Fungal Diversity

, Volume 84, Issue 1, pp 101–117 | Cite as

Using a temporal phylogenetic method to harmonize family- and genus-level classification in the largest clade of lichen-forming fungi

  • Pradeep K. Divakar
  • Ana Crespo
  • Ekaphan Kraichak
  • Steven D. Leavitt
  • Garima Singh
  • Imke Schmitt
  • H. Thorsten Lumbsch


Although classification at supra-specific ranks is inherently arbitrary, comparable taxonomic ranks within clades can facilitate more consistent classifications and objective comparisons among taxa. Different circumscriptions of the hyper-diverse lichen-forming fungal family Parmeliaceae and widely different generic circumscriptions among authors have been proposed. For this study, we use a recently developed temporal approach that uses time-calibrated chronograms to identify temporal bands for specific ranks in Parmeliaceae and allied groups with the overarching goal of establishing a consistent, stable classification. A data set of 330 species, representing 73 genera in the family and 52 species of related families was used to address the circumscription of Parmeliaceae and its genera following the proposed temporal approach. Based on the results of this study, we propose a revised, temporal-based classification for Parmeliaceae, including all clades that share a common ancestor 102.13–112.88 Ma for families and a time window of 29.45–32.55 Ma for genera. Forty-five of the currently accepted genera in Parmeliaceae were supported in their current circumscription. Two subfamilies are accepted within Parmeliaceae: Protoparmelioideae Divakar et al. subfam. nov., including Protoparmelia and the resurrected genus Maronina, and Parmelioideae, including the bulk of genera in the family. The new genus Austromelanelixia Divakar et al. is proposed to accommodate a clade of southern Hemisphere species previously included in Melanelixia. Eumitria and tentatively Dolichousnea are resurrected as genera separate from Usnea. The following genera are reduced to synonymy: Allocetraria, Cetrariella, Usnocetraria, and Vulpicida with Cetraria; Arctocetraria, Cetreliopsis, Flavocetraria, Kaernefeltia, Masonhalea, Tuckermanella, and Tuckermannopsis with Nephromopsis; and the lichenicolous genera Nesolechia and Raesaenenia with the lichen-forming genera Punctelia and Protousnea, respectively. A total of 47 new combinations and three new names at the species level are proposed.


Ascomycota Gypsoplacaceae Lecanorales Lichenized fungi Parmeliaceae Phylogeny Protoparmelia Taxonomy Taxonomic ranks 



The project was financially supported by the Spanish Ministerio de Ciencia e Innovacion (CGL2013-42498-P), and the Negaunee Foundation (‘The greatest radiation in the fungal kingdom’). GS was supported by a fellowship from the German Academic Exchange Service (DAAD) and EK by a visiting scholarship from The Field Museum.

Supplementary material

13225_2017_379_MOESM1_ESM.xls (148 kb)
Supplementary material 1 (XLS 148 kb) Online Resource 1. Samples used in the study including voucher information and GenBank accession numbers for the six sampled loci: the nuclear ribosomal internal transcribed spacer region (ITS) and the large subunit (LSU), the mitochondrial small subunit rDNA (mtSSU), and low-copy protein-coding markers; the largest subunit of the RNA polymerase II (RPB1), the mini-chromosome maintenance complex component 7 (Mcm7) and the the pre-rRNA processing Trypanosoma serine–arginine 1 protein (Tsr1); newly obtained sequences for this study are in bold; n/a, missing loci


