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

Organisms Diversity & Evolution volume 16, pages 497–524 (2016)Cite this article

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 florida–U. subfloridana, U. fulvoreagens–U. glabrescens, U. barbata–U. chaetophora–U. dasopoga–U. diplotypus, U. barbata–U. intermedia–U. lapponica–U. 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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References

  • Akaike, H. (1974). A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19(6), 716–723.

    Article  Google Scholar 

  • Articus, K. (2004a). Neuropogon and the phylogeny of Usnea s.l. (Parmeliaceae, Lichenized Ascomycetes). Taxon, 53(4), 925–934.

    Article  Google Scholar 

  • Articus, K. (2004b). Phylogenetic studies in Usnea (Parmeliaceae) and allied genera (Vol. 931, Acta Universitatis Upsaliensis. Comprehensive summaries of Uppsala Dissertations from the Faculty of Science and Technology). Uppsala: Acta Universitatis Upsaliensis.

  • Articus, K., Mattsson, J.-E., Tibell, L., Grube, M., & Wedin, M. (2002). Ribosomal DNA and β-tubulin data do not support the separation of the lichens Usnea florida and U. subfloridana as distinct species. Mycological Research, 106(4), 412–418.

    CAS  Article  Google Scholar 

  • Boni, M. F., Posada, D., & Feldman, M. W. (2007). An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics, 176, 1035–1047.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., et al. (2014). BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology, 10(4), e1003537. doi:10.1371/journal.pcbi.1003537.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • Carbone, I., & Kohn, L. M. (1999). A method for designing primer sets for speciation studies in filamentous Ascomycetes. Mycologia, 91(3), 553–556.

    CAS  Article  Google Scholar 

  • Carstens, B. C., & Knowles, L. L. (2007). Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers. Systematic Biology, 56(3), 400–411.

    PubMed  Article  Google Scholar 

  • Carstens, B. C., Pelletier, T. A., Reid, N. M., & Satler, J. D. (2013). How to fail at species delimitation. Molecular Ecology, 22(17), 4369–4383.

    PubMed  Article  Google Scholar 

  • Clerc, P. (1984). Contribution à la revision de la systématique des Usnées (Ascomycotina, Usnea) d'Europe. I. Usnea florida (L.) Wigg. emend. Clerc. Cryptogamie. Bryologie and Lichénologie, 5, 333–360.

    Google Scholar 

  • Clerc, P. (1987). Systematics of the Usnea fragilescens aggregate and its distribution in Scandinavia. Nordic Journal of Botany, 7(4), 479–495.

    Article  Google Scholar 

  • Clerc, P. (1998). Species concepts in the genus Usnea (lichenized Ascomycetes). The Lichenologist, 30(4–5), 321–340.

    Google Scholar 

  • Clerc, P. (2004). Notes on the genus Usnea Adanson. II. Bibliotheca Lichenologica, 88, 79–90.

    Google Scholar 

  • Clerc, P. (2007). Usnea. In T. H. Nash III, C. Gries, & F. Bungartz (Eds.), Lichen flora of the Greater Sonoran Desert Region (Vol. 3) (p. 327). Tempe: Arizona State.

    Google Scholar 

  • Clerc, P. (2011). Usnea. In A. Thell, & R. Moberg (Eds.), Nordic Lichen Flora 4. (pp. 107–127): Museum of Evolution, Uppsala University.

  • R Core Team (2014). R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org

  • Cornejo, C., Chabanenko, S., & Scheidegger, C. (2009). Phylogenetic analysis indicates transitions from vegetative to sexual reproduction in the Lobaria retigera group (Lecanoromycetidae, Ascomycota). The Lichenologist, 41(03), 275–284.

