Usnea nipparensis and U. sinensis form a ‘species pair ’ presuming morphological, chemical and molecular phylogenetic data
More details
Hide details
Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
Online publication date: 2020-12-29
Publication date: 2020-12-29
Plant and Fungal Systematics 2020; 65(2): 265–271
Phylogenetic relationships between Usnea nipparensis and U. sinensis, caperatic acid containing Usnea species, were examined based on ITS rDNA, and the phylogenetic position of U. nipparensis was inferred based on multi-locus gene analysis using ITS rDNA, nuLSU, and MCM7. Although U. nipparensis and U. sinensis have a sorediate and an esorediate shrubby thallus, respectively, and in general look quite different, other detailed morphological and chemical features are similar. Analysis of the ITS rDNA sequences suggests their close relationship, but also confirms the independence of both species, and that they most likely form a ‘species pair’ based on morphological, chemical and molecular phylogenetic data. Phylogenetic trees based on both multi-locus gene and ITS rDNA alone strongly support that U. nipparensis and U. angulata belong to the same clade.
Articus, K., Mattsson, J.-E., Tibell, L., Grube, M. & Wedin, M. 2002. Ribosomal DNA and -tubulin data do not support the separation of the lichens Usnea florida and U. subfloridana as distinct species. Mycological Research 106: 412–418. https://doi.org/10.1017/s09537....
Awasthi, G. 1986. Lichen genus Usnea in India. The Journal of the Hattori Botanical Laboratory 61: 333–421.
Buschbom, J. & Mueller, G. M. 2005. Testing ‘species pair’ hypotheses: evolutionary processes in the lichen-forming species complex Porpidia flavocoerulescens and Porpidia melinodes. Molecular Biology and Evolution 23: 574–586. https://doi.org/10.1093/molbev....
Clerc, P. 1984. Contribution à la revision de la systém atique des usnées (Ascomycotina, Usnea) d’Europe. I. – Usnea florida (L.) Wigg. emend. Clerc. Cryptogamie Bryologie et Lichénologie 5: 333–360.
Clerc, P. 1987. Systematics of the Usnea fragilescens aggregate, and its distribution in Scandinavia. Nordic Journal of Botany 7: 479–495. https://doi.org/10.1111/j.1756....
Clerc, P. 1998. Species concepts in the genus Usnea (lichenized Ascomycetes). The Lichenologist 30: 321–340. https://doi.org/10.1006/lich.1....
Clerc, P. & Otte, V. 2018. Usnea viktoriana (Ascomycota, Parmeliaceae), a new European taxon of the Usnea barbata-dasopoga group, with a key to the shrubby-subpendulous sorediate Usnea species in Europe. The Lichenologist 50: 513–527. https://doi.org/10.1017/s00242....
Culberson, C. F. 1969. Chemical and Botanical Guide to Lichen Products. University of North Carolina Press, Chapel Hill. 628 pp.
Culberson, C. F. & Johnson, A. 1982. Substitution of methyl tert.-butyl ether for diethyl ether in the standardized thin-layer chromatographic method for lichen products. Journal of Chromatography 238: 483–487. https://doi.org/10.1016/s0021-....
Divakar, P. K., Crespo, A., Wedin, M., Leavitt, S. D., Hawksworth, D. L., Myllys, L., McCune, B., Randlane, T., Bjerke, J. W., Ohmura, Y., Schmitt, I., Boluda, C. G., Alors, D., Roca-Valiente, B., Del- Prado, R., Ruibal, C., Buaruang, K., Núñez-Zapata, J., Amo de Paz, G., Rico, V. J., Molina, M. C., Elix, J. A., Esslinger, T. L., Tronstad, I. K., Lindgren, H., Ertz, D., Gueidan, C., Saag, L., Mark, K., Singh, G., Dal Grande, F., Parnmen, S., Beck, A., Benatti, M. N., Blanchon, D., Candan, M., Clerc, P., Goward, T., Grube, M., Hodkinson, B. P., Hur, J. S., Kantvilas, G., Kirika, P. M., Lendemer, J., Mattsson, J. E., Messuti, M. I., Miadlikowska, J., Nelsen, M., Ohlson, J. I., Pérez-Ortega, S., Saag, A., Sipman, H. J., Sohrabi, M., Thell, A., Thor, G., Truong, C., Yahr, R., Upreti, D. K., Cubas, P. & Lumbsch, H. T. 2015. Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi. New Phytologist 208: 1217–1226. https://doi.org/10.1111/nph.13....
