Organisms Diversity & Evolution

, Volume 15, Issue 3, pp 447–458 | Cite as

Hidden diversity in the morphologically variable script lichen (Graphis scripta) complex (Ascomycota, Ostropales, Graphidaceae)

  • Ekaphan Kraichak
  • Robert Lücking
  • Andre Aptroot
  • Andreas Beck
  • Patrick Dornes
  • Volker John
  • James C. Lendemer
  • Matthew P. Nelsen
  • Gerhard Neuwirth
  • Aparna Nutakki
  • Sittiporn Parnmen
  • Mohammad Sohrabi
  • Tor Tønsberg
  • H. Thorsten Lumbsch
Original Article

Abstract

Graphis scripta, or script lichen, is a well-known species of crustose lichenized fungi, widely distributed in the temperate region of the Northern Hemisphere. It is now considered to be a species complex, but because of the lack of secondary chemistry and paucity of measurable morphological characters, species delimitation within the complex has been challenging and is thus far based on apothecium and ascospore morphology. In this study, we employed molecular as well as morphological data to assess phylogenetic structure and delimitation of lineages within the G. scripta complex. We generated sequences for four genetic markers (mtSSU, nuLSU, RPB2, and EF-1) and performed phylogenetic analyses. The resulting trees were used to determine the number of distinct lineages by applying a general mixed Yule-coalescent (GMYC) model and species tree estimation through maximum likelihood (STEM). Our analyses suggest between six and seven putative species within the G. scripta complex. However, these did not correspond to the taxa that were recently distinguished based on apothecium morphology and could not be circumscribed with the morphological characters that were traditionally used in the classification of the complex. Any formal taxonomic treatment will require additional sampling and evaluation of additional traits that potentially can characterize these clades.

Keywords

Crustose lichens General mixed Yule-coalescent method Species delimitation Species trees Taxonomy 

Notes

Acknowledgments

We would like to thank Kyle Huff (Roosevelt University) for helping with morphological measurements. The molecular work was performed at the Pritzker Laboratory for Molecular Systematics and Evolution at The Field Museum (Chicago).

