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Using morphological, chemical, and molecular data to study the diversity of Xanthoparmelia species from South Africa (Ascomycota, Parmeliaceae)

Published online by Cambridge University Press:  22 September 2023

Alejandrina Barcenas-Peña*
Affiliation:
The Grainger Bioinformatics Center and Negaunee Integrative Research Center, Science & Education, The Field Museum, Chicago, IL 60605-2496, USA
Harrie J. M. Sipman
Affiliation:
Freie Universität, Botanischer Garten und Botanisches Museum, D-14195 Berlin, Germany
Volkmar Wirth
Affiliation:
Friedrich-Ebert-Straße 68, D-71711 Murr, Germany
Felix Grewe
Affiliation:
The Grainger Bioinformatics Center and Negaunee Integrative Research Center, Science & Education, The Field Museum, Chicago, IL 60605-2496, USA
H. Thorsten Lumbsch
Affiliation:
The Grainger Bioinformatics Center and Negaunee Integrative Research Center, Science & Education, The Field Museum, Chicago, IL 60605-2496, USA
*
Corresponding author: Alejandrina Barcenas-Peña; Email: abarcenas@fieldmuseum.org

Abstract

There is still a high diversity of lichen-forming fungi that remains undescribed, especially cryptic lineages at the species level. Integrating morphological, chemical, and DNA sequence data has proved useful in corroborating species descriptions and delimitations. Here we reviewed morphological features, secondary metabolites and the DNA sequences of ITS, mtSSU and nuLSU markers to study the diversity of Xanthoparmelia in southern Africa. A total of 37 species were recorded. Three of these appear undescribed, and we therefore describe them here as new: Xanthoparmelia nimisii, with a sorediate thallus and broad lobes, is well supported as a clade separate from X. annexa; X. pseudochalybaeizans with a white medulla is phylogenetically distinct from the otherwise similar X. chalybaeizans; and X. sipmaniana, well supported as a separate clade from the similar X. hypoprocetrarica. In addition, the separation of Xanthoparmelia capensis and X. tinctina requires further studies.

Type
Standard Paper
Copyright
Copyright © The Author(s), 2023. Published by Cambridge University Press on behalf of the British Lichen Society

