Miya, M. and Nishida, M., The mitogenomic contributions to molecular phylogenetics and evolution of fishes: a 15-year retrospect, Ichthyol. Res., 2015, vol. 62, no. 1, pp. 29—71. https://doi.org/10.1007/s10228-014-0440-9
Johnston, I.G. and Williams, B.P., Evolutionary inference across eukaryotes identifies specific pressures favoring mitochondrial gene retention, Cell Syst., 2016, vol. 2, no. 2, pp. 101—111. https://doi.org/10.1016/j.cels.2016.01.013
Article CAS PubMed Google Scholar
Popova, O.V., Mikhailov, K.V., Nikitin, M.A., et al., Mitochondrial genomes of Kinorhyncha: trnM duplication and new gene orders within animals, PLoS One, 2016, vol. 11, no. 10, p. e0165072. https://doi.org/10.1371/journal.pone.0165072
Article CAS PubMed PubMed Central Google Scholar
Kern, E.M.A., Kim, T. and Park, J.-K., The mitochondrial genome in nematode phylogenetics, Front. Ecol. Evol., 2020, vol. 8, p. 250. https://doi.org/10.3389/fevo.2020.00250
Botero-Castro, F., Delsuc, F. and Douzery, E.J., Thrice better than once: quality control guidelines to validate new mitogenomes, Mitochondrial DNA, Part A, 2016, vol. 27, no. 1, pp. 449—454. https://doi.org/10.3109/19401736.2014.900666
Balakirev, E.S., Saveliev, P.A. and Ayala, F.J., Complete mitochondrial genomes of the Cherskii’s sculpin Cottus czerskii and Siberian taimen Hucho taimen reveal GenBank entry errors: incorrect species identification and recombinant mitochondrial genome, Evol. Bioinf., 2017, no. 13, pp. 1—7. https://doi.org/10.1177/1176934317726783
Oleinik, A.G., Skurikhina, L.A. and Kukhlevsky, A.D., Clarification of taxonomic assignment of smelt complete mitochondrial genome: GenBank accession number KP281293.1 (NC_026566.1), Mitochondrial DNA, Part B, 2019, vol. 4, pp. 1696—1697. https://doi.org/10.1080/23802359.2019.1607578
Sangster, G. and Luksenburg, J.A., The published complete mitochondrial genome of the milk shark (Rhizoprionodon acutus) is a misidentified Pacific spadenose shark (Scoliodon macrorhynchos) (Chondrichthyes: Carcharhiniformes), Mitochondrial DNA, Part B, 2021, vol. 6, pp. 828—830. https://doi.org/10.1080/23802359.2021.1884019
Sangster, G. and Luksenburg, J.A., Sharp increase of problematic mitogenomes of birds: causes, consequences, and remedies, Genome Biol. Evol., 2021, vol. 13, no. 9, pp. 828—830. https://doi.org/10.1093/gbe/evab210
Teske, P.R., Mitochondrial genome announcements need to consider existing short sequences from closely related species to prevent taxonomic errors, Conserv. Genet. Resour., 2021, vol. 13, pp. 359—365. https://doi.org/10.1007/s12686-021-01214-7
WoRMS Editorial Board, World Register of Marine Species. https://www.marinespecies.org. Accessed March 18, 2024. https://doi.org/10.14284/170.
Toyoshima, M., Taxonomy of the subfamily Lycodinae (family Zoarcidae) in Japan and adjacent waters, Mem. Fac. Fish. Hokkaido Univ., 1985, vol. 32, no. 2, pp. 131—243. http://hdl.handle.net/2115/21878.
Mecklenburg, C.W., Møller, P.R. and Steinke, D., Biodiversity of arctic marine fishes: taxonomy and zoogeography, Mar. Biodiversity, 2011, vol. 41, pp. 109—140. https://doi.org/10.1007/s12526-010-0070-z
Mecklenburg, C.W. and Steinke, D., Ichthyofaunal baselines in the Pacific Arctic region and RUSALCA study area, Oceanography, 2015, vol. 28, no. 3, pp. 158—189. https://doi.org/10.5670/oceanog.2015.64
Dolganov, V.N. and Saveliev, P.A., The formation of the Lycodinae fauna (Perciformes: Zoarcidae) of the Sea of Japan, Rus. J. Mar. Biol., 2013, vol. 39, no. 5, pp. 331—339. https://doi.org/10.1134/S1063074013050027
Andriashev, A.P., Ryby severnykh morei SSSR (Fishes of the Northern Seas of the USSR), Moskva, Leningrad: Akad. Nauk SSSR, 1954.
Lindberg, G.U. and Krasyukova, Z.V., Ryby Yaponskogo morya i sopredel’nykh chastei Okhotskogo i Zheltogo morei (Fishes of the Sea of Japan and the Adjacent Areas of the Sea of Okhotsk and the Yellow Sea), Leningrad: Nauka, 1975.
Anderson, M.E., Systematics and osteology of the Zoarcidae (Teleostei: Perciformes). Ichthyol. Bull. J.L.B. Smith Inst. Ichthyol., 1994, no. 60, pp. 1—120. http://hdl.handle.net/10962/d1019910.
Lee, S.H., Kang, C.B., Shin, M.H., et al., The complete mitochondrial genome of a marbled eelpout Lycodes raridens (Perciformes: Zoarcidae), Mitochondrial DNA, Part B, 2019, vol. 4, no. 2, pp. 4043—4044. https://doi.org/10.1080/23802359.2019.1688698
Zheng, Y., Chen, Y., and Chen, P., The complete mitochondrial genome of an eelpout Lycodes ygreknotatus (Teleostei: Zoarcidae), Mitochondrial DNA, Part B, 2019, vol. 4, pp. 616—617. https://doi.org/10.1080/23802359.2018.1561232
The National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov. Accessed May 3, 2024.