References

  1. Acharius, E. (1809). Förteckning pa de i Sverige växande arter af Lafvarnes famille. Kongliga Vetenskaps Academiens Nya Handlingar, 30, 145–169.Google Scholar
  2. Arup, U., & Åkelius, E. (2009). A taxonomic revision of Caloplaca herbidella and C. furfuracea. The Lichenologist, 41(5), 465–480.CrossRefGoogle Scholar
  3. Bickford, D., Lohman, D. J., Sodhi, N. S., Ng, P. K. L., Meier, R., Winker, K., et al. (2007). Cryptic species as a window on diversity and conservation. Trends in Ecology & Evolution, 22(3), 148–155.CrossRefGoogle Scholar
  4. Blanco, O., Crespo, A., Elix, J. A., Hawksworth, D. L., & Lumbsch, H. T. (2004). A molecular phylogeny and a new classification of parmelioid lichens containing Xanthoparmelia-type lichenan (Ascomycota: Lecanorales). Taxon, 53(4), 959–975.CrossRefGoogle Scholar
  5. Carstens, B. C., & Dewey, T. A. (2010). Species delimitation using a combined coalescent and information-theoretic approach: an example from North American myotis bats. Systematic Biology, 59(4), 400–414.PubMedCentralCrossRefPubMedGoogle Scholar
  6. Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17, 540–552.CrossRefPubMedGoogle Scholar
  7. Coyne, J. A., & Orr, H. A. (2004). Speciation (pp. 1–545). Sinauer Associates Incorporated.Google Scholar
  8. Cracraft, J. (1983). Species concepts and speciation analysis. In R. Johnston (Ed.), Current Ornithology (Vol. 1, pp. 159–187). Springer.Google Scholar
  9. Crespo, A., & Lumbsch, H. T. (2010). Cryptic species in lichen-forming fungi. IMA Fungus, 1(2), 167–170.PubMedCentralCrossRefPubMedGoogle Scholar
  10. Crespo, A., & Ortega, S. P. (2009). Cryptic species and species pairs in lichens: a discussion on the relationship between molecular. Anales del Jardin Botánico de Madrid, 66(1), 71–81.CrossRefGoogle Scholar
  11. Czarnota, P., & Guzow-Krzemińska, B. (2010). A phylogenetic study of the Micarea prasina group shows that Micarea micrococca includes three distinct lineages. The Lichenologist, 42(1), 7–21.CrossRefGoogle Scholar
  12. Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9(8), 772.CrossRefPubMedGoogle Scholar
  13. de Queiroz, K. (2007). Species concepts and species delimitation. Systematic Biology, 56(6), 879–886.CrossRefPubMedGoogle Scholar
  14. Divakar, P. K., & Crespo, A. (2015). Molecular phylogenetic and phylogenomic approaches in studies of lichen systematics and evolution. In Recent Advances in Lichenology (pp. 45–60). New Delhi: Springer.Google Scholar
  15. Drummond, A. J., Ashton, B., Buxton, S., Cheung, M., Cooper, A., Duran, C., et al. (2014). Geneious v. 8.0.3. Biomatters.Google Scholar
  16. Erichsen, C. F. E. (1957). Flechtenflora von Nordwestdeutschland (pp. 1–411). Stuttgart: Gustav Fischer.Google Scholar
  17. Ezard, T., Fujisawa, T., & Barraclough, T. G. (2009). SPLITS: SPecies’ LImits by Threshold Statistics. Retrieved from http://R-Forge.R-project.org/projects/splits/
  18. Fontaneto, D., Iakovenko, N., Eyres, I., Kaya, M., Wyman, M., & Barraclough, T. G. (2011). Cryptic diversity in the genus Adineta Hudson & Gosse, 1886 (Rotifera: Bdelloidea: Adinetidae): a DNA taxonomy approach. Hydrobiologia, 662(1), 27–33.CrossRefGoogle Scholar
  19. Fujisawa, T., & Barraclough, T. G. (2013). Delimiting species using single-locus data and the generalized mixed Yule coalescent approach: a revised method and evaluation on simulated data sets. Systematic Biology, 62(5), 707–724.PubMedCentralCrossRefPubMedGoogle Scholar
  20. Garland, T., Jr., Dickerman, A. W., Janis, C. M., & Jones, J. A. (1993). Phylogenetic analysis of covariance by computer simulation. Systematic Biology, 42(3), 265–292.CrossRefGoogle Scholar
  21. Goldstein, P. Z., DeSalle, R., Amato, G., & Vogler, A. P. (2000). Conservation genetics at the species boundary. Conservation Biology, 14(1), 120–131.CrossRefGoogle Scholar
  22. Guindon, S., & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52(5), 696–704.CrossRefPubMedGoogle Scholar
  23. Hodkinson, B. P., & Lendemer, J. C. (2011). Molecular analyses reveal semi-cryptic species in Xanthoparmelia tasmanica. Bibliotheca Lichenologica, 106, 108–119.Google Scholar
  24. Högnabba, F., & Wedin, M. (2003). Molecular phylogeny of the Sphaerophorus globosus species complex. Cladistics, 19(3), 224–232.CrossRefGoogle Scholar
  25. Hudson, R. R. (1990). Gene genealogies and the coalescent process. In D. J. Futuyma & J. Antonivics (Eds.), Oxford surveys in evolutionary biology (Vol. 7, pp. 1–44). Oxford: Oxford University Press.Google Scholar
  26. Huelsenbeck, J. P., & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics (Oxford, England), 17, 754–755.CrossRefGoogle Scholar
  27. Kraichak, E., Parnmen, S., Lücking, R., Rivas Plata, E., Aptroot, A., Cáceres, M. E. S., et al. (2014). Revisiting the phylogeny of Ocellularieae, the second largest tribe within Graphidaceae (lichenized Ascomycota: Ostropales). Phytotaxa, 189, 52–81.CrossRefGoogle Scholar
  28. Kubatko, L. S., Carstens, B. C., & Knowles, L. L. (2009). STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics (Oxford, England), 25(7), 971–973.CrossRefGoogle Scholar
  29. Leavitt, S. D. S., Fankhauser, J. D. J., Leavitt, D. H. D., Porter, L. D. L., Johnson, L. A. L., & Clair, L. L. L. S. (2011). 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(3), 587–602.CrossRefPubMedGoogle Scholar
