Biodiversity Literature Repository

Submit to community
Liberated Data
Published February 12, 2016 | Version v1
Journal article Restricted

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

Authors/Creators

Description

Mark, Kristiina, Saag, Lauri, Leavitt, Steven D., Will-Wolf, Susan, Nelsen, Matthew P., Tõrra, Tiiu, Saag, Andres, Randlane, Tiina, Lumbsch, H. Thorsten (2016): Evaluation of traditionally circumscribed species in the lichen-forming genus Usnea, section Usnea (Parmeliaceae, Ascomycota) using a six-locus dataset. Organisms Diversity & Evolution (New York, N.Y.) 16 (3): 497-524, DOI: 10.1007/s13127-016-0273-7, URL: http://dx.doi.org/10.1007/s13127-016-0273-7

Files

Restricted

The record is publicly accessible, but files are restricted. <a href="https://zenodo.org/account/settings/login?next=https://zenodo.org/records/13173532">Log in</a> to check if you have access.

Linked records

Additional details

Identifiers

LSID
urn:lsid:plazi.org:pub:7B32EC444E0DF06EFFC3FFEAFFA2CF08

Cites
Publication: 10.1371/journal.pcbi.1003537 (DOI)
Publication: 10.1371/journal.pbio.0040088 (DOI)
Publication: 10.1098/rspb.2013.2765 (DOI)
Publication: 10.1093/sysbio/syv029 (DOI)
Publication: 10.1101/010199 (DOI)
Publication: 10.1038/srep10028 (DOI)
Publication: 10.1371/journal (DOI)
Has part
Figure: 10.5281/zenodo.13173534 (DOI)
Figure: 10.5281/zenodo.13173536 (DOI)
Figure: 10.5281/zenodo.13173538 (DOI)
Figure: 10.5281/zenodo.13173540 (DOI)

