukamoto K, Nishida M. 2001. A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences. Mol. Phylogenet. Evol Mol Phylogenet. E 20:275–285.
   PubMed Web of Science ®Google Scholar
• Kartavtsev YP, Sharina SN, Goto T, Rutenko OA, Zemnukho VV, et al. 2009. Molecular phylogenetics of pricklebacks and other percoid fishes from the Sea of Japan. Aquatic Biol. 8:95–103.
   Web of Science ®Google Scholar
• Kim KH, Horn MH, Sosa AE, German DP. 2014. Sequence and expression of an α-amylase gene in four related species of prickleback fishes (Teleostei: Stichaeidae): ontogenetic, dietary, and species-level effects. J Comp Physiol. 184:221–234.
   Web of Science ®Google Scholar
• Korbie DJ, Mattick JS. 2008. Touchdown PCR for increased specificity and sensitivity in PCR amplification. Nat Protoc. 3:1452–1456.
   PubMed Web of Science ®Google Scholar
• Kwun HJ, Kim J-K. 2013. Molecular phylogeny and new classification of the genera Eulophias and Zoarchias (PISCES, Zoarcoidei). Mol Phylogenet Evol Mol Phylogenet. E 69:787–795.
   PubMed Web of Science ®Google Scholar
• Lanfear R, Calcott B, Ho SYW, Guindon S. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol Mol Biol E. 29:1695–1701.
   PubMed Web of Science ®Google Scholar
• Lanfear R, Calcott B, Kainer D, Mayer C, Stamatakis A. 2014. Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evol Biol. 14:82182–82814.
   Web of Science ®Google Scholar
• Li B, Dettai A, Cruaud C, Couloux A, Desoutter-Meniger M, Lecointre G. 2009. RNF213, a new nuclear marker for acanthomorph phylogeny. Mol Phylogenet Evol Mol Phyl E. 50:345–363.
   PubMed Web of Science ®Google Scholar
• Li C, Ortí G, Zhang G, Lu G. 2007. A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evol Biol. 7:44.
   PubMed Web of Science ®Google Scholar
• Makushok VM. 1958. The morphology and classification of the northern blennioid fishes (Stichaeidae, Blennioidei, Pisces). Trudy Zool Inst Akad Nauk SSSR. 25:3–129. (In Russian).
   Google Scholar
• Makushok VM. 1961. The Neozoarcinae (Zoarcidae, Blennioidei, Pisces) and its place in the classification of fishes. Trudy Inst Oceanol. 43:198–224.
   Google Scholar
• Mecklenburg CW. 2003. Family Bathymasteridae Jordan & Gilbert 1883 ronquils. Annotation Checklist of Fishes. California Acad Sci. 7:1–4.
   Google Scholar
• Miller MA, Pfeiffer W, Schwartz T. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop (GCE).
   Google Scholar
• Miya M, Nishida M. 1999. Organization of the mitochondrial genome of a deep-sea fish, Gonostoma gracile (Teleostei: Stomiiformes): first example of transfer RNA gene rearrangements in bony fishes. Mar Biotechnol. 1:416–426.
   PubMed Web of Science ®Google Scholar
• Miya M, Kawaguchi A, Nishida M. 2001. Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Mol Biol Evol Mol Biol E. 18:1993–2009.
   PubMed Web of Science ®Google Scholar
• Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, et al. 2003. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol Mol Phylogenet E. 26:121–138.
   PubMed Web of Science ®Google Scholar
• Møller PR, Gravlund P. 2003. Phylogeny of the eelpout genus Lycodes (Pisces, Zoarcidae) as inferred from mitochondrial cytochrome b and 12S rDNA. Mol Phylogenet Evol Mol Phyl E. 26:369–388.
   PubMed Web of Science ®Google Scholar
• Nazarkin MV. 1998. New stichaeid fishes (Stichaeidae, Perciformes) from Miocene of Sakhalin. J Ichthyol. 38:279–291.
   Google Scholar
• Near TJ, Eytan RI, Dornberg A, Kuhn KL, Moore JA, et al. 2012. Resolution of ray-finned fish phylogeny and timing of diversification. Proc Natl Acad Sci USA. 109:13698–13703.
   PubMed Web of Science ®Google Scholar
• Near TJ, Eytan RI, Keck BP, Smith WL, Kuhn KL, et al. 2013. Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes. Proc Natl Acad Sci USA. 110:12738–12743.
   PubMed Web of Science ®Google Scholar
• Nelson JS. (2006). Fishes of the world. 4th edn. New York: John Wiley & Sons.
   Google Scholar
• Radchenko OA, Chereshnev IA, Petrovskaya AV, Balanov AA, Turanov SV. 2014a. Position of the Genus Azygopterus (Stichaeidae, Perciformes) in the System of the Suborder Zoarcoidei as Inferred from Sequence Variation of Mitochondrial and Nuclear Genes. Russ J Genet. 50:280–287.