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References

Amo de Paz, G, Lumbsch, HT, Cubas, P, Elix, JA and Crespo, A (2010) The genus Karoowia (Parmeliaceae, Ascomycota) includes unrelated clades nested within Xanthoparmelia. Australian Systematic Botany 23, 173184.Google Scholar
Arup, U, Ekman, S, Lindblom, L and Mattsson, J-E (1993) High performance thin-layer chromatography (HPTLC), an improved technique for screening lichen substances. Lichenologist 25, 6171.Google Scholar
Autumn, K, Barcenas-Peña, A, Kish-Levine, S, Huang, J-P and Lumbsch, HT (2020) Repeated colonization between arid and seasonal habitats, frequent transition among substrate preferences, and chemical diversity in Western Australian Xanthoparmelia lichens. Frontiers in Ecology and Evolution 8, 129.CrossRefGoogle Scholar
Blanco, O, Crespo, A, Elix, JA, Hawksworth, DL and Lumbsch, HT (2004) A molecular phylogeny and a new classification of parmelioid lichens containing Xanthoparmelia-type lichenan (Ascomycota: Lecanorales). Taxon 53, 959975.CrossRefGoogle Scholar
Culberson, C and Johnson, A (1982) Substitution of methyl tert.-butyl ether for diethyl ether in standardized thin-layer chromatographic method for lichen products. Journal of Chromatography 238, 438487.Google Scholar
Culberson, CF, Culberson, WL and Esslinger, TL (1977) Chemosyndromic variation in the Parmelia pulla group. Bryologist 80, 125135.Google Scholar
Darriba, D, Taboada, GL, Doallo, R and Posada, D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9, 772.Google Scholar
Divakar, PK, Crespo, A, Wedin, M, Leavitt, SD, Hawksworth, DL, Myllys, L, McCune, B, Randlane, T, Bjerke, JW, Ohmura, Y, et al. (2015) Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi. New Phytologist 208, 12171226.Google Scholar
Elix, JA (1994) Neofuscelia. Flora of Australia 55, 6885.Google Scholar
Elix, JA (1997) New species and new combinations in the lichen family Parmeliaceae (Ascomycotina) from South Africa. Mycotaxon 63, 335343.Google Scholar
Elix, JA (1999 a) New species of Neofuscelia (lichenized Ascomycotina, Parmeliaceae) from the Southern Hemisphere. Mycotaxon 71, 471–456.Google Scholar
Elix, JA (1999 b) New species of Xanthoparmelia (lichenized Ascomycotina, Parmeliaceae) from South Africa. Mycotaxon 73, 5161.Google Scholar
Elix, JA (2001) A revision of the lichen genus Paraparmelia Elix & J. Johnst. Bibliotheca Lichenologica 80, 1224.Google Scholar
Elix, JA (2002) New species of Xanthoparmelia (lichenized Ascomycotina, Parmeliaceae) from Africa. Lichenologist 34, 238291.Google Scholar
Elix, JA (2003) The lichen genus Paraparmelia, a synonym of Xanthoparmelia (Ascomycota, Parmeliaceae). Mycotaxon 87, 395403.Google Scholar
Elix, JA, Johnston, J and Armstrong, PM (1986) A revision of the lichen genus Xanthoparmelia in Australasia. Bulletin of the British Museum (Natural History), Botany Series 15, 163362.Google Scholar
Elix, JA, Becker, U and Follmann, G (1999) New species of Neofuscelia and Xanthoparmelia (lichenized Ascomycotina, Parmeliaceae) from Zimbabwe. Mycotaxon 71, 112.Google Scholar
Esslinger, TL (1977) A chemosystematic revision of the brown Parmeliae. Journal of the Hattori Botanical Laboratory 42, 1211.Google Scholar
Esslinger, TL (1981) Almbornia, a new lichen genus from South Africa. Nordic Journal of Botany 1, 125127.CrossRefGoogle Scholar
Esslinger, TL (1986) Further reports on the brown Parmeliaceae of southern Africa. Nordic Journal of Botany 6, 8791.Google Scholar
Esslinger, TL (2000) Notes on the brown-colored species of Parmeliaceae (lichenized Ascomycota) in southern Africa. Bryologist 103, 568591.Google Scholar
Gardes, M and Bruns, T (1993) ITS primers with enhanced specificity for basidiomycetes – application to the identification of mycorrhizae and rusts. Molecular Ecology 2, 113118.Google Scholar
Gelman, A and Rubin, DB (1992) Inference from iterative simulation using multiple sequences. Statistical Science 7, 457511.Google Scholar
Guindon, S and Gascuel, O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52, 696704.Google Scholar
Hale, ME (1974) Bulbothrix, Parmelina, Relicina and Xanthoparmelia, four new genera in the Parmeliaceae. Phytologia 28, 479490.Google Scholar
Hale, ME (1985) Xanthomaculina Hale, a new lichen genus in the Parmeliaceae (Ascomycotina). Lichenologist 17, 255265.Google Scholar
Hale, ME (1986) New species of the lichen genus Xanthoparmelia from southern Africa (Ascomycotina: Parmeliaceae). Mycotaxon 27, 563610.Google Scholar
