References
- Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25: 3389–3402.
- Barcytė, D., Hodač, L. & Nedbalová, L. (2017). Lunachloris lukesovae gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel coccoid green alga isolated from soil in South Bohemia, Czech Republic. European Journal of Phycology, 52: 281–291.
- Barcytė, D., Hodač, L., Nedbalová, L. & Elster, J. (2018a). Chloromonas svalbardensis n. sp. with insights into the phylogroup Chloromonadinia (Chlorophyceae). Journal of Eukaryotic Microbiology, 65: 882–892.
- Barcytė, D., Hodač, L., Nedbalová, L. & Elster, J. (2018b). Chloromonas arctica sp. nov., a psychrotolerant alga from snow in the High Arctic (Chlamydomonadales, Chlorophyta). International Journal of Systematic and Evolutionary Microbiology, 68: 851–859.
- Barcytė, D., Nedbalová, L., Culka, A., Košek, F. & Jehlička, J. (2018c). Burning coal spoil heaps as a new habitat for the extremophilic red alga Galdieria sulphuraria. Fottea, 18: 19–29.
- Bischoff, H.W. & Bold, H.C. (1963). Phycological studies IV. Some soil algae from Enchanted Rock and related algal species. University of Texas Publication, 6318: 1–95.
- Bourrelly, P. (1951). Volvocales rares ou nouvelles. Hydrobiologia, 3: 251–281.
- Christen, H.R. (1959). Flagellaten aus dem Schützenweiher bei Veltheim. Mitteilungen der naturwissenschaftlichen gesellschaft in Winterthur, 29: 167–189.
- Darty, K., Denise, A. & Ponty, Y. (2009). VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25: 1974–1975.
- Ettl, H. (1976). Die Gattung Chlamydomonas Ehrenberg. Beihefte zur Nova Hedwigia, 49: 1–1122.
- Ettl, H. (1983). Chlorophyta I. Phytomonadina. In Süßwasserflora von Mitteleuropa (Ettl, H., Gerloff, J., Heynig, H. & Mollenhauer, D., editors). Gustav Fischer Verlag, Jena.
- Flint, E.A. & Ettl, H. (1966). Some new and uncommon Chlamydomonas species from New Zealand. New Zealand Journal of Botany, 4: 418–433.
- Hall, T.A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41: 95–98.
- Helms, G., Friedl, T., Rambold, G. & Mayrhofer, H. (2001). Identification of photobionts from the lichen family Physciaceae using algal-specific ITS rDNA sequences. Lichenologist, 33: 73–86.
- Hepperle, D. (2004). SeqAssem©. A sequence analysis tool, contig assembler and trace data visualization tool for molecular sequences. Win32-Version. Distributed by the author via: http://www.sequentix.de.
- Hoham, R.W., Bonome, T.A., Martin, C.W. & Leebens-Mack, J.H. (2002). A combined 18S rDNA and rbcL phylogenetic analyses of Chloromonas and Chlamydomonas (Chlorophyceae, Volvocales) emphasizing snow and other cold-temperature habitats. Journal of Phycology, 38: 1051–1064.
- Hoham, R.W. & Mullet, J.E. (1978). Chloromonas nivalis (Chod.) Hoh. & Mull. comb. nov., and additional comments on the snow alga, Scotiella. Phycologia, 17: 106–107.
- Hoham, R.W., Mullet, J.E. & Roemer, S.C. (1983). The life history and ecology of the snow alga Chloromonas polyptera comb. nov. (Chlorophyta, Volvocales). Canadian Journal of Botany, 61: 2416–2429.
- Hoham, R.W., Roemer, S.C. & Mullet, J.E. (1979). The life history and ecology of the snow alga Chloromonas brevispina comb. nov. (Chlorophyta, Volvocales). Phycologia, 18: 55–70.
- Katana, A., Kwiatowski, J., Spalik, K., Zakryś, B., Szalacha, E. & Szymańska, H. (2001). Phylogenetic position of Koliella (Chlorophyta) as inferred from nuclear and chloroplast small subunit rDNA. Journal of Phycology, 37: 443–451.
- Katoh, K. & Toh, H. (2008). Recent developments in the MAFFT multiple sequence alignment program. Briefing in Bioinformatics, 9: 286–298.
- Klebs, G.A. (1886). Über die Organisation der Gallerte bei einigen Algen und Flagellaten. Untersuchungen Botanische Institut Tübingen, 2: 333–417, pls III, IV.
- Koetschan, C., Hackl, T., Müller, T., Wolf, M., Förster, F. & Schultz, J. (2012). ITS2 database IV: interactive taxon sampling for internal transcribed spacer 2 based phylogenies. Molecular Phylogeny and Evolution, 63: 585–588.
