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Evaluation of traditionally circumscribed species in the lichen-forming genus Usnea, section Usnea (Parmeliaceae, Ascomycota) using a six-locus dataset

An Erratum to this article was published on 05 December 2016

Abstract

Recent taxonomic and DNA sequence-based studies in several groups of lichen-forming fungi have revealed incongruence between the morphological and molecule-based circumscriptions of species. While the cosmopolitan genus Usnea is well-known and easily recognized by the yellowish beard-like thallus with central cord, delimitation of many Usnea species is difficult due to the high variation and complexity of diagnostic characters. In this study, we assessed the monophyly of 18 species from section Usnea occurring in North America and Europe, including sorediate and sexually reproducing taxa with both pendent and shrubby thalli. Six nuclear markers (ribosomal internal transcribed spacer (ITS) and intergenic spacer (IGS), and protein-coding beta-tubulin, MCM7, RPB1 and RPB2) were sequenced for 144 samples. All analyzed loci show weak genetic structure and short branch lengths in single-locus topologies, suggesting recent diversification history of the sampled taxa. Concatenated, multi-locus analyses conducted in Bayesian and maximum likelihood frameworks, as well as coalescent-based species delimitation and species tree methods, recover several distinct clades, some represent traditional morphology-based species (Usnea cavernosa, U. praetervisa, U. silesiaca, U. wasmuthii), while others form clusters of two or more species (Usnea floridaU. subfloridana, U. fulvoreagensU. glabrescens, U. barbataU. chaetophoraU. dasopogaU. diplotypus, U. barbataU. intermediaU. lapponicaU. substerilis). We propose synonymization of U. substerilis under U. lapponica. The status of several other species within intermixed clusters requires further evaluation with more extensive sampling and the inclusion of more variable markers before taxonomic consequences can be considered. A new species, Usnea parafloridana is described from Wisconsin, USA.

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Acknowledgments

We thank the collectors who provided the specimens used here and anonymous reviewers for useful comments. The study was financially supported by the Estonian Research Council (grants ETF9109 and PUT1017 to TR) and European Union Social Fund through the ESF Doctoral Studies and Internationalisation Programme Activity 6. The molecular work was performed in the DNA Genotyping and Sequencing Core Facility of the Estonian Biocentre and Institute of Molecular and Cell Biology at the University of Tartu (Tartu, Estonia) and in the Pritzker Laboratory for Molecular Systematics at the Field Museum (Chicago, IL, USA). Computationally demanding analyses were carried out in the High Performance Computing Center at the University of Tartu.

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An erratum to this article is available at http://dx.doi.org/10.1007/s13127-016-0311-5.

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Online Resource 1

Fig. S1–S6 Majority rule consensus trees inferred from ML analysis on ITS (Fig. S1), IGS (Fig. S2), beta-tubulin (Fig. S3), MCM7 (Fig. S4), RPB1 (Fig. S5) and RPB2 (Fig. S6) datasets together with nonparametric bootstrap support (BP) and posterior probability (PP) values from Bayesian inference. Above branch is indicated ML bootstrap probabilities (BP) and below Bayesian posterior probability (PP) scores. Branches marked in bold indicate strong support (BP ≥ 70 and PP ≥ 0.95) for specified clade. Scale bar shows the number of substitutions per site (PDF 339 kb)

Online Resource 2

Fig. S7 Majority rule consensus tree of all available Usnea fulvoreagens, U. glabrescens s.str. and U. pacificana sequences (Table 1) with U. silesiaca as an outgroup, based on six concatenated loci, inferred in RAxML. Clade bootsrap probabilites (BP) are given above branch and strongly supported clades (BP ≥ 70 %) are marked in bold. Scale bar shows the number of substitutions per site. In brackets are given specimen code, country, and secondary chemistry. Secondary metabolites in fulvoreagens-glabrescens clade: bar − barbatic acid; BMY − baeomycesic acid; NSTI − norstictic acid; pro − protocetraric acid; SAL − salazinic acid; SQU − squamatic acid; STI-comp − stictic acid complex with connorstictic cryptostictic acids; unid rfcl x − unidentified substance from reference class x. Capital letters denotes major compounds in chemotype, lower case accessory substances (PDF 136 kb)

Online Resource 3

Fig. S8 Majority rule consensus tree of all studied Usnea parafloridana specimens with some representatives from florida-subfloridana and wasmuthii clades, based on six concatenated loci, inferred in RAxML. Clade bootsrap probabilites (BP) are given above branch and strongly supported clades (BP ≥ 70 %) are marked in bold. Scale bar shows the number of substitutions per site. In brackets are given specimen codes and secondary chemistry. Secondary metabolites in U. parafloridana: NSTI − norstictic acid; SAL − salazinic acid; unid rfcl x − unidentified substance from reference class x. Capital letters denotes major compounds in chemotype, lower case accessory substances (PDF 274 kb)

Online Resource 4

Fig. S9 Examples of lichen substances of some studied Usnea specimens, incl. U. parafloridana sp. nov., identified in thin layer chromatography analyses. Secondary metabolites are visualized in solvent system A, after treatment with sulphuric acid and heating (Orange et al. 2001). Identified secondary metabolites: al – alectorialic acid; bar − barbatic acid; bmy − baeomycesic acid; cnsti – connorstictic acid; csti – cryptostictic acid; nsti – norstictic acid; sal – salazinic acid; squ − squamatic acid; sti – stictic acid; tha – thamnolic acid; usn − usnic acid (PDF 1398 kb)

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Mark, K., Saag, L., Leavitt, S.D. et al. Evaluation of traditionally circumscribed species in the lichen-forming genus Usnea, section Usnea (Parmeliaceae, Ascomycota) using a six-locus dataset. Org Divers Evol 16, 497–524 (2016). https://doi.org/10.1007/s13127-016-0273-7

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Keywords

  • Lichenized fungi
  • Rapid radiation
  • Species delimitation
  • Species trees
  • Taxonomy
  • Usnea