Divakar, P. K., Crespo, A., Kraichak, E., Leavitt, S. D., Singh, G., Schmitt, I. & Lumbsch, H. T. 2017. Using a temporal phylogenetic method to harmonize family- and genus-level classification in the largest clade of lichen-forming fungi. Fungal Diversity 84: 101–117. https://doi.org/10.1007/s13225....
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17: 368–376. https://doi.org/10.1007/bf0173....
Felsenstein, J. 1985. Confidence limits on phylogenies an approach using the bootstrap. Evolution 39: 783–791. https://doi.org/10.2307/240867....
Gardes, M. & Bruns, T. D. 1993. ITS primers with enhanced specificity for Basidiomycetes – application to the identification of mycorrhizae and rusts. Molecular Ecology 2: 113–118. https://doi.org/10.1111/j.1365....
Gerlach, A. C. L., Clerc, P. & Da Silveira, R. M. B. 2017. Taxonomy of the corticolous, shrubby, esorediate, neotropical species of Usnea Adans. (Parmeliaceae) with an emphasis on southern Brazil. The Lichenologist 49: 199–238. https://doi.org/10.1017/s00242....
Gerlach, A. C. L., Toprak, Z., Naciri, Y., Caviró, E. A., de Silveira, R. M. B. & Clerc, P. 2019. New insights into the Usnea cornuta aggregate (Parmeliaceae, lichenized Ascomycota): Molecular analysis reveals high genetic diversity correlated with chemistry. Molecular Phylogenetics and Evolution 131: 125–137. https://doi.org/10.1016/j.ympe....
Grewe, F., Lagostina, E., Wu, H., Printzen, C. & Lumbsch, H. T. 2018. Population genomic analyses of RAD sequences resolves the phylogenetic relationship of the lichen-forming fungal species Usnea antarctica and Usnea aurantiacoatra. MycoKeys 43: 91–113. https://doi.org/10.3897/mycoke....
Hosaka, K. 2009. Phylogeography of the genus Pisolithus revisited with some additional taxa from New Caledonia and Japan. Bulletin of the National Museum of Nature and Science, Series B 35: 151–167.
Huneck, S., Feige, G. B. & Lumbsch, H. T. 1994. High performance liquid chromatographic analysis of aliphatic lichen acids. Phytochemical Analysis 5: 57–60. https://doi.org/10.1002/pca.28....
Katoh, K., Rozwicki, J. & Yamada, K. D. 2019. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20: 1160–1166. https://doi.org/10.1093/bib/bb....
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. https://doi.org/10.1111/j.1469....
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. https://doi.org/10.1007/bf0173....
Kumar, S., Stecher, G., Li, G., Knyaz, C. & Tamura, K. 2018. MEGAX: Molecular Evolutionary Genetics Analysis accross computing platforms. Molecular Biology and Evolution 35: 1547–1549. https://doi.org/10.1093/molbev....
Lagostina, E., Dal Grande, F., Andreev, M. & Printzen, C. 2018. The use of microsatellite markers for species delimitation in Antarctic Usnea subgenus Neuropogon. Mycologia 110: 1047–1057. https://doi.org/10.1080/002755....
Leavitt, S. D., Johnson, L. & St Clair, L. L. 2011. 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: 175–188. https://doi.org/10.3732/ajb.10....
Lücking, R., Hodkinson, B. P. & Leavitt, S. T. 2017. The 2016 classification of lichenized fungi in the Ascomycota and Basidiomycota – Approaching one thousand genera. The Bryologist 119: 361–416. https://doi.org/10.1639/0007-2....
Lumbsch, H. T. & Wirtz, N. 2011. Phylogenetic relationships of the neuropogonoid core group in the genus Usnea (Ascomycota: Parmeliaceae). The Lichenologist 43: 553–559. https://doi.org/10.1017/s00242....
Mark, K., Saag, L., Leavitt, S. D., Will-Wolf, S., Nelsen, M. P., Tõrra, T., Saag, A., Randlane, T. & Lumbsch, H. T. 2016. Evaluation of traditionally circumscribed species in the lichen-forming genus Usnea, section Usnea (Parmeliaceae, Ascomycota) using a six-locus dataset. Organisms Diversity & Evolution 16: 497–524. https://doi.org/10.1007/s13127....
