Phenotypical plasticity and homoplasy complicate species delimitation in the Cladonia gracilis group (Cladoniaceae, Ascomycota)

Organisms Diversity and Evolution

Volumn 11, Issue 5, 2011, Pages 343-355

  Pino Bodas, Raquel ^a   Burgaz, Ana Rosa ^a   Martín, María P ^b   Lumbsch, H Thorsten ^c  

^a UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

^b CSIC   (Spain)

^c FIELD MUSEUM OF NATURAL HISTORY   (United States)

Author keywords

Genealogical concordance phylogenetic species recognition; Lichens; Morphology; Taxonomy; Variability

Indexed keywords

CONSPECIFIC; FUNGUS; LICHEN; MORPHOLOGY; PHENOTYPIC PLASTICITY; PHYLOGENETICS; PHYLOGENY; SPECIMEN BANK; TAXONOMY;

ASCOMYCOTA; CLADONIA CONIOCRAEA; CLADONIA GRACILIS; CLADONIACEAE;

EID: 84855664997     PISSN: 14396092     EISSN: 16181077     Source Type: Journal    
DOI: 10.1007/s13127-011-0062-2     Document Type: Article

References (83)

1. Agapow, P. M., & Burt, A. (2001). Indices of multilocus linkage disequilibrium. Molecular Ecology Notes, 1, 101-102. (Pubitemid 33691862)
2. Ahti, T. (1980a). Taxonomic revision of Cladonia gracilis and its allies. Annales Botanici Fennici, 17, 195-243.
3. Ahti, T. (1980b). Nomenclatural notes on Cladonia species. The Lichenologist, 12, 125-133.
4. Ahti, T. (2000). Cladoniaceae. Flora Neotropica Monographs, 78, 1-362.
5. Ahti, T., & Hammer, S. (2002). Cladonia. In T. H. Nash III, B. D. Ryan, C. Gries, & F. Bungartz (Eds.), Lichen Flora of the Greater Sonora Desert Region, volumen 1 (pp. 131-158). Tempe: Thomson-Shore.
6. Ahti, T., & DePriest, P. (2005). 1657-1665) Proposals to conserve eight names and reject one species name in Cladoniaceae (Fungi. Taxon, 54, 183-188.
7. Articus, K., Mattsson, J. E., Tibell, L., Grube, M., & Wedin, M. (2002). Ribosomal DNA β-tubulin data do not support the separation of the lichens Usnea florida and U. subfloridana as distinct species. Mycological Research, 106, 412-418. (Pubitemid 34805337)
8. Boni, M. F., Posada, D., & Feldman, M. W. (2007). An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics, 176, 1035-1047. (Pubitemid 46961105)
9. Briggs, D. (1964). Experimental taxonomy of some British species of the genus Dicranum. New Phytologist, 64, 366-386.
10. Brodo, I., & Ahti, T. (1996). Lichen and lichenicolous fungi of Queen Charlotte Islands, British Columbia, Canada. 2. The Cladoniaceae. Canadian Journal of Botany, 74, 1147-1180.
11. Brodo, I. M., Duran Sharnoff, S., & Sharnoff, S. (2001). Lichens of North America. New Haven & London: Yale University Press.
12. Brown, A. H. D., Feldman, M. W., & Nevo, E. (1980). Multilocus structure of natural populations of Hordeum spontaneum. Genetics, 96, 523-536.
13. Bruen, T., Philippe, H., & Bryant, D. (2006). A quick and robust statistical test to detect the presence of recombination. Molecular Biology and Evolution, 172, 2665-2681.
14. Burt, A., Carter, D. A., Koenig, G. L., White, T. J., & Taylor, J. W. (1996).Molecular markers reveal cryptic sex in the human pathogen Coccidioides immitis. Proceedings of the National Academy of Sciences of the United States of America, 93, 770-773. (Pubitemid 26041166)
15. Burgaz, A. R., & Ahti, T. (2009). Cladoniaceae. Flora Ibérica Liquenológica, 4, 1-111.
16. Buschbom, J., & Mueller, G. M. (2006). Testing "Species Pair" hypotheses: Evolutionary processes in the lichen-forming species complex Porpidia flavocoerulescens and Porpidia melinodes. Molecular Biology and Evolution, 23, 574-586. (Pubitemid 43278269)