  30. Leavitt, S. D., Moreau, C. S., & Lumbsch, H. T. (2015). The dynamic discipline of species delimitation: progress toward effectively recognizing species boundaries in natural populations. In Recent Advances in Lichenology (pp. 11–44). New Delhi: Springer.Google Scholar
  31. Lendemer, J. C. J. (2011). A taxonomic revision of the North American species of Lepraria s.l. that produce divaricatic acid, with notes on the type species of the genus L. incana. Mycologia, 103(6), 1216–1229.CrossRefPubMedGoogle Scholar
  32. Lendemer, J. C., & Hodkinson, B. P. (2013). A radical shift in the taxonomy of Lepraria s.l.: molecular and morphological studies shed new light on the evolution of asexuality and lichen growth form diversification. Mycologia, 105(4), 994–1018.CrossRefPubMedGoogle Scholar
  33. Linnaeus, C. (1753). Species plantarum (pp. 1–639). Stockholm: Salvius.Google Scholar
  34. Lücking, R., Archer, A. W., & Aptroot, A. (2009). A world-wide key to the genus Graphis (Ostropales: Graphidaceae). The Lichenologist, 41(04), 363–452.CrossRefGoogle Scholar
  35. Lücking, R., Dal-Forno, M., Lawrey, J. D., Bungartz, F., Rojas, M. E. H., Hernández, J. E., et al. (2013). Ten new species of lichenized Basidiomycota in the genera Dictyonema and Cora (Agaricales: Hygrophoraceae), with a key to all accepted genera and species in the Dictyonema clade. Phytotaxa, 139(1), 1–38.CrossRefGoogle Scholar
  36. Lücking, R., Johnston, M. K., Aptroot, A., Kraichak, E., Lendemer, J. C., Boonpragob, K., et al. (2014). One hundred and seventy five new species of Graphidaceae: closing the gap or a drop in the bucket? Phytotaxa, 189, 7–38.CrossRefGoogle Scholar
  37. Lumbsch, H. T., & Leavitt, S. D. (2011). Goodbye morphology? A paradigm shift in the delimitation of species in lichenized fungi. Fungal Diversity, 50(1), 59–72.CrossRefGoogle Scholar
  38. Lumbsch, H. T., Mangold, A., Martin, M. P., & Elix, J. A. (2008). Species recognition and phylogeny of Thelotrema species in Australia (Ostropales, Ascomycota). Australian Systematic Botany, 21(3), 217–227.CrossRefGoogle Scholar
  39. Lumbsch, H. T., Parnmen, S., Rangsiruji, A., & Elix, J. A. (2010). Phenotypic disparity and adaptive radiation in the genus Cladia (Lecanorales, Ascomycota). Australian Systematic Botany, 23(4), 239–247.CrossRefGoogle Scholar
  40. Lumbsch, H. T., Parnmen, S., Kraichak, E., Papong, K. B., & Lücking, R. (2014). High frequency of character transformations is phylogenetically structured within the lichenized fungal family Graphidaceae (Ascomycota: Ostropales). Systematics and Biodiversity, 12(3), 271–291.CrossRefGoogle Scholar
  41. Mangold, A., Martin, M. P., Lücking, R., & Lumbsch, H. T. (2008). Molecular phylogeny suggests synonymy of Thelotremataceae within Graphidaceae (Ascomycota : Ostropales). Taxon, 57, 476–486.Google Scholar
  42. Mayr, E. (1963). Animal species and evolution (pp. 1–797). Cambridge: Harvard University Press.CrossRefGoogle Scholar
  43. McCune, B., & Schoch, C. (2009). Hypogymnia minilobata (Parmeliaceae), a New Lichen from Coastal California. The Bryologist, 112(1), 94–100.CrossRefGoogle Scholar
  44. Miller, M. A., Pfeiffer, W., & Schwartz, T. (2010). Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop (GCE), 2010, 1–8.Google Scholar
  45. Moncada, B., Coca, L. F., & Lücking, R. (2013). Neotropical members of Sticta (lichenized Ascomycota: Lobariaceae) forming photosymbiodemes, with the description of seven new species. The Bryologist, 116(2), 169–200.CrossRefGoogle Scholar
  46. Nee, S., May, R. M., & Harvey, P. H. (1994). The reconstructed evolutionary process. Philosophical Transactions: Biological Sciences, 344(1309), 305–311.CrossRefGoogle Scholar
  47. Neuwirth, G., & Aptroot, A. (2011). Recognition of four morphologically distinct species in the Graphis scripta complex in Europe. Herzogia, 24, 207–230.CrossRefGoogle Scholar
  48. Paradis, E. (2010). pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics (Oxford, England), 26, 419–420.CrossRefGoogle Scholar
  49. Paradis, E. (2013). Molecular dating of phylogenies by likelihood methods: a comparison of models and a new information criterion. Molecular Phylogenetics and Evolution, 67(2), 436–444. doi:10.1016/j.ympev.2013.02.008.CrossRefPubMedGoogle Scholar
  50. Paradis, E., Claude, J., & Strimmer, K. (2004). APE: analyses of phylogeneticsand evolution in R language. Bioinformatics, 20, 289–290.CrossRefPubMedGoogle Scholar
  51. 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(3), 841–849.Google Scholar
  52. Parnmen, S., Rangsiruji, A., Mongkolsuk, P., Boonpragob, K., Nutakki, A., & Lumbsch, H. T. (2012). Using phylogenetic and coalescent methods to understand the species diversity in the Cladia aggregata complex (Ascomycota, Lecanorales). PLoS ONE, 7(12), e52245.PubMedCentralCrossRefPubMedGoogle Scholar
  53. Parnmen, S., Cáceres, M. E. S., Lücking, R., & Lumbsch, H. T. (2013). Myriochapsa and Nitidochapsa, two new genera in Graphidaceae (Ascomycota: Ostropales) for chroodiscoid species in the Ocellularia clade. The Bryologist, 116(2), 127–133.CrossRefGoogle Scholar
  54. Pillon, Y., Hopkins, H. C. F., Rigault, F., Jaffré, T., & Stacy, E. A. (2014). Cryptic adaptive radiation in tropical forest trees in New Caledonia. New Phytologist, 202(2), 521–530.CrossRefPubMedGoogle Scholar
  55. Pons, J., Barraclough, T., Gomez-Zurita, J., Cardoso, A., Duran, D., Hazell, S., et al. (2006). Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology, 55(4), 595–609.CrossRefPubMedGoogle Scholar