    Article  Google Scholar 

  • Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9(8), 772–772.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Delport, W., Poon, A. F., Frost, S. D., & Pond, S. L. (2010). Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics, 26, 2455–2457.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Drummond, A. J., Ho, S. Y., Phillips, M. J., & Rambaut, A. (2006). Relaxed phylogenetics and dating with confidence. PLoS Biology, 4(5), e88. doi:10.1371/journal.pbio.0040088.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • Drummond, A. J., Suchard, M. A., Xie, D., & Rambaut, A. (2012). Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29(8), 1969–1973.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Edwards, S. V. (2009). Is a new and general theory of molecular systematics emerging? Evolution, 63(1), 1–19.

    CAS  PubMed  Article  Google Scholar 

  • Edwards, D. L., & Knowles, L. L. (2014). Species detection and individual assignment in species delimitation: can integrative data increase efficacy? Proceedings of the Royal Society B, 281(1777), 20132765. doi:10.1098/rspb.2013.2765.

    PubMed  PubMed Central  Article  Google Scholar 

  • Elix, J. A., Corush, J., & Lumbsch, H. T. (2009). Triterpene chemosyndromes and subtle morphological characters characterise lineages in the Physcia aipolia group in Australia (Ascomycota). Systematics and Biodiversity, 7(4), 479–487.

    Article  Google Scholar 

  • Fos, S., & Clerc, P. (2000). The lichen genus Usnea on Quercus suber in Iberian cork-oak forests. The Lichenologist, 32(1), 67–88.

    Article  Google Scholar 

  • Fujita, M. K., Leaché, A. D., Burbrink, F. T., McGuire, J. A., & Moritz, C. (2012). Coalescent-based species delimitation in an integrative taxonomy. Trends in Ecology & Evolution, 27(9), 480–488.

    Article  Google Scholar 

  • Gardes, M., & Bruns, T. D. (1993). ITS primers with enhanced specificity for basidiomycetes – application to the identification of mycorrhizae and rusts. Molecular Ecology, 2(2), 113–118.

    CAS  PubMed  Article  Google Scholar 

  • Giarla, T. C., & Esselstyn, J. A. (2015). The challenges of resolving a rapid, recent radiation: empirical and simulated phylogenomics of Philippine shrews. Systematic Biology. doi:10.1093/sysbio/syv029.

    PubMed  Google Scholar 

  • Gibbs, M. J., Armstrong, J. S., & Gibbs, A. J. (2000). Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics, 16, 573–582.

    CAS  PubMed  Article  Google Scholar 

  • Givnish, T. J. (2015). Adaptive radiation versus ‘radiation’ and ‘explosive diversification’: why conceptual distinctions are fundamental to understanding evolution. New Phytologist, 207(2), 297–303.

    PubMed  Article  Google Scholar 

  • Glass, N. L., & Donaldson, G. C. (1995). Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous Ascomycetes. Applied and Environmental Microbiology, 61(4), 1323–1330.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Halonen, P. (2000). Usnea pacificana, sp. nov. and U. wasmuthii (Lichenized Ascomycetes) in Pacific North America. The Bryologist, 103(1), 38–43.

    Article  Google Scholar 

  • Halonen, P., Clerc, P., Goward, T., Brodo, I. M., & Wulff, K. (1998). Synopsis of the genus Usnea (lichenized Ascomycetes) in British Columbia, Canada. Bryologist, 101, 36–60.

    Article  Google Scholar 

  • Halonen, P., Myllys, L., Ahti, T., & Petrova, O. V. (1999). The lichen genus Usnea in East Fennoscandia. III. The shrubby species. Annales Botanici Fennici, 36, 235–256.

    Google Scholar 

  • Heled, J., & Drummond, A. J. (2010). Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution, 27(3), 570–580.

    CAS  PubMed  Article  Google Scholar 

  • Huelsenbeck, J. P., & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17(8), 754–755.

    CAS  PubMed  Article  Google Scholar 

  • Jones, G. R. (2015). STACEY: species delimitation and phylogeny estimation under the multispecies coalescent. doi:10.1101/010199. Preprint in biorxiv.org.