17. Canfield, M. R., Greene, E., Moreau, C. S., Chen, N., & Pierce, N. E. (2008). Exploring phenotypic plasticity and biogeography in emerald moths: A phylogeny of genus Nemoria (Lepidoptera: Geometridae). Molecular Phylogenetics and Evolution, 49, 477-487.
18. Cunningham, C. W. (1997). Can three incongruences tests predict when data should be combined? Molecular Biology and Evolution, 14, 733-740. (Pubitemid 27287294)
19. Dahl, E. (1950). Studies in the macrolichen flora of southwest Greenland. Meddelelser om Gronland, 150, 1-176.
20. Awasthi, D. D., & Ahti, T. (2007). Cladonia. In D. D. Awasthi (Ed.), A compendium of the macrolichens from India, Nepal and Sri Lanka (pp. 79-116). Dehra Dun: Bishen Singh Mahandra Pal Singh.
21. Davis, J. I. (1983). Phenotypic plasticity and the selection of taxonomic characters in Puccinellia (Poaceae). Systematic Botany, 8, 341-353.
22. Farris, J. S., Källersjö, M., Kluge, A. G., & Bult, C. (1994). Testing significance of incongruence. Cladistics, 10, 315-319.
23. Felsentein, J. (1985). Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution, 39, 783-791.
24. Fontaine, K. M., Ahti, T., & Piercey-Normore, M. D. (2010). Convergent evolution in Cladonia gracilis and allies. The Lichenologist, 42, 323-338.
25. Gardes, M., & Bruns, T. D. (1993). ITS primers with enhanced specificity for Basidiomycetes-aplication to the identification of mycorrhize and rust. Molecular Ecology, 2, 113-118.
26. Gibbs, M. J., Armstrong, J. S., & Gibbs, A. J. (2000). Sister-Scanning: A Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics, 16, 573-582.
27. Hammer, S. (1991). A preliminary synopsis of the species of Cladonia in California and adjacent Oregon. Mycotaxon, 40, 169-197.
28. Hammer, S. (1993). Development in Cladonia ochrochlora. Mycologia, 85, 84-92.
29. Hammer, S. (1995). A synopsis of the genus Cladonia in the Northwestern United States. Bryologist, 98, 1-28.
30. Hammer, S., & Ahti, T. (1990). New and interesting species of Cladonia from California. Mycotaxon, 37, 335-348.
31. Hollander, J., & Butlin, R. K. (2010). The adaptive value of phenotypic plasticity in two ecotypes of a marine gastropod. BMC Evolutionary Biology, 10, 333
32. Huelsenbeck, J. P., & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17, 754-755. (Pubitemid 32851390)
33. Huson, D. H., & Bryant, D. (2006). Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution, 23, 254-267. (Pubitemid 43100040)
34. James, P. W. (2009). Cladonia. In C. W. Smith et al. (Eds.), The lichens of Great Britain and Ireland (pp. 309-338). London: Natural History Museum Publications.
35. Kaplan, Z. (2002a). Phenotipic plasticity in Potamogeton (Potamogenaceae). Folia Geobotanica, 37, 141-170.
36. Liu, Y. J., Whelen, S., & Hall, B. D. (1999). Phylogenetic relationships among Ascomycetes: Evidence from an RNA polymerase II subunit. Molecular Biology and Evolution, 16, 1808-1999.
37. Lohtander, K., Myllys, L., Sundin, R., Källersjö, M., & Tehler, A. (1998a). The species pair concept in the lichen Dendrographa leucophaea (Arthoniales): Analyses based on ITS sequences. Bryologist, 101, 404-411. (Pubitemid 28460973)
38. Lohtander, K., Källersjö, M., & Tehler, A. (1998b). Dispersal strategies in Rocellina capensis (Arthoniales). The Lichenologist, 30, 341-350. (Pubitemid 28478401)
39. Lortie, C. J., & Aarssen, L. W. (1996). The speciation hypothesis for phenotypic plasticity in plants. International Journal of Plant Sciences, 157, 484-487.
40. Lumbsch, H. T. (2004). Comparison of homoplasy supports that characters have no a priori value in phylogenetic analyses of lichenized ascomycetes. Bibliotheca Lichenologica, 88, 427-431.
