Two independent genetic markers support separation of the myxomycete Lycogala epidendrum into numerous biological species

LITERATURE CITED

• Adl SM, Habura A, Eglit Y. 2014. Amplification primers of SSU rDNA for soil protists. Soil Biol Biochem. 69:328–342.
   Web of Science ®Google Scholar
• Borg Dahl M, Brejnrod AD, Unterseher M, Hoppe T, Feng Y, Novozhilov Y, Sørensen SJ, Schnittler M. 2018. Genetic barcoding of dark-spored myxomycetes (Amoebozoa). Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies. Mol Ecol Resour. 18(2):306–318.
   PubMed Web of Science ®Google Scholar
• Chen C, Frankhouser D, Bundschuh R, Ioshikhes I. 2012. Comparison of insertional RNA editing in Myxomycetes. PLoS Comput Biol. 8(2):11.
   Web of Science ®Google Scholar
• Dagamac NHA, Rojas C, Novozhilov YK, Moreno GH, Schlueter R, Schnittler M, Janke A. 2017. Speciation in progress? A phylogeographic study among populations of Hemitrichia serpula (Myxomycetes). PLoS ONE. 12(4):e0174825.
   PubMed Web of Science ®Google Scholar
• Estrada-Torres A, Gaither TW, Miller DL, Lado C, Keller HW. 2005. The myxomycete genus Schenella, morphological and DNA sequence evidence for synonymy with the gasteromycete genus Pyrenogaster. Mycologia. 97:139–149.
   PubMed Web of Science ®Google Scholar
• Feng Y, Schnittler M. 2015. Sex or no sex? Group I introns and independent marker genes reveal the existence of three sexual but reproductively isolated biospecies. Trichia varia (Myxomycetes). Org Divers Evol. 15(4):631–650.
   Web of Science ®Google Scholar
• Fiore-Donno AM, Meyer M, Baldauf SL, Pawlowski J. 2008. Evolution of dark-spored myxomycetes (slime-molds), molecules versus morphology. Mol Phylogenet Evol. 46:878–889.
   PubMed Web of Science ®Google Scholar
• Fiore-Donno AM, Nikolaev SI, Nelson M, Pawlowski J, Cavalier-Smith T, Baldauf S. 2010. Deep phylogeny and evolution of slime moulds (Mycetozoa). Protist. 161:55–70.
   PubMed Web of Science ®Google Scholar
• Frankham R, Ballou JD, Eldridge MDB, Lacy RC, Ralls K, Dudash MR, Fenster CB. 2011. Predicting the probability of outbreeding depression. Conserv Biol. 25(3):465–475.
   PubMed Web of Science ®Google Scholar
• Fries EM. 1829 . Myxogastres. In: Systema Mycologicum. Vol. 3. Uppsala (Sweden): Gryphiswaldiae. p. 1–202. https://archive.org/details/systemamycologi02hoffgoog/page/n4/mode/2up.
   Google Scholar
• García-Martín JM, Zamora JC, Lado C. 2019. Evidence of intra-individual SSU polymorphisms in dark-spored Myxomycetes (Amoebozoa). Protist. 170(5):125681.
   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. Nucleic Acids Symposium Series; 41:95–98.
   Google Scholar
• Horton T, Landweber L. 2000. Evolution of four types of RNA editing in myxomycetes. RNA. 6(10):1339–46.
   PubMed Web of Science ®Google Scholar
• Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. 2017. ModelFinder, fast model selection for accurate phylogenetic estimates. Nat Methods. 14:587–589.
   PubMed Web of Science ®Google Scholar
• Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780.
   PubMed Web of Science ®Google Scholar
• Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE. 2015. The Phyre2 web portal for protein modelling prediction and analysis. Nat Protoc. 10:845–858.
   PubMed Web of Science ®Google Scholar
• Lado C. 2005–2022. An online nomenclatural information system of Eumycetozoa. Real Jardín Botánico CSIC Madrid Spain; [ accessed 2022 Jul 25]. http://www.nomeneumycetozoa.com.
   Google Scholar
• Larsson A. 2014. AliView, a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics. 30(22):3276–3278.
   PubMed Web of Science ®Google Scholar
• Leontyev DV, Schnittler M, Ishchenko Y, Quade A, Kahlert H, Rojas Alvarado C, Stephenson SL. 2022. Another species complex in myxomycetes: diversity of peridial structures. Lycogala epidendrum. 114(3−4):413–434. Nova Hedwigia.
   Google Scholar
• Leontyev D, Schnittler M, Moreno Horcajada G, Stephenson S, Mitchell DW, Rojas C. 2014. The genus Alwisia (Myxomycetes) revalidated, with two species new to science. Mycologia. 106(5):936–948.
   PubMed Web of Science ®Google Scholar
• Leontyev D, Schnittler M, Stephenson SL. 2015. A critical revision of the Tubifera ferruginosa complex. Mycologia. 107(5):959–985.
   PubMed Web of Science ®Google Scholar
• Leontyev DV, Schnittler M. 2017. Phylogeny of myxomycetes. In: Rojas Alvarado C, Stephenson SL, editors. Myxomycetes. 1st ed. Amsterdam (Netherlands): Elsevier. p. 83–106.