    Google Scholar 

  • Jones, G., Zeynep, A., & Oxelman, B. (2014). DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Bioinformatics, 31, 991–998.

    PubMed  Article  CAS  Google Scholar 

  • Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772–780.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Katoh, K., & Toh, H. (2008). Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics, 9(4), 286–298.

    CAS  PubMed  Article  Google Scholar 

  • Kelly, L. J., Hollingsworth, P. M., Coppins, B. J., Ellis, C. J., Harrold, P., Tosh, J., et al. (2011). DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context. New Phytologist, 191(1), 288–300.

    PubMed  Article  Google Scholar 

  • Kimura, M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111–120.

    CAS  PubMed  Article  Google Scholar 

  • Knowles, L. L., & Kubatko, L. S. (2010). Estimating species trees: practical and theoretical aspects. Hoboken: Wiley-Blackwell.

    Google Scholar 

  • Kosakovsky Pond, S. L., Posada, D., Gravenor, M. B., Woelk, C. H., & Frost, S. D. W. (2006). GARD: a genetic algorithm for recombination detection. Bioinformatics, 22(24), 3096–3098.

    PubMed  Article  CAS  Google Scholar 

  • Kraichak, E., Divakar, P. K., Crespo, A., Leavitt, S. D., Nelsen, M. P., Lücking, R., et al. (2015a). A tale of two hyper-diversities: diversification dynamics of the two largest families of lichenized fungi. Scientific Reports, 5, 10028. doi:10.1038/srep10028.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Kraichak, E., Lücking, R., Aptroot, A., Beck, A., Dornes, P., John, V., et al. (2015b). Hidden diversity in the morphologically variable script lichen (Graphis scripta) complex (Ascomycota, Ostropales, Graphidaceae). Organisms Diversity & Evolution, 15(3), 447–458.

    Article  Google Scholar 

  • Leaché, A. D. (2009). Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus). Systematic Biology, 58(6), 547–559.

    PubMed  Article  Google Scholar 

  • Leavitt, S. D., Fankhauser, J. D., Leavitt, D. H., Porter, L. D., Johnson, L. A., & St. Clair, L. L. (2011a). Complex patterns of speciation in cosmopolitan "rock posy" lichens – discovering and delimiting cryptic fungal species in the lichen-forming Rhizoplaca melanophthalma species-complex (Lecanoraceae, Ascomycota). Molecular Phylogenetics and Evolution, 59(3), 587–602.

    PubMed  Article  Google Scholar 

  • Leavitt, S. D., Johnson, L., & St. Clair, L. L. (2011b). Species delimitation and evolution in morphologically and chemically diverse communities of the lichen-forming genus Xanthoparmelia (Parmeliaceae, Ascomycota) in western North America. American Journal of Botany, 98(2), 175–188.

    PubMed  Article  Google Scholar 

  • Linda in Arcadia. (2013). Usnea dasopoga, a name to be reinstated for U. filipendula, and its orthography. Taxon, 62(3), 604–605.

    Article  Google Scholar 

  • Lindblom, L., & Ekman, S. (2006). Genetic variation and population differentiation in the lichen-forming ascomycete Xanthoria parietina on the island Storfosna, central Norway. Molecular Ecology, 15(6), 1545–1559.

    CAS  PubMed  Article  Google Scholar 

  • Liu, Y. L., Whelen, S., & Hall, B. D. (1999). Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Molecular Biology and Evolution, 16, 1799–1808.

    CAS  PubMed  Article  Google Scholar 

  • Lumbsch, H. T., & Wirtz, N. (2011). Phylogenetic relationships of the neuropogonoid core group in the genus Usnea (Ascomycota: Parmeliaceae). The Lichenologist, 43(6), 553–559.

    Article  Google Scholar 

  • Lumbsch, H. T., Ahti, T., Altermann, S., Amo De Paz, G., Aptroot, A., Arup, U., et al. (2011). One hundred new species of lichenized fungi: a signature of undiscovered global diversity. Phytotaxa, 18, 1–127.