   Web of Science ®Google Scholar
• Radchenko OA, Chereshnev IA, Petrovskaya AV, Balanov AA. 2009a. Molecular systematics and phylogeny of the Eelpouts of the suborder Zoarcoidei. Vestn DVO RAN. 3:40–47. (In Russian).
   Google Scholar
• Radchenko OA, Chereshnev IA, Petrovskaya AV. 2009b. Relationships and divergence of some taxa of the subfamily Lycodinae (Zoarcidae, Pisces) based on molecular-genetic and morphological data. J Ichthyol. 49:585–598.
   Google Scholar
• Radchenko OA, Chereshnev IA, Petrovskaya AV. 2010a. Relationships and position of the genus Neozoarces of the subfamily neozoarcinae in the system of the suborder Zoarcoidei (Pisces, Perciformes) by molecular-genetic data. J Ichthyol. 50:246–251.
   Google Scholar
• Radchenko OA, Chereshnev IA, Petrovskaya AV. 2010b. Phylogenetic relations in the family pholidae (Perciformes: Zoarcoidei) based on genetic and morphological data. J Ichthyol. 50:728–739.
   Google Scholar
• Radchenko OA, Chereshnev IA, Petrovskaya AV. 2012a. Position of the genera Lycenchelys Gill and Lycodapus Gilbert in the family zoarcidae (Perciformes: Zoarcoidei) inferred from molecular genetic analysis. Russ J Genet. 48:310–320.
   Web of Science ®Google Scholar
• Radchenko OA, Chereshnev IA, Petrovskaya AV. 2012b. Position of neck banded blenny Leptostichaeus pumilus (Perciformes: Zoarcoidei) in the system of the suborder Zoarcoidei as inferred from molecular genetic data. J Ichthyol. 52:592–598.
   Google Scholar
• Radchenko OA, Chereshnev IA, Petrovskaya AV. 2014b. Genetic differentiation of species and taxonomic structure of the superfamily Stichaeoidea (Perciformes: Zoarcoidei). Russ J Mar Biol. 40:473–485.
   Web of Science ®Google Scholar
• Ronquist F, Teslenko M, Mark PVD, Ayres DL, Darling A, et al. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. MrBayes3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space. Syst Biol. 61:539–542.
   PubMed Web of Science ®Google Scholar
• Sambrook JF, Fritsch EF, Maniatis T. 1989. Molecular cloning: A laboratory manual. 2nd edn. New York: Cold Spring Harbor Laboratory Press.
   Google Scholar
• Saveliev PA. 2012. On the systematic position of the genus Petroschmidtia Taranetz et Andriashev, 1934 (Perciformes: Zoarcidae). Russ J Mar Biol. 38:139–148.
   Web of Science ®Google Scholar
• Scornavacca C, Zickmann F, Huson DH. 2011. Tanglegrams for rooted phylogenetic trees and networks. Bioinformatics. 27:i248–i256.
   PubMed Web of Science ®Google Scholar
• Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30:1312–1313.
   PubMed Web of Science ®Google Scholar
• Stevenson DE, Matarese AC. 2005. The ronquils: a review of the North Pacific fish family Bathymasteridae (Actinopterygii: Perciformes: Zoarcoidei). Proceedings of the Biological Society of Washington. 118:367–406.
   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 Mol Biol E. 30:2725–2729.
   PubMed Web of Science ®Google Scholar
• Turanov SV, Kartavtsev YPh, Lipinsky VV, Zemnukhov VV, Balanov AA, Lee Y-H, et al. 2016. DNA-barcoding of perch-like fishes (Actinopterygii: Perciformes) from far-eastern seas of Russia with taxonomic remarks for some groups. Mitochondrial DNA. 27:1188–1209.
   PubMed Web of Science ®Google Scholar
• Turanov SV, Kartavtsev YPh, Zemnukhov VV. 2012. Molecular phylogenetic study of several eelpout fishes (Perciformes, Zoarcoidei) from Far Eastern seas on the basis of the nucleotide sequences of the mitochondrial cytochrome oxidase 1 gene (Co-1). Russ J Genet. 48:208–233.
   Web of Science ®Google Scholar
• Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD. 2005. DNA barcoding Australia's fish species. Philos Trans R Soc London B Biol Sci. 360:1847–1857.
   PubMed Web of Science ®Google Scholar
• Yatsu A. 1981. A revision of the gunnel family Pholididae (Pisces, Blennioidei). Bull Nat Sci Mus Tokyo Ser a. 7:165–190.
   Google Scholar
• Zemnukhov VV, Savelyev PA. 2011. Neck banded blenny Leptostichaeus pumilus Miki, 1985 (Perciformes: Stichaeidae): A new genus and species for Russian waters. Russ J Mar Biol. 37:163–164.
   Web of Science ®Google Scholar
• Zemnukhov VV. 2012. Genus Leptostichaeus and its position in the taxonomy of fishes (Perciformes: Zoarcoidei, Stichaeidae). J Ichthyol. 52:363–368.
   Google Scholar