REFERENCES
- Altenburger A., Blossom H.E., Garcia-Cuetos L., Jakobsen H.H., Carstensen J., Lundholm N., Hansen P.J., Moestrup Ø. & Haraguchi L. 2020. Dimorphism in cryptophytes – the case of Teleaulax amphioxeia/Plagioselmis prolonga and its ecological implications. Science Advances 6: Article eabb1611. DOI: https://doi.org/10.1126/sciadv.abb1611.
- Andersen R.A. 2005. Algal culturing techniques. Elsevier Academic Press, New York, New York, USA. 577 pp.
- Annenkova N.V., Giner C.R. & Logares R. 2020. Tracing the origin of planktonic protists in an ancient lake. Microorganisms 8: Article 543. DOI: https://doi.org/10.3390/microorganisms8040543.
- Bagley M., Pilgrim E., Knapp M., Yoder C., Domingo J.S. & Banerji A. 2019. High-throughput environmental DNA analysis informs a biological assessment of an urban stream. Ecological Indicators 104: 378–389. DOI: https://doi.org/10.1016/j.ecolind.2019.04.088.
- Bock C., Jensen M., Forster D., Marks S., Nuy J., Psenner R., Beisser D. & Boenigk J. 2020. Factors shaping community patterns of protists and bacteria on a European scale. Environmental Microbiology 22: 2243–2260. DOI: https://doi.org/10.1111/1462-2920.14992.
- Boenigk J., Wodniok S., Bock C., Beisser D., Hempel C., Grossmann L., Lange A. & Jensen M. 2018. Geographic distance and mountain ranges structure freshwater protist communities on a European scale. Metabarcoding and Metagenomics 2: Article e21519. DOI: https://doi.org/10.3897/mbmg.2.21519.
- Byun Y. & Han K. 2006. PseudoViewer: web application and webservice for visualizing RNA pseudoknots and secondary structures. Nucleic Acids Research 34: 416–422. DOI: https://doi.org/10.1093/nar/gkl210.
- Caisová L., Marin B. & Melkonian M. 2013. A consensus secondary structure of ITS2 in the Chlorophyta identified by phylogenetic reconstruction. Protist 164: 482–496. DOI: https://doi.org/10.1016/j.protis.2013.04.005.
- Cerino F. & Zingone A. 2006. A survey of cryptomonad diversity and seasonality at a coastal Mediterranean site. European Journal of Phycology 41: 363–378. DOI: https://doi.org/10.1080/09670260600839450.
- Choi B., Son M., Kim J.I. & Shin W. 2013. Taxonomy and phylogeny of the genus Cryptomonas (Cryptophyceae, Cryptophyta) from Korea. Algae 28: 307–330. DOI: https://doi.org/10.4490/algae.2013.28.4.307.
- Coleman A.W. 2000. The significance of a coincidence between evolutionary landmarks found in mating affinity and a DNA sequence. Protist 151: 1–9. DOI: https://doi.org/10.1078/1434-4610-00002.
- Coleman A.W. 2009. Is there a molecular key to the level of “biological species” in eukaryotes? A DNA guide. Molecular Phylogenetics and Evolution 50: 197–203. DOI: https://doi.org/10.1016/j.ympev.2008.10.008.
- Darriba D., Taboada G.L., Doallo R. & Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772. DOI: https://doi.org/10.1038/nmeth.2109.
- Deane J.A., Strachan I.M., Saunders G.W., Hill D.R. & McFadden G.I. 2002. Cryptomonad evolution: nuclear 18S rDNA phylogeny versus cell morphology and pigmentation. Journal of Phycology 38: 1236–1244. DOI: https://doi.org/10.1046/j.1529-8817.2002.01250.x.
- Eddy S.R. 1998. Profile hidden Markov models. Bioinformatics 14: 755–763. DOI: https://doi.org/10.1093/bioinformatics/14.9.755.