  1. Amo de Paz G, Cubas P, Divakar PK, Lumbsch HT, Crespo A (2011) Origin and diversification of major clades in parmelioid lichens (Parmeliaceae, Ascomycota) during the Paleogene inferred by Bayesian analysis. PLoS ONE 6(12):e2816. doi: 10.1371/journal.pone.0028161 CrossRefGoogle Scholar
  2. Aptroot A, Oliveira MMDD, Cáceres MES (2013) Protoparmelia capitata (Ascomycota: Parmeliaceae): new record for South America. Acta Bot Bras 27:498–501CrossRefGoogle Scholar
  3. Articus K (2004) Neuropogon and the phylogeny of Usnea s.l. (Parmeliaceae, lichenized Ascomycetes). Taxon 53:925–934CrossRefGoogle Scholar
  4. Arup U, Ekman S, Grube M, Mattsson J-E, Wedin M (2007) The sister group relation of Parmeliaceae (Lecanorales, Ascomycota). Mycologia 99:42–49CrossRefPubMedGoogle Scholar
  5. Arup U, Søchting U, Frödén P (2013) A new taxonomy of the family Teloschistaceae. Nord J Bot 31:16–83CrossRefGoogle Scholar
  6. Avise JC, Johns GC (1999) Proposal for a standardized temporal scheme of biological classification for extant species. Proc Natl Acad Sci USA 96:7358–7363. doi: 10.1073/pnas.96.13.7358 CrossRefPubMedPubMedCentralGoogle Scholar
  7. Avise JC, Liu JX (2011) On the temporal inconsistencies of Linnean taxonomic ranks. Biol J Lin Soc 102:707–714. doi: 10.1111/j.1095-8312.2011.01624.x CrossRefGoogle Scholar
  8. Avise JC, Mitchell D (2007) Time to standardize taxonomies. Syst Biol 56:130–133CrossRefPubMedGoogle Scholar
  9. Barraclough TG, Humphreys AM (2015) The evolutionary reality of species and higher taxa in plants: a survey of post-modern opinion and evidence. New Phytol 207:291–296. doi: 10.1111/nph.13232 CrossRefPubMedGoogle Scholar
  10. Blanco O, Crespo A, Divakar PK, Esslinger TL, Hawksworth DL, Lumbsch HT (2004) Melanelixia and Melanohalea, two new genera segregated from Melanelia (Parmeliaceae) based on molecular and morphological data. Mycol Res 108:873–884CrossRefPubMedGoogle Scholar
  11. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552CrossRefPubMedGoogle Scholar
  12. Coyne JA, Orr HA (2004) Speciation. Sinauer Associates, SunderlandGoogle Scholar
  13. Crespo A, Lumbsch HT, Mattsson JE, Blanco O, Divakar PK, Articus K, Wiklund E, Bawingan PA, Wedin M (2007) Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene. Mol Phylogenet Evol 44:812–824CrossRefPubMedGoogle Scholar
  14. Crespo A, Kauff F, Divakar PK, Amo G, Arguello A, Blanco O, Cubas P, del Prado R, Elix JA, Esslinger TL, Ferencova Z, Hawksworth DL, Lutzoni F, Millanes AM, Molina MC, Perez-Ortega S, Wedin M, Ahti T, Bungartz F, Calvelo S, Aptroot A, Barreno E, Candan M, Cole M, Ertz D, Goffinet B, Lindblom L, Lücking R, Mattsson JE, Messuti MI, Miadlikowska J, Piercey-Normore M, Rico V, Sipman HJM, Schmitt I, Spribille T, Thell A, Thor G, Lumbsch HT (2010) Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence. Taxon 59:1735–1753Google Scholar
  15. Crespo A, Divakar PK, Hawksworth DL (2011) Generic concepts in parmelioid lichens, and the phylogenetic value of characters used in their circumscription. Lichenologist 43:511–535CrossRefGoogle Scholar
  16. De Queiroz K (2006) The PhyloCode and the distinction between taxonomy and nomenclature. Syst Biol 55:160–162CrossRefPubMedGoogle Scholar
