Hostname: page-component-cd9895bd7-p9bg8 Total loading time: 0 Render date: 2024-12-23T14:01:33.643Z Has data issue: false hasContentIssue false

The cetrarioid core group revisited (Lecanorales: Parmeliaceae)

Published online by Cambridge University Press:  05 October 2011

Matthew P. NELSEN
Affiliation:
Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th Street, Chicago, Illiniois 60637, USA; and Department of Botany, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605, USA. Email: [email protected]
Natali CHAVEZ
Affiliation:
Department of Botany, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605, USA; and Department of Biological Sciences, DePaul University, 2325 North Clifton Avenue, Chicago, Illinois 60614, USA.
Erin SACKETT-HERMANN
Affiliation:
Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605, USA.
Arne THELL
Affiliation:
The Biological Museums, Lund University, Östra Vallgatan 18-20, SE-223 61 Lund, Sweden.
Tiina RANDLANE
Affiliation:
Institute of Ecology and Earth Sciences, University of Tartu, Lai Street 38, 51005 Tartu, Estonia.
Pradeep K. DIVAKAR
Affiliation:
Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, E-28040 Madrid, Spain.
Víctor J. RICO
Affiliation:
Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, E-28040 Madrid, Spain.
H. Thorsten LUMBSCH
Affiliation:
Department of Botany, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605, USA.

Abstract

The cetrarioid core group has been the focus of numerous taxonomic and phylogenetic studies in recent years, yet the phylogenetic resolution and support among these clades remains unclear. Here we use four commonly employed loci to estimate if their use increases phylogenetic resolution and support. The present study largely confirms the topologies of previous studies, but with increased support. Approximately half of the genera in the cetrarioid core were not monophyletic. Melanelia sorediella was clustered within Cetrariella, and the combination Cetrariella sorediella (Lettau) V. J. Rico & A. Thell comb. nov. is made. Additionally, the genus Flavocetrariella was supported as part of Nephromopsis and is considered to be a synonym of the latter. Finally, a comparison of genetic distances shows that the maximum intrageneric genetic distance encompassed by many cetrarioid genera is lower than that of many other genera in Parmeliaceae.