- Ehrenberg C.G. 1831. Animalia Evertebrata. Symbolae physicae seu icones et descriptiones animalium evertebratorum sepositis insectis quae ex itinere per Africanum Borealem et Asiam Occidentalem Friderici Guilelmi Hemprich et Christiani Godofredi Ehrenberg medicinae et chirurgiae doctorum studio novae aut illustratae redierunt. In: Symbolae physicae … Pars Zoologica IV [ Text] (Ed. by P.C. Hemprich, and C.G. Ehrenberg), unpaginated. Mittler, Berlin, Germany.
- Gillespie J.J., Johnston J.S., Cannone J.J. & Gutell R.R. 2006. Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements. Insect Molecular Biology 15: 657–686. DOI: https://doi.org/10.1111/j.1365-2583.2006.00689.x.
- Guiry M.D. & Guiry G.M. 2021. AlgaeBase. World-wide electronic publication, National University of Ireland, Galway, Ireland. http://www.algaebase.org; searched on 30 March 2021.
- Gusev E., Podunay Y., Martynenko N., Shkurina N. & Kulikovskiy M. 2020. Taxonomic studies of Cryptomonas lundii clade (Cryptophyta: Cryptophyceae) with description of a new species from Vietnam. Fottea, Olomouc 20: 137–143. DOI: https://doi.org/10.5507/fot.2020.004.
- Hill D.R. & Wetherbee R. 1986. Proteomonas sulcata gen. et sp. nov. (Cryptophyceae), a cryptomonad with two morphologically distinct and alternating forms. Phycologia 25: 521–543. DOI: https://doi.org/10.2216/i0031-8884-25-4-521.1.
- Hoef-Emden K. 2005. Multiple independent losses of photosynthesis and differing evolutionary rates in the genus Cryptomonas (Cryptophyceae): combined phylogenetic analyses of DNA sequences of the nuclear and the nucleomorph ribosomal operons. Journal of Molecular Evolution 60: 183–195. DOI: https://doi.org/10.1007/s00239-004-0089-5.
- Hoef-Emden K. 2007. Revision of the genus Cryptomonas (Cryptophyceae) II: incongruences between classical morphospecies concept and molecular phylogeny in smaller pyrenoid-less cells. Phycologia 46: 402–428. DOI: https://doi.org/10.2216/06-83.1.
- Hoef-Emden K. 2012. Pitfalls of establishing DNA barcoding systems in protists: the Cryptophyceae as a test case. PLOS One 7: Article e43652. DOI: https://doi.org/10.1371/journal.pone.0043652.
- Hoef-Emden K. 2018. Revision of the genus Chroomonas Hansgirg: the benefits of DNA-containing specimens. Protist 169: 662–681. DOI: https://doi.org/10.1016/j.protis.2018.04.005.
- Hoef-Emden K. & Archibald J.M. 2017. Cryptophyta (Cryptomonads). In: Handbook of the protists (Ed. by J.M. Archibald, A.G.B. Simpson, C.H. Slamovits, L. Margulis, M. Melkonian, D.J. Chapman, and J.O. Corliss), pp 851–891. Springer, Cham, Switzerland. DOI: https://doi.org/10.1007/978-3-319-28149-0_35.
- Hoef-Emden K. & Melkonian M. 2003. Revision of the genus Cryptomonas (Cryptophyceae): a combination of molecular phylogeny and morphology provides insights into a long-hidden dimorphism. Protist 154: 371–409. DOI: https://doi.org/10.1078/143446103322454130.
- Katoh K. & Toh H. 2010. Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics 26: 1899–1900. DOI: https://doi.org/10.1093/bioinformatics/btq224.
- Keller A., Schleicher T., Schultz J., Müller T., Dandekar T. & Wolf M. 2009. 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene 430: 50–57. DOI: https://doi.org/10.1016/j.gene.2008.10.012.
- Kim J.I., Moore C.E., Archibald J.M., Bhattacharya D., Yi G., Yoon H.S. & Shin W. 2017. Evolutionary dynamics of cryptophyte plastid genomes. Genome Biology and Evolution 9: 1859–1872. DOI: https://doi.org/10.1093/gbe/evx123.