41. Lutzoni, F., Kauff, F., Cox, C., McLaughlin, D., Celio, G., Dentinger, B., et al. (2004). Assembling the fungal tree of life: Progress, classification, and evolution of subcellular traits. American Journal of Botany, 91, 1446-1480. (Pubitemid 43193713)
42. Maddison, W. P., Maddison, D. R. (2007). Mesquite: A modular system for evolutionary analysis. Version 2.74. http://mesquiteproject.org.
43. Martin, D. P., Williamson, C., & Posada, D. (2005). RDP2: Recombination detection and analysis from sequence alignments. Bioinformatics, 21, 260-262. (Pubitemid 40202028)
44. Maynard Smith, J. (1992). Analyzing the mosaic structure of genes. Journal of Molecular Evolution, 34, 126-129.
45. Maynard Smith, J., Smith, N. H., O'Rourke, E. M., & Spratt, B. G. (1993). How clonal are bacteria? Proceedings National Academy of Sciences Of the United States of America, 90, 4384-4388. (Pubitemid 23148908)
46. Myllys, L., Lohtander, K., Källersjö, M., & Tehler, A. (1999). Sequence insertions and ITS data provide congruent information on Roccella canariensis and R. tuberculata (Arthoniales, Euascomycetes) phylogeny. Molecular Phylogenetics and Evolution, 12, 295-309. (Pubitemid 129499309)
47. Myllys, L., Lohtander, K., & Tehler, A. (2001). β-tubulin, ITS and group I intron sequences challenge the species pair concept in Physcia aipolia and P. caesia. Mycologia, 93, 335-343.
48. Nash, T. H., III, Boucher, V. L., Gebauer, R., & Larson, D. W. (1990). Morphological and physiological plasticity in Ramalina menziesii: Studies with reciprocal transplants between a coastal and inland site. In H. M. Jahns (Ed.), Contributions to Lichenology in Honour of A. Henssen. Bibliotheca Lichenologica, 38 (pp. 357- 365). Berlin-Stuttgart: J. Cramer.
49. Nelsen, M. P., & Gargas, A. (2009). Assessing clonality and chemotype monophyly in Thamnolia (Icmadophilaceae). Bryologist, 112, 42-53.
50. Nimis, P. L. (1993). The lichens of Italy. An annotated catalogue. Torino: Museo Regionale di Scienze Naturali Monografie XII
51. Nylander, J. A. A. (2004). MrModelTest 2.1. Program distributed by the author. Uppsala: Evolutionary Biology Centre, Uppsala University.
52. Nylander, J. A. 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, 581-583. (Pubitemid 351256305)
53. Padidam, M., Sawyer, S., & Fauquet, C. M. (1999). Possible emergence of new geminiviruses by frequent recombination. Virology, 265, 218-225. (Pubitemid 30022217)
54. Piercey-Normore, M. D., & DePriest, P. T. (2001). Algal switching among lichen symbionts. American Journal of Botany, 88, 1490-1498.
55. Pigliucci, M., Cammell, K., & Schmitt, J. (1999). Evolution of phenotypic plasticity a comparative approach in the phylogenetic neighbourhood of Arabidopsis thaliana. Journal of Evolution and Biology, 12, 779-791. (Pubitemid 29311752)
56. Pino-Bodas, R., Burgaz, A. R., & Martín, M. P. (2010). Elucidating the taxonomic rank of Cladonia subulata versus C. rei (Cladoniaceae). Mycotaxon, 113, 311-326.
57. Pintado, A., Valladares, F., & Sancho, L. G. (1997). Exploring phenotypic plasticity in the lichen Ramalina capitata: Morphology, water relations and chlorophyll content in north- and southfacing populations. Annals of Botany, 80, 345-353. (Pubitemid 27393069)
58. Poelt, J., Vezda, A. (1981). Bestimmungsschlüssel europäischer Flechten. Ergänzungsheft II. Bibliotheca Lichenologica, 16. Vaduz: J. Cramer.
59. Posada, D., & Crandall, K. A. (2001). Evaluation of methods for detecting recombination from DNA sequences: Computer simulations. Proceedings of the National Academy of Sciences of the United States of America, 98, 13757-13762. (Pubitemid 33115971)