  56. Printzen, C., & Ekman, S. (2002). Genetic variability and its geographical distribution in the widely disjunct Cavernularia hultenii. The Lichenologist, 34(2), 101–111.CrossRefGoogle Scholar
  57. Printzen, C., Ekman, S., & Tønsberg, T. (2003). Phylogeography of Cavernularia hultenii: evidence of slow genetic drift in a widely disjunct lichen. Molecular Ecology, 12(6), 1473–1486.Google Scholar
  58. Rambaut, A. (2012). FigTree. Version 1.4.2.Google Scholar
  59. Rehner, S. (2001). Primers for Elongation Factor 1-α (EF1-α). Assembling the fungal tree of life. Retrieved from http://www.aftol.org/pdfs/EF1primer.pdf
  60. Revell, L. J. (2011). phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3, 217–223.CrossRefGoogle Scholar
  61. Rivas Plata, E., & Lumbsch, H. T. (2011). Parallel evolution and phenotypic divergence in lichenized fungi: a case study in the lichen-forming fungal family Graphidaceae (Ascomycota: Lecanoromycetes: Ostropales). Molecular Phylogenetics and Evolution, 61(1), 45–63.CrossRefPubMedGoogle Scholar
  62. Rivas Plata, E., Lücking, R., & Lumbsch, H. T. (2012). A new classification for the lichen family Graphidaceae s.lat. (Ascomycota: Lecanoromycetes: Ostropales). Fungal Diversity, 52, 107–121.CrossRefGoogle Scholar
  63. Rivas Plata, E., Parnmen, S., Staiger, B., Mangold, A., Frisch, A., Weerakoon, G., Hernandez, J., et al. (2013). A molecular phylogeny of Graphidaceae (Ascomycota, Lecanoromycetes, Ostropales) including 428 species. MycoKeys, 6, 55–94.CrossRefGoogle Scholar
  64. Ruprecht, U., Lumbsch, H. T., Brunauer, G., Green, T. A., & Türk, R. (2010). Diversity of Lecidea (Lecideaceae, Ascomycota) species revealed by molecular data and morphological characters. Antarctic Science, 22(6), 727.CrossRefGoogle Scholar
  65. Sanderson, M. J. (2002). Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution, 19(1), 101–109.CrossRefPubMedGoogle Scholar
  66. Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9, 671–675.CrossRefPubMedGoogle Scholar
  67. Spribille, T., Klug, B., & Mayrhofer, H. (2011). A phylogenetic analysis of the boreal lichen Mycoblastus sanguinarius (Mycoblastaceae, lichenized Ascomycota) reveals cryptic clades correlated with fatty acid profiles. Molecular Phylogenetics and Evolution, 59(3), 603–614.CrossRefPubMedGoogle Scholar
  68. Staiger, B. (2002). Die Flechtenfamilie Graphidaceae. Stuttgart: Schweizerbart’sche Verlagsbuchhandlung.Google Scholar
  69. Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (Oxford, England), 22, 2688–2690.CrossRefGoogle Scholar
  70. Stamatakis, A., Hoover, P., & Rougemont, J. (2008). A Rapid Bootstrap Algorithm for the RAxML Web Servers. Systematic Biology, 57, 758–771.CrossRefPubMedGoogle Scholar
  71. Stenroos, S. K., & DePriest, P. T. (1998). SSU rDNA phylogeny of cladoniiform lichens. American Journal of Botany, 85(11), 1548–1559.CrossRefPubMedGoogle Scholar
  72. Talavera, G., & Castresana, J. (2007). Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology, 56, 564–577.CrossRefPubMedGoogle Scholar
  73. Tehler, A., & Irestedt, M. (2007). Parallel evolution of lichen growth forms in the family Roccellaceae (Arthoniales, Ascomycota). Cladistics, 23(5), 432–454.CrossRefGoogle Scholar
  74. 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.PubMedCentralPubMedGoogle Scholar
  75. Vogler, A. P., & Monaghan, M. T. (2007). Recent advances in DNA taxonomy. Journal of Zoological Systematics and Evolutionary Research, 45(1), 1–10.CrossRefGoogle Scholar
  76. Vondrák, J. (2012). Biomonitoring, ecology, and systematics of lichens. The Bryologist, 115(4), 636–637.CrossRefGoogle Scholar
  77. Vondrák, J., Říha, P., Arup, U., & Søchting, U. (2009). The taxonomy of the Caloplaca citrina group (Teloschistaceae) in the Black Sea region; with contributions to the cryptic species concept in lichenology. The Lichenologist, 41(6), 571–604.CrossRefGoogle Scholar
  78. Wedin, M., & Döring, H. (1999). The phylogenetic relationship of the Sphaerophoraceae, Austropeltum and Neophyllis (lichenized Ascomycota) inferred by SSU rDNA sequences. Mycological Research, 103(9), 1131–1137.CrossRefGoogle Scholar
  79. Wedin, M., Westberg, M., Crewe, A. T., & Tehler, A. (2009). Species delimitation and evolution of metal bioaccumulation in the lichenized Acarospora smaragdula (Ascomycota, Fungi) complex. Cladistics, 25(2), 161–172.CrossRefGoogle Scholar
  80. Wiens, J. J., & Penkrot, T. A. (2002). Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Systematic Biology, 51(1), 69–91.CrossRefPubMedGoogle Scholar
  81. 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.CrossRefPubMedGoogle Scholar
  82. Yost, J. M., Barry, T., Kay, K. M., & Rajakaruna, N. (2012). Edaphic adaptation maintains the coexistence of two cryptic species on serpentine soils. American Journal of Botany, 99(5), 890–897.CrossRefPubMedGoogle Scholar
  83. Zahlbruckner, A. (1923). Catalogus lichenum universalis (Vol. 2, pp. 1–701). Leipzig: Gebrüder Borntraeger.Google Scholar
  84. Zhang, J., Kapli, P., Pavlidis, P., & Stamatakis, A. (2013). A general species delimitation method with applications to phylogenetic placements. Bioinformatics (Oxford, England), 29(22), 2869–2876.CrossRefGoogle Scholar
  85. Zoller, S., Scheidegger, C., & Sperisen, C. (1999). PCR primers for the amplification of mitochondrial small subunit ribosomal DNA of lichen-forming ascomycetes. The Lichenologist, 31, 511–516.CrossRefGoogle Scholar