    Article  Google Scholar 

  • Madden, T. (2002). The BLAST sequence analysis tool. In J. McEntyre & J. Ostell (Eds.), The NCBI handbook. Bethesda: National Center for Biotechnology Information.

    Google Scholar 

  • Maddison, W. P. (1997). Gene trees in species trees. Systematic Biology, 46(3), 523–536.

    Article  Google Scholar 

  • Maddison, W. P., & Maddison, D. R. (2011). Mesquite: a modular system for evolutionary analysis. Version 2.75. http://mesquiteproject.org.

    Google Scholar 

  • Martin, D., & Rybicki, E. (2000). RDP: detection of recombination amongst aligned sequences. Bioinformatics, 16, 562–563.

    CAS  PubMed  Article  Google Scholar 

  • Martin, D. P., Posada, D., Crandall, K. A., & Williamson, C. (2005). A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Research and Human Retroviruses, 21, 98–102.

    CAS  PubMed  Article  Google Scholar 

  • Martin, D. P., Lemey, P., Lott, M., Moulton, V., Posada, D., & Lefeuvre, P. (2010). RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics, 26(19), 2462–2463.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Mason-Gamer, R. J., & Kellogg, E. A. (1996). Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Systematic Biology, 45(4), 524–545.

    Article  Google Scholar 

  • Matheny, P. B., Liu, Y. J., Ammirati, J. F., & Hall, B. D. (2002). Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales). American Journal of Botany, 89(4), 688–698.

    CAS  PubMed  Article  Google Scholar 

  • Maynard Smith, J. (1992). Analyzing the mosaic structure of genes. Journal of Molecular Evolution, 34, 126–129.

    Google Scholar 

  • McCune, B. (2005). Usnea in Pacific Northwest. http://people.oregonstate.edu/~mccuneb/Usnea.PDF Accessed 25 Feb 2015.

  • McEvoy, M., Nybakken, L., Solhaug, K. A., & Gauslaa, Y. (2006). UV triggers the synthesis of the widely distributed secondary lichen compound usnic acid. Mycological Progress, 5(4), 221–229.

    Article  Google Scholar 

  • Molina, M. C., Del-Prado, R., Divakar, P. K., Sánchez-Mata, D., & Crespo, A. (2011). Another example of cryptic diversity in lichen-forming fungi: the new species Parmelia mayi (Ascomycota: Parmeliaceae). Organisms Diversity & Evolution, 11(5), 331–342.

    Article  Google Scholar 

  • Motyka, J. (1936). Lichenum generis Usnea studium monographicum. Pars systematica (2 vol. in 1 bd.). Lublin: Editio et proprietas auctoris.

  • Ohmura, Y. (2001). Taxonomic study of the genus Usnea (lichenized Ascomycetes) in Japan and Taiwan. Journal of Hattori Botanical Laboratory, 90, 1–96.

    Google Scholar 

  • Ohmura, Y. (2002). Phylogenetic evaluation of infrageneric groups of the genus Usnea based on ITS regions in rDNA. Journal of Hattori Botanical Laboratory, 92, 231–243.

    Google Scholar 

  • Ohmura, Y., & Kanda, H. (2004). Taxonomic status of section Neuropogon in the genus Usnea elucidated by morphological comparisons and ITS rDNA sequences. The Lichenologist, 36(3–4), 217–225.

    Article  Google Scholar 

  • O'Meara, B. C., Ané, C., Sanderson, M. J., & Wainwright, P. C. (2006). Testing for different rates of continuous trait evolution using likelihood. Evolution, 60(5), 922–933.

    PubMed  Article  Google Scholar 

  • Orange, A., James, P. W., & White, F. J. (2001). Microchemical methods for the identification of Lichens. London: British Lichen Society.

