Using genetic distances in addition to ITS molecular phylogeny to identify potential species in the Parmotrema reticulatum complex: A case study

Lichenologist

Volumn 43, Issue 6, 2011, Pages 569-583

  Del Prado, Ruth ^a   Divakar, Pradeep K ^a   Crespo, Ana ^a  

^a UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

Author keywords

cryptic species; lichens; Parmeliaceae; species complexes; species identification

Indexed keywords

EID: 84856396817     PISSN: 00242829     EISSN: 10961135     Source Type: Journal    
DOI: 10.1017/S0024282911000582     Document Type: Article

References (78)

1. Argüello, A., Del-Prado, R., Cubas, P. & Crespo, A. (2007) Parmelina quercina (Parmeliaceae, Lecanorales) includes four phylogenetically supported morphospecies. Biological Journal of the Linnean Society 91: 455-467.
2. Clauzade, G. & Roux, C. (1986) ['1985'] Likenoj de Okcidenta Europo. Ilustrita Determinlibro. Bulletin de la Société Botanique du Centre-Ouest, Nouvelle Séries, Numero Special 7: 1-893.
3. Crespo, A. & Lumbsch, H. T. (2010) Cryptic species in lichen-forming fungi. IMA Fungus 1: 167-170.
4. Crespo, A. & Pérez-Ortega, S. (2009) Cryptic species and species pairs in lichens: a discussion on the relationship between molecular phylogenies and morphological characters. Anales del Jardín Botánico de Madrid 66: 71-81.
5. Crespo, A., Blanco, O. & Hawksworth, D. L. (2001) The potential of mitochondrial DNA for establishing phylogeny and stabilising generic concepts in the parmelioid lichens. Taxon 50: 807-819.
6. 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: 1735-1753.
7. Culberson, C. F. (1972) Improved conditions and new data for the identification of lichen products by a standardized thin-layer chromatographic method. Journal of Chromatography 72: 113-125.
8. 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: 125-133.
9. De Queiroz, K. (2007) Species concepts and species delimitation. Systematic Biology 56: 879-886.
10. Divakar, P. K. & Upreti, D. K. (2005) Parmelioid Lichens in India (A Revisionary Study). Dehra Dun: Bishen Singh Mahendra Pal Singh.
11. Divakar, P. K., Upreti, D. K. & Elix, J. A. (2001) New species and new records in the lichen family Parmeliaceae (Ascomycotina) from India. Mycotaxon 80:355-362.
12. Divakar, P. K., Molina, M. C., Lumbsch, H. T. & Crespo, A. (2005a) Parmelia barrenoae, a new lichen species related to Parmelia sulcata (Parmeliaceae) based on molecular and morphological data. Lichenologist 37: 37-46.
13. Divakar, P. K., Blanco, O., Hawksworth, D. L. & Crespo, A. (2005b) Molecular phylogenetic studies on the Parmotrema reticulatum (syn. Rimelia reticulata) complex, including the confirmation of P. pseudoreticulatum. Lichenologist 37: 55-65.
14. Divakar, P. K., Figueras, G., Hladun, N. & Crespo, A. (2010a) Morphological versus phylogenetic species: an example from Melanelixia glabra (Parmeliaceae, Ascomycota). Fungal Diversity 42: 47-55.
15. Divakar, P. K., Cubas, P., Blanco, O., Del-Prado, R., Núñez-Zapata, J., Roca-Valiente, B., Lumbsch, H. T & Crespo, A. (2010b) An overview on hidden diversity in lichens: Parmeliaceae. 〈imc9.info/prog-sig3-detail-divakar.htm〉
16. Elix, J. A. (1994a) Rimelia. Flora of Australia 55: 186-188.
17. Elix, J. A. (1994b) Lichens, Lecanorales 2, Parmeliaceae. Flora Australia 55: 1-360.
18. Elix, J. A. & Ernst-Russell, K. D. (1993) A Catalogue of Standardized Thin Layer Chromatographic Data and Biosynthetic Relationships for Lichen Substances, 2nd edn. Canberra: Australian National University.
19. Elix, J. A., Corush, J. & Lumbsch, H.T. (2009) Triterpene chemosyndromes and subtle morphological characters characterise lineages in the Physcia aipolia group in Australia (Ascomycota). Systematics and Biodiversity 7: 479-487.
20. Fazekas, A. J., Kesanakurti, P. R., Burgess, K. S., Percy, D. M., Graham, S. W., Barrett, S. C. H., Newmaster, S. G., Hajibabaei, M. & Husband, B. C. (2009) Are plant species inherently harder to discriminate than animal species using DNA barcoding markers? Molecular Ecology Resources 9: 130-139.
21. Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
22. Gardes, M. & Bruns, T. D. (1993) ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Molecular Ecology 2: 113-118.
23. Grube, M. & Kroken, S. (2000) Molecular approaches and the concept of species and species complexes in lichenized fungi. Mycological Research 104: 1284-1294.
24. Hale, M. E. (1965) A monograph of Parmelia subgenus Amphigymnia. Contributions from the United States National Herbarium 36: 193-358.