Type
Research Article
Copyright
Copyright © British Lichen Society 2011

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Aguileta, G., Marthey, S., Chiapello, H., Lebrun, M.-H., Rodolphe, F., Fournier, E., Gendrault-Jacquemard, A. & Giraud, T. (2008) Assessing the performance of single-copy genes for recovering robust phylogenies. Systematic Biology 57: 613627.CrossRefGoogle ScholarPubMed
Awasthi, D. D. (2007) A Compendium of the Macrolichens from India, Nepal and Sri Lanka. Dehra Dun: Bishen Singh Mahendra Pal Singh.Google Scholar
Blanco, O., Crespo, A., Divakar, P. K., Esslinger, T. L., Hawksworth, D. L. & Lumbsch, H. T. (2004a) Melanelixia and Melanohalea, two new genera segregated from Melanelia (Parmeliaceae) based on molecular and morphological data. Mycological Research 108: 873884.CrossRefGoogle ScholarPubMed
Blanco, O., Crespo, A., Elix, J. A., Hawksworth, D. L. & Lumbsch, H. T. (2004b) A molecular phylogeny and a new classification of parmelioid lichens containing Xanthoparmelia-type lichenan (Ascomycota: Lecanorales). Taxon 53: 959975.CrossRefGoogle Scholar
Blanco, O., Crespo, A., Divakar, P. K., Elix, J. A. & Lumbsch, H. T. (2005) Molecular phylogeny of parmotremoid lichens (Ascomycota, Parmeliaceae). Mycologia 97: 150159.Google Scholar
Bruns, T. D., White, T. J. & Taylor, J. W. (1991) Fungal molecular systematics. Annual Review of Ecology and Systematics 22: 525564.CrossRefGoogle Scholar
Castresana, J. (2001) Cytochrome b phylogeny and the taxonomy of great apes and mammals. Molecular Biology and Evolution 18: 465471.CrossRefGoogle ScholarPubMed
Crespo, A., Blanco, O. & Hawksworth, D. L. (2001) The potential of mitochondrial DNA for establishing phylogeny and stabilizing concepts in the parmelioid lichens. Taxon 50: 807819.CrossRefGoogle Scholar
Crespo, A., Lumbsch, H. T., Mattsson, J. –E., Blanco, O., Divakar, P. K., Articus, K., Wiklund, E., Bawingan, P. A. & Wedin, M. (2007) Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene. Molecular Phylogenetics and Evolution 44: 812824.CrossRefGoogle ScholarPubMed
Crespo, A., Kauff, F., Divakar, P. K., del Prado, R., Pérez-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: 17351753.CrossRefGoogle Scholar
Crespo, A., Divakar, P. K. & Hawksworth (2011) Generic concepts in parmelioid lichens, and the phylogenetic value of characters used in their circumscription. Lichenologist 43: 511535.CrossRefGoogle 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: 125133.Google Scholar
Divakar, P, K., Lumbsch, H. T., Ferencova, Z., del Prado, R. & Crespo, A. (2010) Remototrachyna, a newly recognized tropical lineage of lichens in the Hypotrachyna clade (Parmeliaceae, Ascomycota), originated in the Indian subcontinent. American Journal of Botany 97: 579590.CrossRefGoogle ScholarPubMed
Döring, H., Clerc, P., Grube, M. & Wedin, M. (2000) Mycobiont-specific PCR primers for the amplification of nuclear ITS and LSU rDNA from lichenized ascomycetes. Lichenologist 32: 200204.CrossRefGoogle Scholar
Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 17921797.CrossRefGoogle ScholarPubMed
Elix, J. A. (1993) Progress in the generic delimitation of Parmelia sensu lato lichens (Ascomycotina: Parmeliaceae). Bryologist 96: 359383.CrossRefGoogle Scholar
Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783791.CrossRefGoogle ScholarPubMed
Goward, T. (1985) Ahtiana, a new lichen genus in the Parmeliaceae. Bryologist 88: 367371.CrossRefGoogle Scholar
Guindon, S. & Gascuel, O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52: 696704.CrossRefGoogle ScholarPubMed
Hale, M. E. (1990) A synopsis of the lichen genus Xanthoparmelia (Vainio) Hale (Ascomycotina, Parmeliaceae). Smithsonian Contributions to Botany 74: 1250.Google Scholar
Huelsenbeck, J. P. & Ronquist, F. (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754755.CrossRefGoogle ScholarPubMed
Kärnefelt, I. (1979) The brown fruticose species of Cetraria. Opera Botanica 46: 1150.Google Scholar
Kärnefelt, I., Mattsson, J. -E. & Thell, A. (1992) Evolution and phylogeny of cetrarioid lichens. Plant Systematics and Evolution 183: 113160.CrossRefGoogle Scholar
Kirk, P. M., Cannon, P. F., Minter, M. W. & Stalpers, J. A. (eds) (2008) Ainsworth & Bisby's Dictionary of the Fungi. 10th edn. Wallingford: CAB International.CrossRefGoogle Scholar
Larget, B. & Simon, D. L. (1999) Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Molecular Biology and Evolution 16: 750759.CrossRefGoogle Scholar
Lumbsch, H. T. (2002) How objective are genera in euascomycetes? Perspectives in Plant Ecology, Evolution and Systematics 5: 91101.CrossRefGoogle Scholar
Maddison, W. P. & Maddison, D. R. (2010) Mesquite: A Modular System for Evolutionary Analysis. Version 2.73 http://mesquiteproject.orgGoogle 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: 688698.CrossRefGoogle ScholarPubMed
Miller, M. A., Holder, M. T., Vos, R., Midford, P. E., Liebowitz, T., Chan, L., Hoover, P. & Warnow, T. (2009) The CIPRES Portals. CIPRES. 2009-08-04. URL: http://www.phylo.org/sub_sections/portal. Accessed: 2009-08-04. (Archived by WebCite(r) at http://www.webcitation.org/5imQlJeQa)Google Scholar
Nilsson, R. H., Kristiansson, E., Ryberg, M., Hallenberg, N. & Larsson, K-H. (2008) Intraspecific ITS variability in the kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evolutionary Bioinformatics 4: 193201.CrossRefGoogle ScholarPubMed