- Kryvenda, A., Rybalka, N., Wolf, M. & Friedl, T. (2018). Species distinctions among closely related strains of Eustigmatophyceae (Stramenopiles) emphasizing ITS2 sequence-structure data: Eustigmatos and Vischeria. European Journal of Phycology, 53: 471–491.
- Lund, J.W.G. (1947). Observations on soil algae. III. Species of Chlamydomonas Ehr. in relation to variability within the genus. New Phytologist, 46: 185–194.
- Matsuzaki, R., Hara, Y. & Nozaki, H. (2012). A taxonomic revision of Chloromonas reticulata (Volvocales, Chlorophyceae), the type species of the genus Chloromonas, based on multigene phylogeny and comparative light and electron microscopy. Phycologia, 51: 74–85.
- Matsuzaki, R., Hara, Y. & Nozaki, H. (2014). A taxonomic study of snow Chloromonas species (Volvocales, Chlorophyceae) based on light and electron microscopy and molecular analysis of cultured material. Phycologia, 53: 293–304.
- Matsuzaki, R., Nakada, T., Hara, Y. & Nozaki, H. (2010). Light and electron microscopy and molecular phylogenetic analyses of Chloromonas pseudoplatyrhyncha (Volvocales, Chlorophyceae). Phycological Research, 58: 202–209.
- Matsuzaki, R., Nozaki, H. & Kawachi, M. (2018). Taxonomic revision of Chloromonas nivalis (Volvocales, Chlorophyceae) strains, with the new description of two snow-inhabiting Chloromonas species. PLoS ONE, 13: e0193603.
- Matsuzaki, R., Nozaki, H., Takeuchi, N., Hara, Y. & Kawachi, M. (2019). Taxonomic re-examination of “Chloromonas nivalis (Volvocales, Chlorophyceae) zygotes” from Japan and description of C. muramotoi sp. nov. PLoS ONE, 14: e0210986.
- Nakada, T., Misawa, K. & Nozaki, H. (2008). Molecular systematics of Volvocales (Chlorophyceae, Chlorophyta) based on exhaustive 18S rRNA phylogenetic analyses. Molecular Phylogenetics and Evolution, 48: 281–291.
- Nakada, T., Tomita, M., Wu, J.T. & Nozaki, H. (2016). Taxonomic revision of Chlamydomonas subg. Amphichloris (Volvocales, Chlorophyceae), with resurrection of the genus Dangeardinia and descriptions of Ixipapillifera gen. nov. and Rhysamphichloris gen. nov. Journal of Phycology, 52: 283–304.
- Posada, D. (2008). jModelTest: phylogenetic model averaging. Molecular Biology and Evolution, 25: 1253–1256.
- Pröschold, T., Marin, B., Schlösser, U.G. & Melkonian, M. (2001). Molecular phylogeny and taxonomic revision of Chlamydomonas (Chlorophyta). I. Emendation of Chlamydomonas Ehrenberg and Chloromonas Gobi, and description of Oogamochlamys gen. nov. and Lobochlamys gen. nov. Protist, 152: 265–300.
- Rambaut, A. (2007). Figtree, a graphical viewer of phylogenetic trees. In http://tree.bio.ed.ac.uk/software/figtree/.
- Remias, D., Schwaiger, S., Aigner, S., Leya, T., Stuppner, H. & Lütz, C. (2012). Characterization of an UV- and VIS-absorbing, purpurogallin-derived secondary pigment new to algae and highly abundant in Mesotaenium berggrenii (Zygnematophyceae, Chlorophyta), an extremophyte living on glaciers. FEMS Microbiology Ecology, 79: 638–648.
- Reuter, J.S. & Mathews, D.H. (2010). RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics, 11: 129.
- Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D.L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M.A. & Huelsenbeck, J.P. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61: 539–542.
- Rybalka, N., Wolf, M., Andersen, R.A. & Friedl, T. (2013). Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae). BMC Evolutionary Biology, 13: 39.
- Seibel, P.N., Müller, T., Dandekar, T. & Wolf, M. (2008). Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. BMC Research Notes, 1: 91.
- Stamatakis, A., Hoover, P. & Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology, 57: 758–771.
- Stat, M., Bird, C.E., Pochon, X., Chasqui, L., Chauka, L.J., Concepcion, G.T., Logan, D., Takabayashi, M., Toonen, R.J. & Gates, R.D. (2011). Variation in Symbiodinium ITS2 sequence assemblages among coral colonies. PLoS ONE, 6: e15854.
- 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.
- White, T.J., Bruns, T., Lee, S. & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR protocols: A Guide to Methods and Applications (Innis, N., Gelfand, D., Sninsky, J. & White, T., editors), 315–322. Academic Press, New York.
- 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: e66726.
- Zwickl, D.J. (2006). Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD dissertation, The University of Texas at Austin.