  17. Divakar PK, Crespo A, Blanco O, Lumbsch HT (2006) Phylogenetic significance of morphological characters in the tropical Hypotrachyna clade of parmelioid lichens (Parmeliaceae, Ascomycota). Mol Phylogenet Evol 40:448–458CrossRefPubMedGoogle Scholar
  18. Divakar PK, Ferencova Z, Del Prado R, Lumbsch HT, Crespo A (2010) Remototrachyna, a new tropical lineage in hypotrachynoid lichens (Parmeliaceae, Ascomycota): a multigene and morphological approach. Am J Bot 97:579–590CrossRefPubMedGoogle Scholar
  19. Divakar PK, Del Prado R, Lumbsch HT, Wedin M, Esslinger TL, Leavitt SD, Crespo A (2012) Diversification of the newly recognized lichen forming fungal lineage Montanelia (Parmeliaceae, Ascomycota) and its relation to key geological and climatic events. Am J Bot 99:2014–2026CrossRefPubMedGoogle Scholar
  20. Divakar PK, Crespo A, Núñez-Zapata J, Flakus A, Sipman HJM, Elix JA, Lumbsch HT (2013) A molecular perspective on generic concepts in the Hypotrachyna clade (Parmeliaceae, Ascomycota). Phytotaxa 132:21–38CrossRefGoogle Scholar
  21. Divakar PK, Crespo A, Wedin M, Leavitt SD, Hawksworth DL, Myllys L, McCune B, Randlane T, Bjerke JW, Ohmura Y, Schmitt I, Boluda CG, Alors D, Roca-Valiente B, Del-Prado R, Ruibal C, Buaruang K, Núñez-Zapata J, Amo de Paz G, Rico VJ, Molina MC, Elix JA, Esslinger TL, Tronstad IKK, Lindgren H, Ertz D, Gueidan C, Saag L, Mark K, Singh G, Dal Grande F, Parnmen S, Beck A, Benatti MN, Blanchon D, Candan M, Clerc P, Goward T, Grube M, Hodkinson BP, Hur J-S, Kantvilas G, Kirika PM, Lendemer J, Mattsson J-E, Messuti MI, Miadlikowska J, Nelsen M, Ohlson JI, Pérez-Ortega S, Saag A, Sipman HJM, Sohrabi M, Thell A, Thor G, Truong C, Yahr R, Upreti DK, Cubas P, Lumbsch HT (2015) Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi. New Phytol 208:1217–1226. doi: 10.1111/nph.13553 CrossRefPubMedGoogle Scholar
  22. Drummond AJ, Rambaut A (2007) Beast: Bayesian evoluionary analysis by sampling trees. BMC Evol Biol 7:214CrossRefPubMedPubMedCentralGoogle Scholar
  23. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4:699–710CrossRefGoogle Scholar
  24. Elix JA (1993) Progress in the generic delimitation of Parmelia sensu lato lichens (Ascomycotina: Parmeliaceae) and a synoptic key to the Parmeliaceae. Bryologist 96:359–383CrossRefGoogle Scholar
  25. Elix JA, Hale ME (1987) Canomaculina, Myelochroa, Parmelinella, Parmelinopsis and Parmotremopsis, five new genera in the Parmeliaceae (lichenized Ascomycotina). Mycotaxon 29:233–244Google Scholar
  26. Ferencova Z, Cubas P, Divakar PK, Molina MC, Crespo A (2014) Notoparmelia, a new genus of Parmeliaceae (Ascomycota) based on overlooked anatomical features, phylogeny and distribution pattern. Lichenologist 46:51–67CrossRefGoogle Scholar
  27. Gaya E, Navarro-Rosines P, Llimona X, Hladun N, Lutzoni F (2008) Phylogenetic reassessment of the Teloschistaceae (lichen-forming Ascomycota, Lecanoromycetes). Mycol Res 112:528–546. doi: 10.1016/j.mycres.2007.11.005 CrossRefPubMedGoogle Scholar
  28. Gaya E, Högnabba F, Holguin Á, Molnar K, Fernández-Brime S, Stenroos S, Arup U, Søchting U, Pvd Boom, Lücking R, Sipman HJM, Lutzoni F (2012) Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota). Mol Phylogenet Evol 63:374–387CrossRefPubMedGoogle Scholar
  29. Hale ME Jr (1974) Bulbothrix, Parmelina, Relicina, and Xanthoparmelia, four new genera in the Parmeliaceae. Phytologia 28:479–490Google Scholar