   Google Scholar
• Leonytev DV, Schnittler M. 2022. Phylogeny and phylogenetically based classification of Myxomycetes. In: Rojas Alvarado C, Stephenson SL, editors. The Myxomycetes: biology, systematics, biogeography and ecology. Amsterdam (Netherlands): Elsevier. p. 91–124.
   Google Scholar
• Leontyev DV, Schnittler M, Stephenson SL, Novozhilov YK. 2019a. Systematic revision of the Tubifera casparyi – t. dictyoderma complex, resurrection of the genus Siphoptychium and introduction of the new genus Thecotubifera. Mycologia. 111(6):981–997.
   PubMed Web of Science ®Google Scholar
• Leontyev DV, Schnittler M, Stephenson S, Novozhilov YK, Shchepin OV. 2019b. Towards a phylogenetic classification of Myxomycetes. Phytotaxa. 339(3):209–238.
   Web of Science ®Google Scholar
• Liu T, Bundschuh R. 2005. Model for codon position bias in RNA editing. Phys Rev Lett. 95(8):088101.
   PubMed Web of Science ®Google Scholar
• Lloyd SJ, Leontyev DV, Dagamac NH. 2019. Three new species of Tubifera from Tasmania and New South Wales. Phytotaxa. 414(5):240–252.
   Web of Science ®Google Scholar
• Mahendran R, Spottswood MR, Miller DL. 1991. RNA editing by cytidine insertion in mitochondria of Physarum polycephalum. Nature. 349:434–438.
   PubMed Web of Science ®Google Scholar
• Mayr E. 1991. Principles of systematic zoology. New York (NY): McGraw-Hill.
   Google Scholar
• Mikhailyuk T, Lukešová A, Glaser K, Holzinger A, Obwegeser S, Nyporko S, Friedl T, Karsten U. 2018. New taxa of Streptophyte algae (Streptophyta) from terrestrial habitats revealed using an integrative approach. Protist. 169(3):406–431.
   PubMed Web of Science ®Google Scholar
• Miller D, Padmanabhan R, Sarcar SN. 2017. Genomics and gene expression. In: Rojas Alvarado C, Stephenson SL, editors. Myxomycetes. 1st ed. Amsterdam (Netherlands): Elsevier. p.107–143.
   Google Scholar
• Nannenga-Bremekamp NE. 1991. A guide to temperate myxomycetes. Bristol (UK): Biopress.
   Google Scholar
• Pankovius T. 1654. Herbarium Portatile oder Behendes Kräuter und Gewächs-Buch. Leipzig (Germany): Christian Kirchners.
   Google Scholar
• Phillips R. 2010. Mushrooms and other Fungi of North America. Buffalo (New York (NY)): Firefly Books.
   Google Scholar
• Puillandre N, Lambert A, Brouillet S, Achaz G. 2011. ABGD automatic barcode gap discovery for primary species delimitation. [ accessed 2022 Jul 25]. http://bioinfomnhnfr/abi/public/abgd/.
   Google Scholar
• Rambaut A. 2018. FigTree v144. [ accessed 2022 Jul 25]. http://treebioedacuk/software/.
   Google Scholar
• Reynolds CR, Islam SA, Sternberg MJE. 2018. EzMol, a web server wizard for the rapid visualisation and image production of protein and nucleic acid structures. J Mol Biol. 430(15):2244–2248.
   PubMed Web of Science ®Google Scholar
• Schnittler M, Dagamac NH, Leontyev D, Shchepin O, Novozhilov Y, Klahr A. 2020. Quick n’ cheap – a simplified workflow to barcode plasmodial slime molds (Myxomycetes). Karstenia. 58(2):385–392.
   Google Scholar
• Schnittler M, Günther K-F. 1999. Central European vascular plants requiring priority conservation measures - an analysis from national red lists and distribution maps. Biodivers Conserv. 8:891–925.
   Web of Science ®Google Scholar
• Schnittler M, Shchepin ON, Dagamac NHA, Borg Dahl M, Novozhilov YK. 2017. Barcoding myxomycetes with molecular markers, challenges and opportunities. Nova Hedwigia. 104(1–3):323–341.
   Web of Science ®Google Scholar
• Shchepin ON, Novozhilov YK, Woyzichovski J, Bog M, Prikhodko I, Fedorova N, Gmoshinsky V, Borg Dahl M, Dagamac NHA, Yajima Y, et al. 2022. Cryptic speciation as a possible way to enable local adaption: genetic structure of the prostist Physarum albescens (Amoebozoa) revealed by multiple markers and genotyping by sequencing. Mol Ecol. 31(1):372–390.
   PubMed Web of Science ®Google Scholar
• Takano H, Abe T, Sakurai R, Moriyama Y, Miyazawa Y, Nozaki H, Kawano S, Sasaki S, Kuroiwa T. 2001. The complete DNA sequence of the mitochondrial genome of Physarum polycephalum. Mol Genet Genom. 264(5):539–545.
   Web of Science ®Google Scholar
• Technelysium Pty Ltd. 1998. Chromas Technelysium Pty Ltd. [ accessed 2022 Jul 25]. http://technelysiumcomau/wp/chromas/.
   Google Scholar
• Trifinopoulos J, Nguyen L-T, von Haeseler A, Minh BQ. 2016. IQ-TREE, a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 44(W1):W232–W235.
   PubMed Web of Science ®Google Scholar