Mattsson J.-E. & Lumbsch, H. T. 1989. The use of the species pair concept in lichen taxonomy. Taxon 38: 238–241. https://doi.org/10.2307/122084....
Ohmura, Y. 2001. Taxonomic study of the genus Usnea (lichenized Ascomycetes) in Japan and Taiwan. The Journal of the Hattori Botanical Laboratory 90: 1–96.
Ohmura, Y. 2002. Phylogenetic evaluation of infrageneric groups of the genus Usnea based on ITS regions in rDNA. The Journal of the Hattori Botanical Laboratory 92: 231–243.
Ohmura, Y. 2008. Molecular phylogeny of Usnea rubicunda and U. rubrotincta (Parmeliaceae, lichenized Ascomycotina) based on ITS rDNA sequences. Journal of Japanese Botany 83: 347–355.
Ohmura, Y. 2012. A synopsis of the lichen genus Usnea (Parmeliaceae, Ascomycota) in Taiwan. Memoirs of the National Museum of Nature and Science 48: 91–137.
Ohmura, Y. & Clerc, P. 2019. Lectotypification of Usnea confusa (Parmeliaceae, Ascomycota). Bulletin of the National Museum of Nature and Science, Series B 45: 63–70.
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: 217–225. https://doi.org/10.1017/s00242....
Poelt, J. 1970. Das Konzept der Artenpaare bei den Flechten. Vorträge aus dem Gesamtgebiet der Botanik herausgegeben von der Deutschen Botanischen Gesellschaft, neue Folge 4: 187–198.
Poelt, J. 1972. Die Taxonomische Behandlung von Artenpaaren bei den Flechten. Botaniska Notiser 125: 77–81.
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: 427–444. https://doi.org/10.1017/s00242....
Saitou, N. & Nei, M. 1987. The Neighbor-Joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406–425. https://doi.org/10.1093/oxford....
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: 71–82. https://doi.org/10.1017/s09541....
Shen, Y.-M., Hsieh, H.-J., Yeh, R.-Y. & Hung, T.-H. 2012. Five apothecium- producing lichenized fungi of the genus Usnea in Taiwan. Fungal Science 27: 31–44.
Stevens, G. N. 1999. A revision of the lichen family Usneaceae in Australia. Bibliotheca Lichenologica 72: 1–128.
Tamura, K. & Nei, M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10: 512–526. https://doi.org/10.1093/oxford....
Tehler, A. 1982. The species pair concept in lichenology. Taxon 31: 708–714. https://doi.org/10.2307/121968....
Truong, C. & Clerc, P. 2016. New species and new records in the genus Usnea (Parmeliaceae, lichenized Ascomycota) from tropical South America. The Lichenologist 48: 71–93. https://doi.org/10.1017/s00242....
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: 357–372. https://doi.org/10.1016/j.ympe....
van den Boom, P. P. G., Clerc, P. & Ertz, D. 2015. New records of lichens and lichenicolous fungi from La Gomera (Canary Islands, Spain), including the new species: Usnea boomiana P. Clerc. Candollea 70: 165–177. https://doi.org/10.15553/c2015....
Vilgalys, R. & Hester, M. 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology 172: 4238–4246. https://doi.org/10.1128/jb.172....
Walker, F. J. 1985. The lichen genus Usnea subgenus Neuropogon. Bulletin of the British Museum (Natural History), Botany Series 13: 1–130.
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. https://doi.org/10.1016/j.mycr....
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: 17–37. https://doi.org/10.1007/s13127....
Yoshimura, I. & Kurokawa, T. 1976. Simple identification of lichen aliphatic acids by using thin-layer chromatography and microcrystal test. Bulletin of Kochi Gakuen Junior College 7: 55–60.
Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics
Robert Lücking, Steven Leavitt, David Hawksworth
Fungal Diversity
Mycobiont-specific primers facilitate the amplification of mitochondrial small subunit ribosomal DNA: a focus on the lichenized fungal genus Melanelia (Ascomycota, Parmeliaceae) in Iceland
Maonian Xu, Yingkui Liu, Erik Möller, Scott LaGreca, Patricia Moya, Xinyu Wang, Einar Timdal, Boer de, Eva Barreno, Lisong Wang, Holger Thüs, Ólafur Andrésson, Kristinn Magnússon, Elín Ólafsdóttir, Starri Heiðmarsson