- Kisselev I.A. 1954. Pyrrophyta. In: Identification guide for freshwater algae of the USSR, vol. 6 (Ed. by M.M. Hollerbach, and V.I. Poljansky), Sovetskaya Nauka, Moscow, Russia. 212 pp [ in Russian].
- Kulizin P.V., Martynenko N.A., Gusev E.S., Kapustin D.A., Vodeneeva E.L. & Kulikovskiy M.S. 2022. New species of genus Cryptomonas for the flora of Russia. Inland Water Biology 15.
- Kumar S., Stecher G., Li M., Knyaz C. & Tamura K. 2018. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution 35: 1547–1549. DOI: https://doi.org/10.1093/molbev/msy096.
- Lane C.E. & Archibald J.M. 2008. New marine members of the genus Hemiselmis (Cryptomonadales, Cryptophyceae). Journal of Phycology 44: 439–450. DOI: https://doi.org/10.1111/j.1529-8817.2008.00486.x.
- Lisin Y.V. [Ed.] 2011. Atlas of the Komi Republic. Feoriya, Moscow, Russia. 448 pp [ in Russian].
- Marin B., Klingberg M. & Melkonian M. 1998. Phylogenetic relationships among the Cryptophyta: analyses of nuclear-encoded SSU rRNA sequences support the monophyly of extant plastid-containing lineages. Protist 149: 265–276. DOI: https://doi.org/10.1016/S1434-4610(98)70033-1.
- Martynenko N.A., Gusev E.S., Kapustin D.A., Guseva E.E. & Kulikovskiy M.S. 2020a. Cryptomonas cattiensis sp. nov. (Cryptophyceae: Cryptomonadales), a new species described from Vietnam. Phytotaxa 454: 127–136. DOI: https://doi.org/10.11646/phytotaxa.454.2.4.
- Martynenko N.A., Gusev E.S., Kulizin P.V., Guseva E.E., McCartney K. & Kulikovskiy M.S. 2020b. A new species of Cryptomonas (Cryptophyceae) from the Western Urals (Russia). European Journal of Taxonomy 649: 1–12. DOI: https://doi.org/10.5852/ejt.2020.649.
- Matvienko O.M. & Litvinenko R.M. 1977. Pyrrophyta. Identification guide for freshwater algae of the Ukrainian SSR, vol. 3, 2. Naukova Dumka, Kiev, Ukraine. 387 pp [ in Ukrainian].
- McFadden G.I. & Melkonian M. 1986. Use of Hepes buffer for microalgal culture media and fixation for electron microscopy. Phycologia 25: 551–557. DOI: https://doi.org/10.2216/i0031-8884-25-4-551.1.
- Müller T., Philippi N., Dandekar T., Schultz J. & Wolf M. 2007. Distinguishing species. RNA 13: 1469–1472. DOI: https://doi.org/10.1261/rna.617107.
- Nakayama T., Watanabe S., Mitsui K., Uchida H. & Inouye I. 1996. The phylogenetic relationship between the Chlamydomonadales and Chlorococcales inferred from 18SrDNA sequence data. Phycological Research 44: 47–55. DOI: https://doi.org/10.1111/j.1440-1835.1996.tb00037.x.
- Nazarov N.N. 2006. Geography of the Perm region. Part I. Natural (physical) geography. Publishing House of Perm State University, Perm, Russia. 138 pp [ in Russian].
- Patova E., Novakovskaya I., Martynenko N., Gusev E. & Kulikovskiy M. 2021. Mychonastes frigidus sp. nov. (Sphaeropleales/Chlorophyceae), a new species described from a mountain stream in the Subpolar Urals (Russia). Fottea, Olomouc 21: 8–15. DOI:https://doi.org/10.5507/fot.2020.012.
- Pruesse E., Peplies J. & Glöckner F.O. 2012. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28: 1823–1829. DOI: https://doi.org/10.1093/bioinformatics/bts252.
- Rambaut A., Drummond A.J., Xie D., Baele G. & Suchard M.A. 2018. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology 67: 901–904. DOI: https://doi.org/10.1093/sysbio/syy032.