    Google Scholar 

  • Padidam, M., Sawyer, S., & Fauquet, C. M. (1999). Possible emergence of new geminiviruses by frequent recombination. Virology, 265, 218–225.

    CAS  PubMed  Article  Google Scholar 

  • Poelt, J. (1970). Das Konzept der Artenpaare bei den Flechten. Vorträge aus dem Gesamtgebiet der Botanik, Neue Folge, 4, 187–198.

    Google Scholar 

  • Pons, J., Barraclough, T. G., Gomez-Zurita, J., Cardoso, A., Duran, D. P., Hazell, S., et al. (2006). Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology, 55(4), 595–609.

    PubMed  Article  Google Scholar 

  • Posada, D., & Crandall, K. A. (2001). Evaluation of methods for detecting recombination from DNA sequences: computer simulations. PNAS, 98, 13757–13762.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Rambaut, A. (2009). FigTree. Version 1.3.1. http://tree.bio.ed.ac.uk/software/figtree. Edinburgh: Institute of Evolutionary Biology, University of Edinburgh.

  • Rambaut, A., & Drummond, A. (2007). Tracer. Version 1.4. http://beast.bio.ed.ac.uk.

    Google Scholar 

  • Rambaut, A., & Drummond, A. (2012a). LogCombiner Version 1.7.2. http://beast.bio.ed.ac.uk.

    Google Scholar 

  • Rambaut, A., & Drummond, A. (2012b). TreeAnnotator Version 1.7.2. http://beast.bio.ed.ac.uk.

    Google Scholar 

  • Randlane, T., Tõrra, T., Saag, A., & Saag, L. (2009). Key to European Usnea species. The Diversity of Lichenology: Jubilee Volume, 100(100), 419–462.

    Google Scholar 

  • Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., et al. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61(3), 539–542.

    PubMed  PubMed Central  Article  Google Scholar 

  • Saag, L., Tõrra, T., Saag, A., Del-Prado, R., & Randlane, T. (2011). Phylogenetic relations of European shrubby taxa of the genus Usnea. The Lichenologist, 43(05), 427–444.

    Article  Google Scholar 

  • Saag, L., Mark, K., Saag, A., & Randlane, T. (2014). Species delimitation in the lichenized fungal genus Vulpicida (Parmeliaceae, Ascomycota) using gene concatenation and coalescent-based species tree approaches. American Journal of Botany, 101(12), 2169–2182.

    PubMed  Article  Google Scholar 

  • Sanderson, M. J., & Donoghue, M. J. (1996). Reconstructing shifts in diversification rates on phylogenetic trees. Trends in Ecology & Evolution, 11(1), 15–20.

    CAS  Article  Google Scholar 

  • Scherrer, S., Zippler, U., & Honegger, R. (2005). Characterisation of the mating-type locus in the genus Xanthoria (lichen-forming ascomycetes, Lecanoromycetes). Fungal Genetics and Biology, 42(12), 976–988.

    CAS  PubMed  Article  Google Scholar 

  • Schmitt, I., & Lumbsch, H. T. (2004). Molecular phylogeny of the Pertusariaceae supports secondary chemistry as an important systematic character set in lichen-forming ascomycetes. Molecular Phylogenetics and Evolution, 33(1), 43–55.

    CAS  PubMed  Article  Google Scholar 

  • Schmitt, I., Crespo, A., Divakar, P. K., Fankhauser, J. D., Herman-Sackett, E., Kalb, K., et al. (2009). New primers for promising single-copy genes in fungal phylogenetics and systematics. Persoonia, 23, 35–40.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Seymour, F. A., Crittenden, P. D., Wirtz, N., Øvstedal, D. O., Dyer, P. S., & Lumbsch, H. T. (2007). Phylogenetic and morphological analysis of Antarctic lichen-forming Usnea species in the group Neuropogon. Antarctic Science, 19(1), 71–82.