60. Rambaut, A. (2002). Sel-Al: Sequences aligment editor v 2.0011. Edinburgh: Institute of Evolutionary Biology, University of Edinburgh. http://tree.bio.ed.ac.uk/software/.
61. Rikkinen, J. (1997). Habitat shifts and morphological variation of Pseudevernia furfuracea along a topographical gradient. Symbolae Botanicae Upsalienses, 32, 223-245.
62. Salminen, M. O., Carr, J. K., Burke, D. S., & McCutchan, F. E. (1995). Identification of breakpoints in intergenotypic recombinants of HIV type 1 by Bootscanning. AIDS Research and Human Retroviruses, 11, 1423-1425.
63. Sandstede, H. (1931). Die Gattung Cladonia. Rabenhorst's Kryptogamen-Flora von Deutschland, Österreich und der Schweiz, 9, 1-531.
64. Schichting, C. D. (2002). Phenotypic plasticity in plants. Plant Species Biology, 17, 85-88.
65. Schmidt, H. A., Strimmer, K., Vingron, M., & von Haeseler, A. (2002). TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics, 18, 502-504. (Pubitemid 34284960)
66. Schwerdtner, H., & Cordes, H. (1992). Zur Bedeutung von Mikrostandorten für kleinräumige Verteilung von Flechten auf Totholz. International Journal of Mycology and Lichenology, 5, 121-136.
67. Shimodaira, H., & Hasegawa, M. (1999). Multiple comparisons of log-likehoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16, 1114-1116. (Pubitemid 29368141)
68. Stamatakis, A. (2006). RAxML-VI-HPC: Maximum-likelihood-based phylogenetic 1118 analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688-2690. (Pubitemid 44642609)
69. Stenroos, S., Hyvönen, J., Myllys, L., Thell, A., & Ahti, T. (2002). Phylogeny of the genus Cladonia s. lat. (Cladoniaceae, Ascomycetes) inferred from molecular, morphological, and chemical data. Cladistics, 18, 237-278.
70. Stenroos, S., Ferraro, L., & Ahti, T. (1992). Cladoniaceae. Flora Criptogámica de Tierra del Fuego, 13, 1-111.
71. Strimmer, K., & Rambaut, A. (2002). Inferring confidence sets of possibly misspecified gene trees. Proceedings of the Royal Society B, 269, 137-142. (Pubitemid 34107156)
72. Sultan, S. D. (1987). Evolutionary implications of phenotypic plasticity in plants. Evolutionary Biology, 21, 127-178.
73. Swofford, D. L. (2003). PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10. Sunderland. Massachusetts: Sinauer Associates.
74. Taylor, J. W., Jacobson, D. J., Kroken, S., Kasuga, T., Geiser, D. M., Hibbett, D. S., et al. (2000). Species recognition and species concepts in fungi. Fungal Genetics and Biology, 29, 21-32.
75. Thomson, J. W. (1968). The lichen genus Cladonia in North America. Toronto: University of Toronto Press.
76. Thomson, J. W. (2003). Lichens of Wisconsin. Madison: University of Wisconsin.
77. Trussell, G. C. (1996). Phenotypic plasticity in an intertidal snail: The role of a common crab predator. Evolution, 50, 448-454.
78. White, T. J., Bruns, T., Lee, S., & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, & T. J. White (Eds.), PCR protocols (pp. 315-322). San Diego: Academy Press.
79. Whitman, D., & Ananthakrishnan, T. N. (2008). Phenotypic plasticity in insects: Mechanisms and consequences. US: Science Publisher.
80. Wirth, V. (1995). Flechtenflora. Stuttgart: Ulmer.
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.
82. Yahr, R., Vilgalys, R.,&DePriest, P. T. (2006).Geographic variation in algal partners ofCladonia subtenuis (Cladoniaceae) highlights the dynamic nature of a lichen symbiosis. New Phytologist, 171, 847-860. (Pubitemid 44175204)
83. Zhang, X., Ren, A., Ci, H., & Gao, Y. (2010). Genetic diversity and structure of Neotyphodium species and their host Achnatherum sibiricum in a natural grass-endophyte system. Microbial Ecology, 59, 744-756.