Copyright information

© Gesellschaft für Biologische Systematik 2015

Authors and Affiliations

  • Ekaphan Kraichak
    • 1
    • 2
  • Robert Lücking
    • 1
  • Andre Aptroot
    • 3
  • Andreas Beck
    • 4
  • Patrick Dornes
    • 5
  • Volker John
    • 6
  • James C. Lendemer
    • 7
  • Matthew P. Nelsen
    • 1
  • Gerhard Neuwirth
    • 8
  • Aparna Nutakki
    • 9
  • Sittiporn Parnmen
    • 10
  • Mohammad Sohrabi
    • 11
  • Tor Tønsberg
    • 12
  • H. Thorsten Lumbsch
    • 1
  1. 1.Science and EducationThe Field MuseumChicagoUSA
  2. 2.Department of Botany, Faculty of ScienceKasetsart UniversityBangkokThailand
  3. 3.ABL HerbariumSoestThe Netherlands
  4. 4.Botanische StaatssammlungMünchenGermany
  5. 5.PforzheimGermany
  6. 6.Pfalzmuseum für NaturkundeBad DürkheimGermany
  7. 7.Institute of Systematic BotanyNew York Botanical GardenBronxUSA
  8. 8.Ried/TumeltshamAustria
  9. 9.Department of Biological SciencesUniversity of ChicagoChicagoUSA
  10. 10.Department of Medical SciencesMinistry of Public HealthNonthaburiThailand
  11. 11.Iranian Research Organization for Science and Technology (IROST)TehranIran
  12. 12.Museum of Natural HistoryUniversity of BergenBergenNorway

Personalised recommendations