Edgar, R.C., MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 2004, vol. 32, no. 5, pp. 1792—1797. https://doi.org/10.1093/nar/gkh340
Article CAS PubMed PubMed Central Google Scholar
Altschul, S., Gish, W., Miller, W., et al., Basic local alignment search tool, J. Mol. Biol., 1990, no. 215, pp. 403—410. https://doi.org/10.1016/S0022-2836(05)80360-2
Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., et al., DnaSP6: DNA sequence polymorphism analysis of large datasets, Mol. Biol. Evol., 2017, vol. 34, pp. 3299—3302. https://doi.org/10.1093/molbev/msx248
Article CAS PubMed Google Scholar
Filatov, D.A., PROSEQ: a software for preparation and evolutionary analysis of DNA sequence data sets, Mol. Ecol. Notes, 2002, no. 2, pp. 621—624. https://doi.org/10.1046/j.1471-8286.2002.00313.x
Tamura, K., Stecher, G., and Kumar, S., MEGA11: molecular evolutionary genetics analysis version 11, Mol. Biol. Evol., 2021, vol. 38, no. 7, pp. 3022–3027. https://doi.org/10.1093/molbev/msab120
Article CAS PubMed PubMed Central Google Scholar
Collins, R.A., Boykin, L.M., Cruickshank, R.H., et al., Barcoding’s next top model: an evaluation of nucleotide substitution models for specimen identification, Methods Ecol. Evol., 2012, no. 3, pp. 457—465. https://doi.org/10.1111/j.2041-210x.2011.00176.x
Nguyen, L.T., Schmidt, H.A., von Haeseler, A., et al., IQ-TREE: a fast and effective stochastic algorithm for estimating maximum likelihood phylogenies, Mol. Biol. Evol., 2015, vol. 32, pp. 268—274. https://doi.org/10.1093/molbev/msu300
Article CAS PubMed Google Scholar
Akaike, H., A new look at the statistical model identification, IEEE Trans. Automat. Contr., 1974, no. 19, pp. 716—723. https://doi.org/10.1109/TAC.1974.1100705
Schwarz, G.E., Estimating the dimension of a model, Ann. Stat., 1978, vol. 6, no. 2, pp. 461—464. https://doi.org/10.1214/aos/1176344136
Hoang, D.T., Chernomor, O., von Haeseler, A., et al., UFBoot2: improving the ultrafast bootstrap approximation, Mol. Biol. Evol., 2018, vol. 35, no. 2, pp. 518—522. https://doi.org/10.1093/molbev/msx281
Article CAS PubMed Google Scholar
Johns, G.C. and Avise, G.C., A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene, Mol. Biol. Evol., 1998, vol. 15, no. 11, pp. 1482—1490. https://doi.org/10.1093/oxfordjournals.molbev.a025875
Kartavtsev, Y.P., Rozhkovan, K.V. and Masalkova, N.A., Phylogeny based on two mtDNA genes (Co-1, Cyt-B) among sculpins (Scorpaeniformes, Cottidae) and some other scorpionfish in the Russian Far East, Mitochondrial DNA, Part A, 2016, vol. 27, no. 3, pp. 2225—2240. https://doi.org/10.3109/19401736.2014.984164
Coulson, M.W., Marshall, H.D., Pepin, P., et al., Mitochondrial genomics of gadine fishes: implications for taxonomy and biogeographic origins from whole-genome data sets, Genome, 2006, vol. 49, no. 9, pp. 1115—1130. https://doi.org/10.1139/g06-083
Article CAS PubMed Google Scholar
Balakirev, E.S., Kravchenko,A.Y. and Semenchenko, A.A., Genetic evidence for a mixed composition of the genus Myoxocephalus (Cottoidei: Cottidae) necessitates generic realignment, Genes, 2020, vol. 11, no. 9, p. 1071. https://doi.org/10.3390/genes11091071
Article CAS PubMed PubMed Central Google Scholar
Balakirev, E.S., Recombinant mitochondrial genomes reveal recent interspecific hybridization between invasive salangid fishes, Life, 2022, no. 12, p. 661. https://doi.org/10.3390/life12050661
Radchenko, O.A., Chereshnev, I.A., Petrovskaya, A.V., et al., Nucleotide sequence variation of the mitochondrial COI gene in several eelpout species of the genus Zoarces (Zoarcidae, Pisces), Russ. J. Genet., 2008, vol. 44, no. 7, pp. 799—807. https://doi.org/10.1134/S1022795408070077
Turanov, S.V., Kartavtsev, Y.P. and Zemnukhov, V.V., 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., 2012, vol. 48, pp. 208—223. https://doi.org/10.1134/S1022795412020159
Turanov, S., Kartavtsev, Y., Lipinsky, et al., DNA-barcoding of perch-like fishes (Actinopterygii: Perciformes) from far-eastern seas of Russia with taxonomic remarks for some groups, Mitochondrial DNA, Part A, 2014, vol. 27, no. 2, pp. 1188—1209. https://doi.org/10.3109/19401736.2014.945525
Dettai, A., Lautredou, A.-C., Bonillo, C., et al., The actinopterygian diversity of the CEAMARC cruises: barcoding and molecular taxonomy as a multi-level tool for new findings, Deep Sea Res., Part II: Top. Stud. Oceanogr., 2011, no. 58, pp. 250—263. https://doi.org/10.1016/j.dsr2.2010.05.021
Smith, P.J., Steinke, D., Dettai, A., et al., DNA barcodes and species identifications in Ross Sea and Southern Ocean fishes, Polar Biol., 2012, vol. 35, pp. 1297—1310. https://doi.org/10.1007/s00300-012-1173-8
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