References

  • Akaike, H. (1974). A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19(6), 716-723.
  • Articus, K. (2004a). Neuropogon and the phylogeny of Usnea s.l. (Parmeliaceae, Lichenized Ascomycetes). Taxon, 53(4), 925-934.
  • 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.
  • Boni, M. F., Posada, D., & Feldman, M. W. (2007). An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics, 176, 1035-1047.
  • Bouckaert, R., Heled, J., Kuhnert, 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.
  • Carbone, I., & Kohn, L. M. (1999). A method for designing primer sets for speciation studies in filamentous Ascomycetes. Mycologia, 91(3), 553-556.
  • 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.
  • 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.
  • Clerc, P. (1984). Contribution a la revision de la systematique des Usnees (Ascomycotina, Usnea) d'Europe. I. Usnea florida (L.) Wigg. emend. Clerc. Cryptogamie. Bryologie and Lichenologie, 5, 333- 360.
  • Clerc, P. (1987). Systematics of the Usnea fragilescens aggregate and its distribution in Scandinavia. Nordic Journal of Botany, 7(4), 479- 495.
  • Clerc, P. (1998). Species concepts in the genus Usnea (lichenized Ascomycetes). The Lichenologist, 30(4-5), 321-340.
  • Clerc, P. (2004). Notes on the genus Usnea Adanson. II. Bibliotheca Lichenologica, 88, 79-90.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Edwards, S. V. (2009). Is a new and general theory of molecular systematics emerging? Evolution, 63(1), 1-19.
  • 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.
  • 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.
  • Fos, S., & Clerc, P. (2000). The lichen genus Usnea on Quercus suber in Iberian cork-oak forests. The Lichenologist, 32(1), 67-88.
  • Fujita, M. K., Leache, 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Halonen, P. (2000). Usnea pacificana, sp. nov. and U. wasmuthii (Lichenized Ascomycetes) in Pacific North America. The Bryologist, 103(1), 38-43.
  • 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.
  • 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.
  • Heled, J., & Drummond, A. J. (2010). Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution, 27(3), 570- 580.
  • Huelsenbeck, J. P., & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17(8), 754-755.
  • Jones, G. R. (2015). STACEY: species delimitation and phylogeny estimation under the multispecies coalescent. doi:10.1101/010199. Preprint in biorxiv.org.
  • Jones, G., Zeynep, A., & Oxelman, B. (2014). DISSECT: an assignmentfree Bayesian discovery method for species delimitation under the multispecies coalescent. Bioinformatics, 31, 991-998.
  • 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.
  • Katoh, K., & Toh, H. (2008). Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics, 9(4), 286-298.
  • 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.
  • 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.
  • Knowles, L. L., & Kubatko, L. S. (2010). Estimating species trees: practical and theoretical aspects. Hoboken: Wiley-Blackwell.
  • 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.
  • Kraichak, E., Divakar, P. K., Crespo, A., Leavitt, S. D., Nelsen, M. P., Lucking, 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.
  • Kraichak, E., Lucking, 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.
  • Leache, A. D. (2009). Species tree discordance traces to phylogeographic clade boundaries in North American fence lizards (Sceloporus). Systematic Biology, 58(6), 547-559.
  • 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.
  • 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.
  • Linda in Arcadia. (2013). Usnea dasopoga, a name to be reinstated for U. filipendula, and its orthography. Taxon, 62(3), 604-605.
  • 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.
  • 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.
  • 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.
  • 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.
  • Madden, T.(2002).The BLAST sequence analysis tool. In J. McEntyre & J. Ostell (Eds.), The NCBI handbook. Bethesda: National Center for Biotechnology Information.
  • Maddison, W. P. (1997). Gene trees in species trees. Systematic Biology, 46(3), 523-536.
  • Maddison, W. P., & Maddison, D. R. (2011). Mesquite: a modular system for evolutionary analysis. Version 2.75. http://mesquiteproject.org.
  • Martin, D., & Rybicki, E. (2000). RDP: detection of recombination amongst aligned sequences. Bioinformatics, 16, 562-563.
  • 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.
  • 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.
  • 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.
  • 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.
  • Maynard Smith, J. (1992). Analyzing the mosaic structure of genes. Journal of Molecular Evolution, 34, 126-129.
  • 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.
  • Molina, M. C., Del-Prado, R., Divakar, P. K., Sanchez-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.
  • 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.
  • 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.
  • 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.
  • O'Meara, B. C., Ane, C., Sanderson, M. J., & Wainwright, P. C. (2006). Testing for different rates of continuous trait evolution using likelihood. Evolution, 60(5), 922-933.
  • Orange, A., James, P. W., & White, F. J. (2001). Microchemical methods for the identification of Lichens. London: British Lichen Society.
  • Padidam, M., Sawyer, S., & Fauquet, C. M. (1999). Possible emergence of new geminiviruses by frequent recombination. Virology, 265, 218-225.
  • Poelt, J. (1970). Das Konzept der Artenpaare bei den Flechten. Vortrage aus dem Gesamtgebiet der Botanik, Neue Folge, 4, 187-198.
  • 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.
  • Posada, D., & Crandall, K. A. (2001). Evaluation of methods for detecting recombination from DNA sequences: computer simulations. PNAS, 98, 13757-13762.
  • 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.
  • Rambaut, A., & Drummond, A. (2012a). LogCombiner Version 1.7.2. http://beast.bio.ed.ac.uk.
  • Rambaut, A., & Drummond, A. (2012b). TreeAnnotator Version 1.7.2. http://beast.bio.ed.ac.uk.
  • Randlane, T., Torra, T., Saag, A., & Saag, L. (2009). Key to European Usnea species. The Diversity of Lichenology: Jubilee Volume, 100(100), 419-462.
  • Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Hohna, 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.
  • Saag, L., Torra, 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.
  • 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.
  • Sanderson, M. J., & Donoghue, M. J. (1996). Reconstructing shifts in diversification rates on phylogenetic trees. Trends in Ecology & Evolution, 11(1), 15-20.
  • 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.
  • 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.
  • 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.
  • Seymour, F. A., Crittenden, P. D., Wirtz, N., Ovstedal, 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.
  • 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.
  • 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.
  • 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.
  • Spitzer, M., Wildenhain, J., Rappsilber, J., & Tyers, M. (2014). BoxPlotR: a web tool for generation of box plots. Nature Methods, 11(2), 121-122.
  • Spribille, T., Klug, B., & Mayrhofer, H. (2011). A phylogenetic analysis of the boreal lichen Mycoblastus sanguinarius (Mycoblastaceae, lichenized Ascomycota) reveals cryptic clades corre lated with fatt y acid p rofile s. Mo lecul ar Phylogenetics and Evolution, 59(3), 603-614.
  • Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22(21), 2688-2690.
  • Stamatakis, A., Hoover, P., & Rougemont, J. (2008). A rapid bootstrap algorithm for the RAxML Web servers. Systematic Biology, 57(5), 758-771.
  • 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.
  • Tehler, A., & Irestedt, M. (2007). Parallel evolution of lichen growth forms in the family Roccellaceae (Arthoniales, Ascomycota). Cladistics, 23(5), 432-454.
  • Thell, A., Crespo, A., Divakar, P. K., Karnefelt, 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.
  • Torra, 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Weiller, G. F. (1998). Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Molecular Biology and Evolution, 15, 326-335.
  • 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.
  • Wiens, J. J. (1998). Combining data sets with different phylogenetic histories. Systematic Biology, 47(4), 568-581.
  • Willis, S. C., Farias, I. P., & Orti, 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.
  • 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.
  • 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.
  • 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.
  • Yang, Z., & Rannala, B. (2010). Bayesian species delimitation using multilocus sequence data. Proceedings of the National Academy of Sciences, 107(20), 9264-9269.
  • Yang, Z., & Rannala, B. (2014). Unguided species delimitation using DNA sequence data from multiple loci. Molecular Biology and Evolution, 31(12), 3125-3135.
  • Zhang, J., Kapli, P., Pavlidis, P., & Stamatakis, A. (2013). A general species delimitation method with applications to phylogenetic placements. Bioinformatics, 29(22), 2869-2876.