  30. Hale ME Jr (1984) An historical review of the genus concept in lichenology. Beiheft zur Nova Hedwigia 79:11–23Google Scholar
  31. Hawksworth DL, Rose F (1970) Qualitative scale for estimating sulphur dioxide air pollution in England and Wales using epiphytic lichens. Nature 227:145–148CrossRefPubMedGoogle Scholar
  32. Hawksworth DL, Rose F (1976) Lichens as pollution monitors. Institute of Biology’s studies in biology no. 66. Edward Arnold, LondonGoogle Scholar
  33. Hennig W (1966) Phylogenetic systematics. University of Illinois Press, ChampaignGoogle Scholar
  34. Ho SYW, Phillips MJ (2009) Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Syst Biol 58:367–380. doi: 10.1093/sysbio/syp035 CrossRefPubMedGoogle Scholar
  35. Holt BG, Jønsson KA (2014) Reconciling hierarchical taxonomy with molecular phylogenies. Syst Biol 63:1010–1017. doi: 10.1093/sysbio/syu061 CrossRefPubMedGoogle Scholar
  36. Humphreys AM, Barraclough TG (2014) The evolutionary reality of higher taxa in mammals. Proc R Soc B 281:20132750. doi: 10.1098/rspb.2013.2750 CrossRefPubMedPubMedCentralGoogle Scholar
  37. Humphreys AM, Rydin C, Jønsson KA, Alsop D, Callender-Crowe LM, Barraclough TG (2016) Detecting evolutionarily significant units above the species level using the generalised mixed Yule coalescent method. Methods Ecol Evol. doi: 10.1111/2041-210X.12603 Google Scholar
  38. Jaklitsch WM, Baral HO, Lücking R, Lumbsch HT (2016) Ascomycota. In: Frey W (ed) Syllabus of plant families—Adolf Engler’s Syllabus der Pflanzenfamilien, vol 1/2, 13th edn. Borntraeger Verlagsbuchhandlung, Stuttgart, Gebr, p 150Google Scholar
  39. Johns GC, Avise JC (1998) A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Mol Biol Evol 15:1481–1490CrossRefPubMedGoogle Scholar
  40. Kaasalainen U, Heinrichs J, Krings M, Myllys L, Grabenhorst H, Rikkinen J, Schmidt AR (2015) Alectorioid morphologies in Paleogene Lichens: new evidence and re-evaluation of the Fossil Alectoria succini Magdefrau. PLoS ONE 10(6):e0129526. doi: 10.1371/journal.pone.0129526 CrossRefPubMedPubMedCentralGoogle Scholar
  41. Kärnefelt I, Thell A (1993) Chemical evolution in cetrarioid lichens. In: Feige GB, Lumbsch HTe (eds) Phytochemistry and chemotaxonomy of lichenized Ascomycetes—A Festschrift in Honour of Siegfried Huneck. Bibliotheca Lichenologica, J. Cramer, Berlin, Stuttgart, pp 115–127Google Scholar
  42. Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9:286–298CrossRefPubMedGoogle Scholar
  43. Kirika PM, Leavitt SD, Divakar PK, Crespo A, Gatheri GW, Mugambi G, Lumbsch HT (2015) The monotypic genus Bulborrhizina belongs to Bulbothrix sensu lato (Parmeliaceae, Ascomycota). Bryologist 118:164–169. doi: 10.1639/0007-2745-118.2.164 CrossRefGoogle Scholar
  44. Kirika P, Divakar PK, Crespo A, Leavitt SD, Mugambi GK, Gatheri GW, Lumbsch HT (2016a) Polyphyly of the genus Canoparmelia—another example of incongruence between phenotype-based classification and molecular phylogeny within lichenized Ascomycota (Parmeliaceae). Phytotaxa 289:36–48CrossRefGoogle Scholar
  45. Kirika P, Divakar PK, Leavitt SD, Buaruang K, Crespo A, Mugambi GK, Gatheri GW, Lumbsch HT (2016b) The genus Relicinopsis is nested within Relicina (Parmeliaceae, Ascomycota). Lichenologist 48 (in press)Google Scholar