25. Hale, B. W. & DePriest, P. T. (1999) Mason E. Hale's list of epithets in the parmelioid genera. Bryologist 102: 462-544.
26. Hale, M. E. & Fletcher, A. (1990) Rimelia Hale & Fletcher, a new lichen genus (Ascomycotina: Parmeliaceae). Bryologist 93: 23-29.
27. Hebert, P. D. N., Cywinska, A., Ball, S. L. & deWaard, J. R. (2003a) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, Series B 270: 313-321.
28. Hebert, P. D. N., Ratnasingham, S. & deWaard, J. R. (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London, Series B 270: S96-S99.
29. Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D. H. & Hallwachs, W. (2004a) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the Natinal Academy of Sciences of the United States of America 101(41): 14812-14817.
30. Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S. & Francis, C. M. (2004b) Identification of birds through DNA barcodes. PLoS Biology 3: e422.
31. Hebert, P. D. N., deWaard, J. R. & Landry, J. F. (2010) DNA barcodes for 1/1000 of the animal kingdom. Biology Letters 6: 359-362.
32. Hey, J. & Wakeley, J. (1997) A coalescent estimator of the population recombination rate. Genetics 145:833-846.
33. Hollingsworth, P. M., Forrest, L. L., Spouge, J. L., Hajibabaei, M., Ratnasingham, S., Van der Bank, M., Chase, M. W., Cowan, R. S., Erickson, D. L., Fazekas, A. J. et al. (2009) A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America 106: 12794-12797.
34. Holsinger, K. E. & Weir, B. S. (2009) Genetics in geographically structured populations: defining, estimating and interpreting FST. Nature Review Genetics 10: 639-650.
35. Hudson, R. R., Slatkin, M. & Maddison, W. P. (1992) Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.
36. Huelsenbeck, J. P. & Ronquist, F. (2001) MrBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
37. Kelly, L. J., Hollingsworth, P. M., Coppins, B. J., Ellis, C .J., Harrold, P., Tosh, J. & Yahr, R. (2011) DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context. New Phytologist in press (doi: 10.1111/j.1469-8137.2011. 03677.x).
38. Kress, W. J., Wurdack, K. J., Zimmer, E. A., Weigt, L. A. & Janzen, D. H. (2005) Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America 102: 8369-8374.
39. Krog, H. & Swinscow, T. D. V. (1981) Parmelia subgenus Amphigymnia (lichens) in East Africa. Bulletin of the British Museum (Natural History), Botany Series 9: 143-231.
40. Kroken, S. & Taylor, J. W. (2001) A gene genealogical approach to recognize phylogenetic species boundaries in the lichenized fungus Letharia. Mycologia 93: 38-53.
41. Kurokawa, S. (1991) Japanese species and genera of Parmeliaceae. Journal of Japanese Botany 66: 152-159.
42. Kurokawa, S. (2003) Checklist of Japanese Lichens. Tokyo: National Science Museum.
43. Larena, I., Salazar, O., González, V., Julián, M. C. & Rubio, V. (1999) Design of a primer for ribosomal DNA internal transcribed spacer with enhanced specificity for ascomycetes. Journal of Biotechnology 75: 187-194.
44. Lefébure, T., Douady, C. J., Gouy, M. & Gibert, J. (2006) Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation. Molecular Phylogenetics and Evolution 40: 435-447.
45. Liu, K., Raghavan, S., Nelesen, S., Linder, C. R. & Warnow, T. (2009) Rapid and accurate largescale coestimation of sequence alignments and phylogenetic trees. Science 324: 1561-1564.
46. Liu, J., Moller, M., Gao, L. M., Zhang, D. Q. & Li, D. Z. (2011) DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species. Molecular Ecology Resources 11: 89-100.
47. Llimona, X. & Hladun, N. L. (2001) Checklist of the lichens and lichenicolous fungi of the Iberian Peninsula and Balearic Islands. Bocconea 14: 1-581.
48. Lohtander, K., Myllys, L., Sundin, R., Källersjö, M. & Tehler, A. (1998) The species pair concept in the lichen Dendrographa leucophaea (Arthoniales): analyses based on ITS sequences. Bryologist 101: 404-411.
49. Lumbsch,H. T. (2002) Analysis of phenolic products in lichens for identification and taxonomy. In Protocols in Lichenology. Culturing, Biochemistry, Ecophysiology and Use in Biomonitoring (I. Kranner, R. P. Beckett & A. K. Varma, eds): 281-295. Berlin: Springer.
50. Meyer, C. P.&Paulay, G. (2005)DNAbarcoding: error rates based on comprehensive sampling. PLoS Biol 3: e422.
51. Molina, M. C., Crespo, A., Blanco, O., Lumbsch,H. T. &Hawksworth,D. L. (2004) Phylogenetic relationships and species concepts in Parmelia s. str. (Parmeliaceae) inferred from nuclear ITS rDNA and β-tubulin sequences. Lichenologist 36: 37-54.