- Ronquist F. & Huelsenbeck J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574. DOI: https://doi.org/10.1093/bioinformatics/btg180.
- Ruppert K.M., Kline R.J. & Rahman M.S. 2019. Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: a systematic review in methods, monitoring, and applications of global eDNA. Global Ecology and Conservation 17: Article e00547. DOI: https://doi.org/10.1016/j.gecco.2019.e00547.
- Schultz J., Maisel S., Gerlach D., Müller T. & Wolf M. 2005. A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA 11: 361–364. DOI: https://doi.org/10.1261/rna.7204505.
- Seibel P.N., Müller T., Dandekar T., Schultz J. & Wolf M. 2006. 4SALE – a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinformatics 7: Article 498. DOI: https://doi.org/10.1186/1471-2105-7-498.
- Shalchian-Tabrizi K., Brate J., Logares R., Klaveness D., Berney C. & Jakobsen K.S. 2008. Diversification of unicellular eukaryotes: cryptomonad colonizations of marine and fresh waters inferred from revised 18S rRNA phylogeny. Environmental Microbiology 10: 2635–2644. DOI: https://doi.org/10.1111/j.1462-2920.2008.01685.x.
- Tanifuji G., Kamikawa R., Moore C.E., Mills T., Onodera N.T., Kashiyama Y. & Hashimoto T. 2020. Comparative plastid genomics of Cryptomonas species reveals fine-scale genomic responses to loss of photosynthesis. Genome Biology and Evolution 12: 3926–3937. DOI: https://doi.org/10.1093/gbe/evaa001.
- Thompson J.D., Higgins D.G. & Gibson T.J. 1994. CLUSTALW: improving the sensitivity of progressive multiple sequence through weighing, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673–4680. DOI: https://doi.org/10.1093/nar/22.22.4673.
- van den Hoff J., Bell E. & Whittock L. 2020. Dimorphism in the Antarctic cryptophyte Geminigera cryophila (Cryptophyceae). Journal of Phycology 56: 1028–1038. DOI: https://doi.org/10.1111/jpy.13004.
- Voloshko L.N. 2009. New taxa of the genus Mallomonas (Chrysophyta, Synurophyceae) from lakes of the Polar Ural. Botanicheskii Zhurnal 94: 1068–1076 [ in Russian].
- Voloshko L.N. 2012. A new species of the genus Mallomonas (Chrysophyta, Synurophyceae) from the lakes in Vorkutinskaya tundra. Botanicheskii Zhurnal 97: 1226–1234 [ in Russian].
- Wolf M., Chen S., Song J., Ankenbrand M. & Müller T. 2013. Compensatory base changes in ITS2 secondary structures correlate with the biological species concept despite intragenomic variability in ITS2 sequences – a proof of concept. PLOS One 8: Article e66726. DOI: https://doi.org/10.1371/journal.pone.0066726.
- Wuyts J., Van de Peer Y. & De Wachter R. 2001. Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucleic Acids Research 29: 5017–5028. DOI: https://doi.org/10.1093/nar/29.24.5017.
- Xia X. & Lemey P. 2009. Assessing substitution saturation with DAMBE. The phylogenetic handbook: a practical approach to DNA and protein phylogeny, vol. 2 (Ed. by P. Lemey, M. Salemi & A. Vandamme), pp 615–630. Cambridge University Press, United Kingdom. DOI: https://doi.org/10.1017/CBO9780511819049.
- Xia X. & Xie Z. 2001. DAMBE: software package for data analysis in molecular biology and evolution. Journal of Heredity 92: 371–373. DOI: https://doi.org/10.1093/jhered/92.4.371.
- Xia X., Xie Z., Salemi M., Chen L. & Wang Y. 2003. An index of substitution saturation and its application. Molecular Phylogenetics and Evolution 26: 1–7. DOI: https://doi.org/10.1016/S1055-7903(02)00326-3.
- Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31: 3406–3415. DOI: https://doi.org/10.1093/nar/gkg595.