  46. Kondratyuk S, Jeong M-H, Yu NH, Kãrnefelt I, Thell A, Elix J, Kim J, Kondratyuk A, Hur J-S (2013) Four new genera of teloschistoid lichens (Teloschistaceae, Ascomycota) based on molecular phylogeny. Acta Bot Hung 55(3–4):251–274CrossRefGoogle Scholar
  47. Kondratyuk SY, Jeong M-H, Yu N-N, Kärnefelt I, Thell A, Elix JA, Kim J, Kondratiuk A, Hur J-S (2014a) A revised taxonomy for the subfamily Caloplacoideae (Teloschistaceae, Ascomycota) based on molecular phylogeny. Acta Botanica Hungarica 56(1–2):93–123CrossRefGoogle Scholar
  48. Kondratyuk SY, Jeong MH, Galanina IA, Yakovchenko LS, Yatsyna AP, Hur JS (2014b) Molecular phylogeny of placodioid lichen-forming fungi reveal a new genus, Sedelnikovaea. Mycotaxon 129:269–282. doi: 10.5248/129.269 CrossRefGoogle Scholar
  49. Kondratyuk SY, Kärnefelt I, Thell A, Elix JA, Kim J, Jeong M-H, Yu N-N, Kondratiuk A, Hur J-S (2014c) A revised taxonomy for the subfamily Xanthorioideae (Teloschistaceae, Ascomycota) based on molecular phylogeny. Acta Botanica Hungarica 56(1–2):141–178CrossRefGoogle Scholar
  50. Kraichak E, Divakar PK, Crespo A, Leavitt SD, Nelsen MP, Lücking R, Lumbsch HT (2015) A Tale of Two Hyper-diversities: diversification dynamics of the two largest families of lichenized fungi. Sci Rep 5:e10028CrossRefGoogle Scholar
  51. Kraichak E, Crespo A, Divakar PK, Leavitt SD, Lumbsch HT (2017) A temporal banding approach for consistent taxonomic ranking above the species level. Scientific Reports in reviewGoogle Scholar
  52. Lanfear R, Calcott B, Ho SY, Guindon S (2012) PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol 29:1695–1701CrossRefPubMedGoogle Scholar
  53. Lawrey JD, Diederich P (2003) Lichenicolous fungi: interactions, evolution, and biodiversity. Bryologist 106:81–120CrossRefGoogle Scholar
  54. Lawrey JD, Diederich P (2016) Lichenicolous fungi—worldwide checklist, including isolated cultures and sequences available.
  55. Linnaeus C (1767) Systema naturae. Edit. XII. StockholmGoogle Scholar
  56. Liu NG, Ariyawansa HA, Hyde KD, Maharachchikumbura SS, Zhao RL, Phillips AJL, Jayawardena RS, Thambugala KM, Dissanayake AJ, Wijayawardene NN, Liu JK, Liu ZY, Jeewon R, Jones EBG, Jumpathong J (2017) Perspectives into the value of genera, families and orders in classification. Mycosphere 7:1649–1668Google Scholar
  57. Lumbsch HT (2002) How objective are genera in euascomycetes? Perspect Plant Ecol Evol Syst 5:91–101CrossRefGoogle Scholar
  58. Lumbsch HT, Huhndorf SM (2010) Myconet Volume 14. Part One. Outline of Ascomycota—2009. Fieldiana (Life and Earth Sciences) 1:1–42CrossRefGoogle Scholar
  59. Magallon S (2010) Using fossils to break long branches in molecular dating: a comparison of relaxed clocks applied to the origin of angiosperms. Syst Biol 59:384–399. doi: 10.1093/sysbio/syq027 CrossRefPubMedGoogle Scholar
  60. Mattsson J-E, Wedin M (1999) A re-assessment of the family Alectoriaceae. Lichenologist 31:431–440CrossRefGoogle Scholar
  61. Miadlikowska J, Schoch CL, Kageyama SA, Molnar K, Lutzoni F, McCune B (2011) Hypogymnia phylogeny, including Cavernularia, reveals biogeographic structure. Bryologist 114:392–400. doi: 10.1639/0007-2745-114.2.392 CrossRefGoogle Scholar