    Article  Google Scholar 

  • Singh, G., Dal Grande, F., Divakar, P. K., Otte, J., Leavitt, S. D., Szczepanska, K., et al. (2015). Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota). PLoS One, 10(5), e0124625. doi:10.1371/journal.pone.0124625.

    PubMed  PubMed Central  Article  CAS  Google Scholar 

  • Sistrom, M., Donnellan, S. C., & Hutchinson, M. N. (2013). Delimiting species in recent radiations with low levels of morphological divergence: a case study in Australian Gehyra geckos. Molecular Phylogenetics and Evolution, 68(1), 135–143.

    PubMed  Article  Google Scholar 

  • Spinks, P. Q., Thomson, R. C., Pauly, G. B., Newman, C. E., Mount, G., & Shaffer, H. B. (2013). Misleading phylogenetic inferences based on single-exemplar sampling in the turtle genus Pseudemys. Molecular Phylogenetics and Evolution, 68, 269–281.

    PubMed  Article  Google Scholar 

  • Spitzer, M., Wildenhain, J., Rappsilber, J., & Tyers, M. (2014). BoxPlotR: a web tool for generation of box plots. Nature Methods, 11(2), 121–122.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Spribille, T., Klug, B., & Mayrhofer, H. (2011). A phylogenetic analysis of the boreal lichen Mycoblastus sanguinarius (Mycoblastaceae, lichenized Ascomycota) reveals cryptic clades correlated with fatty acid profiles. Molecular Phylogenetics and Evolution, 59(3), 603–614.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22(21), 2688–2690.

    CAS  PubMed  Article  Google Scholar 

  • Stamatakis, A., Hoover, P., & Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML Web servers. Systematic Biology, 57(5), 758–771.

    PubMed  Article  Google Scholar 

  • Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731–2739.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Tehler, A., & Irestedt, M. (2007). Parallel evolution of lichen growth forms in the family Roccellaceae (Arthoniales, Ascomycota). Cladistics, 23(5), 432–454.

    Article  Google Scholar 

  • Thell, A., Crespo, A., Divakar, P. K., Kärnefelt, I., Leavitt, S. D., Lumbsch, H. T., et al. (2012). A review of lichen family Parmeliaceae – history, phylogeny and current taxonomy. Nordic Journal of Botany, 30, 641–664.

    Article  Google Scholar 

  • Tõrra, T., & Randlane, T. (2007). The lichen genus Usnea (lichenized Ascomycetes, Parmeliaceae) in Estonia with a key to the species in the Baltic countries. The Lichenologist, 39, 415–438.

    Article  Google Scholar 

  • Trest, M. T., Will-Wolf, S., Keuler, R., Shay, N., Hill, K., Studer, A., et al. (2015). Potential impacts of UV exposure on lichen communities: a pilot study of Nothofagus dombeyi trunks in southernmost Chile. Ecosystem Health and Sustainability, 1(4), art14. doi:10.1890/EHS15-0008R1.1.

    Article  Google Scholar 

  • Truong, C., Divakar, P. K., Yahr, R., Crespo, A., & Clerc, P. (2013). Testing the use of ITS rDNA and protein-coding genes in the generic and species delimitation of the lichen genus Usnea (Parmeliaceae, Ascomycota). Molecular Phylogenetics and Evolution, 68(2), 357–372.

    CAS  PubMed  Article  Google Scholar 

  • Velmala, S., Myllys, L., Halonen, P., Goward, T., & Ahti, T. (2009). Molecular data show that Bryoria fremontii and B. tortuosa (Parmeliaceae) are conspecific. The Lichenologist, 41(03), 231–242.

    Article  Google Scholar 

  • Velmala, S., Myllys, L., Goward, T., Holien, H., & Halonen, P. (2014). Taxonomy of Bryoria section Implexae (Parmeliaceae, Lecanoromycetes) in North America and Europe, based on chemical, morphological and molecular data. Annales Botanici Fennici, 51, 345–371.

