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DNA-based identification of lichen-forming fungi: can publicly available sequence databases aid in lichen diversity inventories of Mount Cameroon (West Africa)?

Published online by Cambridge University Press:  08 October 2012

Elizabeth Ayuk OROCK ,
Steven D. LEAVITT ,
Beatrice Ambo FONGE ,
Larry L. ST. CLAIR  and
H. Thorsten LUMBSCH
Elizabeth Ayuk OROCK
Affiliation:
Department of Botany and Plant Physiology, University of Buea, Cameroon, P. O. Box 63, Buea, Cameroon
Steven D. LEAVITT*
Affiliation:
Department of Botany, Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, Illinois 60605-2496, USA. Email: [email protected]
Beatrice Ambo FONGE
Affiliation:
Department of Botany and Plant Physiology, University of Buea, Cameroon, P. O. Box 63, Buea, Cameroon
Larry L. ST. CLAIR
Affiliation:
M. L. Bean Life Science Museum and Department of Biology, Brigham Young University, Provo, Utah 84602, USA
H. Thorsten LUMBSCH
Affiliation:
Department of Botany, Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, Illinois 60605-2496, USA. Email: [email protected]
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Abstract

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Type
Short Communications
Information
The Lichenologist , Volume 44 , Issue 6 , November 2012 , pp. 833 - 839
Copyright
Copyright © British Lichen Society 2012