  62. Miadlikowska J, Kauff F, Högnabba F, Oliver JC, Molnár K, Fraker E, Gaya E, Hafellner J, Hofstetter V, Gueidan C, Kukwa M, Lücking R, Björk C, Sipman HJM, Burgaz AR, Thell A, Passo A, Myllys L, Goward T, Fernández-Brime S, Hestmark G, Lendemer J, Lumbsch HT, Schmull M, Schoch C, Sérusiaux E, Maddison D, Arnold AE, Lutzoni F, Stenroos S (2014) Multigene phylogenetic synthesis for 1307 fungi representing 1139 infrageneric taxa, 312 genera and 66 families of the class Lecanoromycetes (Ascomycota). Mol Phylogenet Evol 79:132–168CrossRefPubMedGoogle Scholar
  63. Müller J (1888) Lichenes Paraguayenses a cl. Balansa lecti. Revue Mycologique 10:53–68, 113–120, 178–184Google Scholar
  64. Nelsen MP, Chavez N, Sackett-Hermann E, Thell A, Randlane T, Divakar PK, Rico VJ, Lumbsch HT (2011) The cetrarioid core group revisited (Lecanorales: Parmeliaceae). Lichenologist 43:537–551. doi: 10.1017/s0024282911000508 CrossRefGoogle Scholar
  65. Nylander JAA, Wilgenbusch JC, Warren DL, Swofford DL (2008) AWTY (Are We There Yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24:581–583CrossRefPubMedGoogle Scholar
  66. Papong K, Kantvilas G, Lumbsch HT (2011) Morphological and molecular evidence places Maronina into synonymy with Protoparmelia (Ascomycota: Lecanorales). Lichenologist 43:561–567. doi: 10.1017/s0024282911000284 CrossRefGoogle Scholar
  67. Persoh D, Rambold G (2002) Phacopsis - a lichenicolous genus of the family Parmeliaceae. Mycological Progress 1:43–55CrossRefGoogle Scholar
  68. Poinar GO Jr, Peterson EB, Platt JL (2000) Fossil Parmelia in new world amber. Lichenologist 32:263–269CrossRefGoogle Scholar
  69. Rambaut A (2007) TreeEdit v.1.0a10.
  70. Rambaut A (2009) FigTree 1.2.2.
  71. Rambaut A, Drummond AJ (2007) Tracer v1.4, Available from
  72. Rambold G, Triebel D (1992) The inter-lecanoralean associations. Bibl Lichenol 48:1–201Google Scholar
  73. Rikkinen J, Poinar GO (2002) Fossilised Anzia (Lecanorales, lichen-forming Ascomycota) from European Tertiary amber. Mycol Res 106:984–990. doi: 10.1017/s0953756202005907 CrossRefGoogle Scholar
  74. Samarakoon MC, Hyde KD, Promputtha I, Ariyawansa HA, Hongsanan S (2016) Divergence and ranking of taxa across the kingdoms Animalia, Fungi and Plantae. Mycosphere 7:1678–1689Google Scholar
  75. Sanderson MJ (1997) A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol Biol Evol 14:1218–1231CrossRefGoogle Scholar
  76. Schmull M, Miadlikowska J, Pelzer M, Stocker-Wörgötter E, Hofstetter V, Fraker E, Hodkinson BP, Reeb V, Kukwa M, Lumbsch HT, Kauff F, Lutzoni F (2011) Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genus Lecidea sensu Zahlbruckner (Lecanoromycetes, Ascomycota). Mycologia 103:983–1003. doi: 10.3852/10-234 CrossRefPubMedGoogle Scholar
  77. Simpson GG (1990) Principles of animal taxonomy. Columbia University Press, New YorkGoogle Scholar
  78. Singh G, Divakar PK, Dal Grande F, Otte J, Parnmen S, Wedin M, Crespo A, Lumbsch HT, Schmitt I (2013) The sister-group relationships of the largest family of lichenized fungi, Parmeliaceae (Lecanorales, Ascomycota). Fungal Biology 117:715–721. doi: 10.1016/j.funbio.2013.08.001 CrossRefPubMedGoogle Scholar
  79. Singh G, Dal Grande F, Divakar PK, Otte J, Leavitt SD, Szczepanska K, Crespo A, Rico VJ, Aptroot A, da Silva Caceres ME, Lumbsch HT, Schmitt I (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 CrossRefPubMedPubMedCentralGoogle Scholar
  80. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690CrossRefPubMedGoogle Scholar