    Article  Google Scholar 

  • Wagner, C. E., Keller, I., Wittwer, S., Selz, O. M., Mwaiko, S., Greuter, L., et al. (2013). Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Molecular Ecology, 22(3), 787–798.

    CAS  PubMed  Article  Google Scholar 

  • Wedin, M., Westberg, M., Crewe, A. T., Tehler, A., & Purvis, O. W. (2009). Species delimitation and evolution of metal bioaccumulation in the lichenized Acarospora smaragdula (Ascomycota, Fungi) complex. Cladistics, 25(2), 161–172.

    Article  Google Scholar 

  • Weiller, G. F. (1998). Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Molecular Biology and Evolution, 15, 326–335.

    CAS  PubMed  Article  Google Scholar 

  • White, T. J., Bruns, T., Lee, S., & Taylor, J. W. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, & T. J. White (Eds.), PCR protocols: a guide to methods and applications (pp. 315–322). New York: Academic Press.

    Google Scholar 

  • Wiens, J. J. (1998). Combining data sets with different phylogenetic histories. Systematic Biology, 47(4), 568–581.

    CAS  PubMed  Article  Google Scholar 

  • Willis, S. C., Farias, I. P., & Ortí, G. (2013). Multi-locus species tree for the Amazonian peacock basses (Cichlidae: Cichla): emergent phylogenetic signal despite limited nuclear variation. Molecular Phylogenetics and Evolution, 69(3), 479–490.

    PubMed  Article  Google Scholar 

  • Wirtz, N., Printzen, C., Sancho, L. G., & Lumbsch, H. T. (2006). The phylogeny and classification of Neuropogon and Usnea (Parmeliaceae, Ascomycota) revisited. Taxon, 55(2), 367–376.

    Article  Google Scholar 

  • Wirtz, N., Printzen, C., & Lumbsch, H. T. (2008). The delimitation of Antarctic and bipolar species of neuropogonoid Usnea (Ascomycota, Lecanorales): a cohesion approach of species recognition for the Usnea perpusilla complex. Mycological Research, 112, 472–484.

    CAS  PubMed  Article  Google Scholar 

  • Wirtz, N., Printzen, C., & Lumbsch, H. T. (2012). Using haplotype networks, estimation of gene flow and phenotypic characters to understand species delimitation in fungi of a predominantly Antarctic Usnea group (Ascomycota, Parmeliaceae). Organisms Diversity & Evolution, 12(1), 17–37.

    Article  Google Scholar 

  • Yang, Z., & Rannala, B. (2010). Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences, 107(20), 9264–9269.

    CAS  Article  Google Scholar 

  • Yang, Z., & Rannala, B. (2014). Unguided species delimitation using DNA sequence data from multiple loci. Molecular Biology and Evolution, 31(12), 3125–3135.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

  • Zhang, J., Kapli, P., Pavlidis, P., & Stamatakis, A. (2013). A general species delimitation method with applications to phylogenetic placements. Bioinformatics, 29(22), 2869–2876.

    CAS  PubMed  PubMed Central  Article  Google Scholar 

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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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Authors and Affiliations

  1. Institute of Botany and Ecology, University of Tartu, Tartu, Estonia

    Kristiina Mark, Andres Saag & Tiina Randlane

  2. Department of Evolutionary Biology, Estonian Biocentre, Tartu, Estonia

    Lauri Saag

  3. Science and Education, The Field Museum, Chicago, IL, USA

    Steven D. Leavitt & H. Thorsten Lumbsch

  4. Estonia Department of Botany, University of Wisconsin-Madison, Madison, WI, USA

    Susan Will-Wolf

  5. Department of Geological Sciences, Stanford University, Stanford, CA, USA

    Matthew P. Nelsen

  6. Estonian Marine Institute, University of Tartu, Tallinn, Estonia

    Tiiu Tõrra

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  1. Kristiina Mark
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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