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References

Arnold, A. E., Miąowska, J., Higgins, K. L., Sarvate, S. D., Gugger, P., Way, A., Hofstetter, V., Kauff, F. & Lutzoni, F. (2009) A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification? Systematic Biology 58: 283–297.Google Scholar
Bates, S. T., Berg-Lyons, D., Lauber, C. L., Walters, W. A., Knight, R. & Fierer, N. (2012) A preliminary survey of lichen associated eukaryotes using pyrosequencing. Lichenologist 44: 137–146.Google Scholar
Begerow, D., Nilsson, H., Unterseher, M. & Maier, W. (2010) Current state and perspectives of fungal DNA barcoding and rapid identification. Applications in Microbiology and Biotechnology 97: 99–108.CrossRefGoogle Scholar
Bjerke, J. W. (2011) Winter climate change: ice encapsulation at mild subfreezing temperatures kills freeze-tolerant lichens. Environmental and Experimental Botany 72: 404–408.CrossRefGoogle Scholar
Blaxter, M., Mann, J., Chapman, T., Thomas, F., Whitton, C., Floyd, R. & Abebe, E. (2005) Defining operational taxonomic units using DNA barcode data. Philosophical Transactions of the Royal Society B, Biological Sciences 360: 1935–1943.Google Scholar
Bokhorst, S. F., Bjerke, J. W., Tømmervik, H., Callaghan, T. V. & Phoenix, G. K. (2009) Winter warming events damage sub-Arctic vegetation: consistent evidence from an experimental manipulation and a natural event. Journal of Ecology 97: 1408–1415.Google Scholar
Bridge, P. D., Roberts, P. J., Spooner, B. M. & Panchal, G. (2003) On the unreliability of published DNA sequences. New Phytologist 160: 43–48.CrossRefGoogle ScholarPubMed
Bridge, P. D., Spooner, B. M. & Roberts, P. J. (2004) Reliability and use of published sequence data. New Phytologist 161: 15–17.CrossRefGoogle Scholar
Coppins, B. J. (2002) Checklist of Lichens of Great Britain and Ireland. London: British Lichen Society.Google Scholar
Crespo, A. & Lumbsch, H. T. (2010) Cryptic species in lichen-forming fungi. IMA Fungus 1: 167–170.Google Scholar
Crespo, A. & Pérez-Ortega, S. (2009). Cryptic species and species pairs in lichens: a discussion on the relationship between molecular phylogenies and morphological characters Anales del Jardin Botanico de Madrid 66(S1): 71–81.CrossRefGoogle Scholar
Crespo, A., Kauff, F., Divakar, P. K., del Prado, R., Perez-Ortega, S., Amo de Paz, G., Ferencova, Z., Blanco, O., Roca-Valiente, B., Núñez-Zapata, J., et al. (2010) Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence. Taxon 59: 1735–1753.Google Scholar
Del-Prado, R., Cubas, P., Lumbsch, H. T., Divakar, P. K., Blanco, O., Amo de Paz, G., Molina, M. C. & Crespo, A. (2010) Genetic distances within and among species in monophyletic lineages of Parmeliaceae (Ascomycota) as a tool for taxon delimitation. Molecular Phylogenetics and Evolution 56: 125–133.CrossRefGoogle ScholarPubMed
Divakar, P., Figueras, G., Hladun, N. & Crespo, A. (2010) Morphological versus phylogenetic species: an example from Melanelixia glabra (Parmeliaceae, Ascomycota). Fungal Diversity 42: 47–55.CrossRefGoogle Scholar
Feuerer, T. (2011) Checklists of lichens and lichenicolous fungi. Version 1 March 2008. http://www.checklists.deGoogle Scholar
Gueidan, C., Savić, S., Thüs, H., Roux, C., Keller, C., Tibell, L., Prieto, M., Heiðmarsson, S., Breuss, O., Orange, A. et al. (2009) Generic classification of the Verrucariaceae (Ascomycota) based on molecular and morphological evidence: recent progress and remaining challenges. Taxon 58: 184–208.Google Scholar
Harris, D. J. (2003) Can you bank on GenBank? Trends in Ecology & Evolution 18: 317–319.CrossRefGoogle Scholar
Heller, N. E. & Zavaleta, E. S. (2009) Biodiversity management in the face of climate change: a review of 22 years of recommendations. Biological Conservation 142: 14–32.Google Scholar
Jones, M., Ghoorah, A. & Blaxter, M. (2011) JMOTU and Taxonerator: turning DNA Barcode sequences into annotated operational taxonomic units. PLoS ONE 6: e19259.Google Scholar
Kelly, L. J., Hollingsworth, P. M., Coppins, B. J., Ellis, C. J., Harrold, P., Tosh, J. & Yahr, R. (2011) DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context. New Phytologist 191: 288–300.Google Scholar
Kroken, S. & Taylor, J. W. (2001) A gene genealogical approach to recognize phylogenetic species boundaries in the lichenized fungus Letharia. Mycologia 93: 38–53.Google Scholar
Larena, I., Salazar, O., González, V., Julián, M. C. & Rubio, V. (1999) Design of a primer for ribosomal DNA internal transcribed spacer with enhanced specificity for ascomycetes. Journal of Biotechnology 75: 187–194.Google Scholar
Leavitt, S. D. & St. Clair, L. L. (2011) Estimating Xanthoparmelia (Parmeliaceae) population density and community composition in subalpine communities in southern Utah, U.S.A. using two distance methods. Bryologist 114: 625–636.CrossRefGoogle Scholar
Leavitt, S. D., Fankhauser, J. D., Leavitt, D. H., Porter, L. D., Johnson, L. A. & St. Clair, L. L. (2011 a) 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: 587–602.CrossRefGoogle ScholarPubMed
Leavitt, S. D., Johnson, L. A. & St. Clair, L. L. (2011 b) 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: 1–14.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: 1545–1559.Google Scholar
Lumbsch, H. T. (2002) How objective are genera in Euascomycetes? Perspectives in Plant Ecology, Evolution and Systematics 5: 91–101.Google Scholar
Lumbsch, H. T. & Leavitt, S. D. (2011) Goodbye morphology? A paradigm shift in the delimitation of species in lichenized fungi. Fungal Diversity 50: 59–72.Google Scholar
Lumbsch, H. T., Ahti, T., Altermann, S., Amo de Paz, G., Aptroot, A., Arup, U., Barcenas Peña, A., Bawingan, P. A., Benatti, M. N., Betancourt, L. et al. (2011) One hundred new species of lichenized fungi: a signature of undiscovered global diversity. Phytotaxa 18: 1–127.Google Scholar
Miądlikowska, J., Kauff, F., Hofstetter, V., Fraker, E., Grube, M., Hafellner, J., Reeb, V., Hodkinson, B. P., Kukwa, M., Lücking, R. et al. (2006) New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia 98: 1088–1103.Google Scholar
Nayanakantha, N. M. C. & Gajameragedara, S. (2003) A survey of lichens in the Kandy Municipal Region. Ceylon Journal of Science (Biological Sciences) 31: 35–41.Google Scholar
Ndenecho, E. N. (2009) Herbalism and resources for the development of ethnopharmacology in Mount Cameroon region. African Journal of Pharmacy and Pharmacology 3: 078–086.Google Scholar
Nilsson, R. H., Ryberg, M., Kristiansson, E., Abarenkov, K., Larsson, K. H. & Koljalg, U. (2006) Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS ONE 1: e59.Google Scholar
Puillandre, N., Lambert, A., Brouillet, S. & Achaz, G. (2011) ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology 21: 1864–1877.Google Scholar
Rambault, A. (1996) Se-Al v2.0a11: Sequence Alignment Editor. Available from: http://evolve.zoo.ox.ac.uk/.Google Scholar
Ratnasingham, S. & Hebert, P. D. N. (2007) BOLD: The Barcode of Life Data System (http://www.barcodinglife.org). Molecular Ecology Notes 7: 355–364.Google Scholar
Schoch, C. L., Seifert, K. A., Huhndorf, S., Robert, V., Spouge, V. L., Levesque, C. A., Chen, W. & Fungal Barcoding Consortium (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proceedings of the National Academy of Sciences 109: 6241–6246.Google Scholar
Seifert, K. A. (2009) Progress towards DNA barcoding of fungi. Molecular Ecology Resources 9: 83–89.Google Scholar
Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Edgar, R., Federhen, S., et al. (2006) Database resources of the national center for biotechnology information. Nucleic Acids Research, 34: D173–D180.Google Scholar
White, T. J., Bruns, T. D., 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, M. A., Gelfand, D. H., Sninsky, J. J. & White, T. J., eds): 315–322. New York: Academic Press.Google Scholar