Nylander, J. A., Wilgenbusch, J. C., Warren, D. L. & Swofford, D. L. (2008) AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24: 581583.CrossRefGoogle Scholar
Parnmen, S., Rangsiruji, A., Mongkolsuk, P., Boonpragob, K., Elix, J. A. & Lumbsch, H. T. (2010) Morphological disparity in Cladoniaceae: the foliose genus Heterodea evolved from fruticose Cladia species (Lecanorales, lichenized Ascomycota). Taxon 59: 841849.CrossRefGoogle Scholar
Posada, D. (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25: 12531256.CrossRefGoogle ScholarPubMed
Rambaut, A. (1996) Se-Al: Sequence Alignment Editor. http://evolve.zoo.ox.ac.uk/Google Scholar
Rambold, G., Triebel, D. & Hertel, H. (1993) Icmadophilaceae, a new family in the Leotiales. Bibliotheca Lichenologica 53: 217240.Google Scholar
Randlane, T. & Saag, A. (1993) World list of cetrarioid lichens. Mycotaxon 47: 395403.Google Scholar
Randlane, T., Saag, A. & Thell, A. (1997) A second updated world list of cetrarioid lichens. Bryologist 100: 109122.CrossRefGoogle Scholar
Randlane, T., Saag, A. & Obermayer, W. (2001) Cetrarioid lichens containing usnic acid from the Tibetan area. Mycotaxon 80: 389425.Google Scholar
Rico, V. J., van den Boom, P. P. G. & Barrasa, J. M. (2005) Morphology, chemistry and distribution of Melanelia sorediella (Parmeliaceae) and similar species in the Iberian Peninsula. Lichenologist 37: 199215.Google Scholar
Rivas Plata, E., Lücking, R., Aptroot, A., Sipman, H. J. M., Umana, L., Chaves, J. L. & Lizano, D. (2006) A first assessment of the Ticolichen biodiversity inventory in Costa Rica: the genus Coenogonium (Ostropales: Coenogoniaceae). Fungal Diversity 23: 255321.Google Scholar
Ronquist, F., Huelsenbeck, J. P., & van der Mark, P. (2005) MrBayes 3.1 Manual. http://mrbayes.csit.fsu.edu/mb3.1_manual.pdfGoogle Scholar
Ronquist, F., van der Mark, P. & Huelsenbeck, J. P. (2009) Bayesian phylogenetic analysis using MrBayes. In The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing (Lemey, P., Salemi, M. & Vandamme, A.-M., eds): 210266. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Saag, A. & Randlane, T. (1995) Phylogenetic affinities of cetrarioid lichens. Cryptogamic Botany 5: 128136.Google Scholar
Saag, A., Randlane, T., Thell, A. & Obermayer, W. (2002) Phylogenetic analysis of cetrarioid lichens with globose ascospores. Proceedings of the Estonian Academy of Sciences, Biology, Ecology 51: 103123.Google Scholar
Schmitt, I., Crespo, A., Divakar, P. K., Fanhauser, J. D., Herman-Sackett, E., Kalb, K., Nelsen, M. P., Nelson, N. A., Rivas-Plata, E., Shimp, A. D. et al. (2009) New primers for promising single-copy genes in fungal phylogenetics and systematics. Persoonia 23: 3540.Google Scholar
Schoch, C. L., Sung, G.-H., López-Giráldez, F., Townsend, J. P., Miądlikowska, J., Hofstetter, V., Robbertse, B., Matheny, P. B., Kauff, F., Wang, Z. et al. (2009) The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Systematic Biology 58: 224239.Google Scholar
Stamatakis, A. (2006) RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 26882690.CrossRefGoogle ScholarPubMed
Stiller, J. W. & Hall, B. D. (1997) The origin of red algae: implications for plastid evolution. Proceedings of the National Academy of Sciences, USA 94: 45204525.CrossRefGoogle ScholarPubMed
Swofford, D. L. (2002) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Sunderland, Massachusetts: Sinauer Associates.Google Scholar
Thell, A. & Miao, V. (1998) Phylogenetic analysis of ITS and group I intron sequences from European and North American samples of cetrarioid lichens. Annales Botanici Fennici 35: 275286.Google Scholar
Thell, A., Stenroos, S., Feuerer, T., Kärnefelt, I., Myllys, L. & Hyvönen, J. (2002) Phylogeny of cetrarioid lichens (Parmeliaceae) inferred from ITS and β-tubulin sequences, morphology, anatomy and secondary chemistry. Mycological Progress 1: 335354.CrossRefGoogle Scholar
Thell, A., Feuerer, T., Kärnefelt, I., Myllys, L. & Stenroos, S. (2004) Monophyletic groups within the Parmeliaceae identified by ITS rDNA, β-tubulin and GAPDH sequences. Mycological Progress 3: 297314.CrossRefGoogle Scholar
Thell, A., Randlane, T., Saag, A. & Kärnefelt, I. (2005) A new circumscription of the lichen genus Nephromopsis (Parmeliaceae, lichenized ascomycetes). Mycological Progress 4: 303316.CrossRefGoogle Scholar
Thell, A., Högnabba, F., Elix, J. A., Feuerer, T., Kärnefelt, I., Myllys, L., Randlane, T., Saag, A., Stenroos, S., Ahti, T. & Seaward, M. R. D. (2009) Phylogeny of the cetrarioid core (Parmeliaceae) based on five genetic markers. Lichenologist 41: 489511.CrossRefGoogle Scholar
Vilgalys, R. & Hester, M. (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology 172: 42384246.Google Scholar
Wiens, J. J. (2003) Missing data, incomplete taxa, and phylogenetic accuracy. Systematic Biology 52: 528538.CrossRefGoogle ScholarPubMed
Wiens, J. J. (2006) Missing data and the design of phylogenetic analyses. Journal of Biomedical Informatics 39: 3442.CrossRefGoogle ScholarPubMed
Wilgenbusch, J. C., Warren, D. L. & Swofford, D. L. (2004) AWTY: a System for Graphical Exploration of MCMC Convergence in Bayesian Phylogenetic Inference. http://ceb.csit.fsu.edu/awtyGoogle Scholar
Zoller, S., Scheidegger, C. & Sperisen, C. (1999) PCR primers for the amplification of mitochondrial small subunit ribosomal DNA of lichen-forming ascomycetes. Lichenologist 31: 511516.CrossRefGoogle Scholar