Hale, ME (1988) Namakwa, a new lichen genus in the Parmeliaceae (Ascomycotina, Parmeliaceae). Mycotaxon 32, 169174.Google Scholar
Hale, ME (1989) A monograph of the lichen genus Karoowia Hale (Ascomycotina: Parmeliaceae). Mycotaxon 35, 177198.Google Scholar
Hale, ME (1990) A synopsis of the lichen genus Xanthoparmelia (Vainio) Hale (Ascomycotina, Parmeliaceae). Smithsonian Contributions to Botany 74, 1250.Google Scholar
Hale, ME and Kurokawa, S (1964) Studies on Parmelia subgenus Parmelia. Contributions from the United States National Herbarium 36, 121191.Google Scholar
Huelsenbeck, JP and Ronquist, F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754755.Google Scholar
Jaklitsch, W, Baral, H-O, Lücking, R, Lumbsch, HT and Frey, W (2016) Syllabus of Plant Families: Adolf Engler's Syllabus der Pflanzenfamilien, Part 1/2. Stuttgart: Borntraeger Verlagsbuchhandlung.Google Scholar
Katoh, K, Rozewicki, J and Yamada, KD (2019) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20, 11601166.Google Scholar
Kurokawa, S and Elix, JA (1971) Two new Australian Parmeliae. Journal of Japanese Botany 46, 113116.Google Scholar
Leavitt, SD, Lumbsch, HT, Stenroos, S and St Clair, LL (2013) Pleistocene speciation in North American lichenized fungi and the impact of alternative species circumscriptions and rates of molecular evolution on divergence estimates. PLoS ONE 8, e85240.Google Scholar
Leavitt, SD, Kirika, PM, Amo de Paz, G, Huang, J-P, Hur, J-S, Elix, JA, Grewe, F, Divakar, PK and Lumbsch, HT (2018) Assessing phylogeny and historical biogeography of the largest genus of lichen-forming fungi, Xanthoparmelia (Parmeliaceae, Ascomycota). Lichenologist 50, 299312.Google Scholar
Mangold, A, Martín, MP, Lücking, R and Lumbsch, HT (2008) Molecular phylogeny suggests synonymy of Thelotremataceae within Graphidaceae (Ascomycota: Ostropales). Taxon 57, 476486.Google Scholar
Miller, MA, Pfeiffer, W and Schwartz, T (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In Proceedings of the Gateway Computing Environments Workshop (GCE), 14 November 2010, New Orleans, Louisiana, pp. 18.Google Scholar
Orange, A, James, PW and White, FJ (2010) Microchemical Methods for the Identification of Lichens. Second Edition with Additions and Corrections. London: British Lichen Society.Google Scholar
Rambaut, A (2014) FigTree 1.2.2. [WWW resource] URL http://tree.bio.ed.ac.uk/software/figtree. [Accessed 1 September 2022].Google Scholar
Ronquist, F and Huelsenbeck, JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 15721574.Google Scholar
Sipman, H (2017) Compiled Key to Xanthoparmelia in Southern Africa. [WWW document] URL http://www.bgbm.fu-berlin.de/sip-man/keys/Afroxantkey3a.pdf. [Accessed 1 September 2022].Google Scholar
Stamatakis, A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 13121313.Google Scholar
Thell, A, Feuerer, T, Kärnefelt, I, Myllys, L and Stenroos, S (2004) Monophyletic groups within the Parmeliaceae identified by ITS rDNA, β-tubulin and GAPDH sequences. Mycological Progress 3, 297314.Google Scholar
Thell, A, Crespo, A, Divakar, PK, Kärnefelt, I, Leavitt, SD, Lumbsch, HT and Seaward, MRD (2012) A review of the lichen family Parmeliaceae – history, phylogeny and current taxonomy. Nordic Journal of Botany 30, 641664.Google Scholar
Vaidya, G, Lohman, DJ and Meier, R (2011) SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics 27, 171180.CrossRefGoogle ScholarPubMed
Vilgalys, R and Hester, M (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology 172, 42384246.Google Scholar
White, TJ, Bruns, TD, Lee, S and Taylor, J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In Innis, MA, Gelfand, DH, Sninsky, JJ and White, TJ (eds), PCR Protocols: a Guide to Methods and Applications. San Diego: Academic Press, pp. 315322.Google Scholar
Wirth, V and Sipman, HJM (2018) Xanthoparmelia krcmarii, a new species from South Africa with haemathamnolic acid. Herzogia 31, 505509.Google Scholar
Wirth, V, Sipman, HJ and Curtis-Scott, O (2018) A sketch of the lichen biota in a Renosterveld vegetation habitat. Carolinea (Karlsruhe) 76, 3555.Google Scholar
Zoller, S, Scheidegger, C and Sperisen, C (1999) PCR primers for the amplification of mitochondrial small subunit ribosomal DNA of lichen-forming ascomycetes. Lichenologist 31, 511516.Google Scholar
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