  81. Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57:758–771. doi: 10.1080/10635150802429642 CrossRefPubMedGoogle Scholar
  82. Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56:564–577CrossRefPubMedGoogle Scholar
  83. Thell A (1995) Pycnoconidial types and their presence in cetrarioid lichens (Ascomycotina, Parmeliaceae). Cryptogam Bryol Lichenol 16:247–256Google Scholar
  84. Thell A, Högnabba F, Elix JA, Feuerer T, Kärnefelt I, Myllys L, Randlane T, Saag A, Stenroos S, Ahti T, Seaward MRD (2009) Phylogeny of the cetrarioid core (Parmeliaceae) based on five genetic markers. Lichenologist 41:489–511. doi: 10.1017/s0024282909990090 CrossRefGoogle Scholar
  85. Thell A, Crespo A, Divakar PK, Kärnefelt I, Leavitt SD, Lumbsch HT, Seaward MRD (2012) A review of the lichen family Parmeliaceae—history, phylogeny and current taxonomy. Nord J Bot 30:641–664. doi: 10.1111/j.1756-1051.2012.00008.x CrossRefGoogle Scholar
  86. Triebel D, Rambold G (1988) Cecidonia und Phacopsis (Lecanorales): zwei lichenicole Pilzgattungen mit cecidogenen Arten. Nova Hedwigia 47:279–309Google Scholar
  87. Triebel D, Rambold G, Elix JA (1995) A conspectus of the genus Phacopsis (Lecanorales). Bryologist 98:71–83CrossRefGoogle Scholar
  88. Wedin M, Döring H, Mattsson JE (1999) A multi-gene study of the phylogenetic relationships of the Parmeliaceae. Mycol Res 103:1185–1192CrossRefGoogle Scholar
  89. Wedin M, Döring H, Gilenstam G (2004) Saprotrophy and lichenization as options for the same fungal species on different substrata: environmental plasticity and fungal lifestyles in the Stictis-Conotrema complex. New Phytol 164:459–465CrossRefGoogle Scholar
  90. Wirtz N, Printzen C, Sancho LG, Lumbsch HT (2006) The phylogeny and classification of Neuropogon and Usnea (Parmeliaceae, Ascomycota) revisited. Taxon 55:367–376CrossRefGoogle Scholar
  91. Zachos FE (2011) Linnean ranks, temporal banding, and time-clipping: why not slaughter the sacred cow? Biol J Lin Soc 103:732–734CrossRefGoogle Scholar
  92. Zhao X, Leavitt SD, Zhao ZT, Zhang LL, Arup U, Grube M, Perez-Ortega S, Printzen C, Sliwa L, Lumbsch HT (2015) Towards a revised generic classification of lecanoroid lichens (Lecanoraceae, Ascomycota) based on molecular, morphological and chemical evidence. Fungal Diversity 78:293–304CrossRefGoogle Scholar
  93. Zhao R-L, Zhou J-L, Chen J, Margaritescu S, Sánchez-Ramírez S, Hyde KD, Callac P, Parra LA, Li G-J, Moncalvo J-M (2016) Towards standardizing taxonomic ranks using divergence times—a case study for reconstruction of the Agaricus taxonomic system. Fungal Divers 78:239–292. doi: 10.1007/s13225-016-0357-x CrossRefGoogle Scholar

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© School of Science 2017

Authors and Affiliations

  1. 1.Departamento de Biología Vegetal II, Facultad de FarmaciaUniversidad Complutense de MadridMadridSpain
  2. 2.Department of Botany, Faculty of ScienceKasetsart UniversityBangkokThailand
  3. 3.Department of Biology and M.L. Bean Life Science MuseumBrigham Young UniversityProvoUSA
  4. 4.Department of Biological Sciences, Institute of Ecology, Evolution and DiversityGoethe Universität and Senckenberg Biodiversity and Climate Research Centre (BiK-F)Frankfurt am MainGermany
  5. 5.Science & EducationThe Field MuseumChicagoUSA

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