52. Molina, M. C., Del-Prado, R., Divakar, P. K., Sánchez-Mata, D. & Crespo, A. (2011) Another example of cryptic diversity in lichen-forming fungi: the new species Parmelia mayi (Ascomycota: Parmeliaceae). Organism Diversity and Evolution, (in press).
53. Moon, K. H., Kurokawa, S. & Kashiwadani, H. (2000) A list of Thailand species of Parmelia (sens. lat.) preserved in the National Science Museum. In Proceedings of the First and Second Symposia on Collection Building and Natural History Studies in Asia (K., Matsuura, ed): 97-106. Tokyo: National Science Museum Monographs.
54. Moon, K. H., Kurokawa, S. & Kashiwadani, H. (2001) The genus Rimelia (lichens) from the Hawaiian Islands. Journal of Japanese Botany 76: 321-328.
55. 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.
56. Nilsson, R. H., Kristiansson, E., Ryberg, M., Hallenberg, N. & Larsson, K. (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: 193-201.
57. Nylander, J. A. A.,Wilgenbusch, J. C., Warren, D. L. & Swofford, D. L. (2007) AWTY (Are we there yet?): A system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24: 581-583.
58. Posada, D. (2008) jModelTest: Phylogenetic model averaging. Molecular Biology and Evolution 25: 1253-1256.
59. Rambaut, A. & Drummond, A. J. (2003) Tracer [computer program]. Available from website http://tree.bio.ed.ac.uk/software/tracer/
60. Räsänen, A. V. (1944) Lichenes Novi I. Annales Botanici Societatis Zoologicae-Botanicae Fennicae "Vanamo" 20(3): 1-34.
61. Rodríguez, F., Oliver, J. F., Martín, A. & Medina, J. R. (1990) The general stochastic model of nucleotide substitution. Journal of Theoretical Biology 142: 485-501.
62. Ross, K. G., Gotzek, D., Ascunce, M. S. & Shoemaker, D. D. (2010) Species delimitation: a case study in a problematic ant taxon. Systematic Biology 59: 162-184.
63. Seifert, K. A., Samson, R. A., deWaard, J. R., Houbraken, J., Levesque, C. A., Moncalvo, J.-M., Louis-Seize, G. & Hebert, P. D. N. (2007) Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proceedings of the National Academy of Sciences of the United States of America 104: 3901-3906.
64. Simon, U. K. & Weiss, M (2008) Intragenomic variation of fungal ribosomal genes is higher than previously thought. Molecular Biology and Evolution 25: 2251-2254.
65. Smith, M. E., Douhan, G. W. & Rizzo, D. M. (2007) Intra-specific and intra-sporocarp ITS variation of ectomycorrhizal fungi as assessed by rDNA sequencing of sporocarps and pooled ectomycorrhizal roots from a Quercus woodland. Mycorrhiza 18: 15-22.
66. Stamatakis, A., Ludwig, T. & Meier, H. (2005) RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21: 456-463.
67. Stamatakis, A., Hoover, P. & Rougemont, J. (2008) A rapid bootstrap algorithm for the RAxML webservers. Systematic Biology 57: 758-771.
68. Strimmer, K. & von Haeseler, A. (1997) Puzzle. Maximum Likelihood Analysis for Nucleotide, Amino Acid, and two-state Data. Version 4.0. Munich: University of Munich.
69. Swinscow, T. D. V & Krog, H. (1988) Macrolichens of East Africa. London: British Museum (Natural History).
70. Swofford, D. L. (2003). PAUP*. Phylogenetic Analysis Using Parsimony (*and OtherMethods). Sunderland, Massachusetts: Sinauer Associates.
71. Tavares, C. N. (1945) Contribução para o estudo das Parmeliáceas Portuguesas. Portugaliae Acta Biologica, serie B. 1: 1-210.
72. Taylor, T. (1836) Musci, hepaticae and lichens. In Flora Hibernica (J.T. Mackay, ed.) 2: 1-156. Dublin: W. Curry.
73. Taylor, J. W., Jacobson, D. J., Kroken, S., Kasuga, T., Geiser, D. M., Hibbett, D. S. & Fisher, M.C. (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology 31: 21-32.
74. Vialle, A., Feau, N., Allaire, M., Didukh, M., Martin, F., Moncalvo, J. M. & Hamelin, R. C. (2009) Evaluation of mitochondrial genes as DNA barcode for Basidiomycota. Molecular Ecology Resources 9 (suppl 1): 99-113.
75. Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R. & Hebert, P. D. N. (2005) DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society, Biological Sciences 360: 1847-1857.
76. Ward, R. D., Holmes, B. H. & O'Hara, T. D. (2008) DNA barcoding discriminates echinoderm species. Molecular Ecology Resources 8: 1202-1211.
77. Wedin, M., Westberg, M., Crewe, A. T., Tehler, A. & Purvis, O.W. (2009) Species delimitation and evolution of metal bioaccumulation in the lichenized Acarospora smaragdula (ascomycota, fungi) complex. Cladistics 25: 161-172.
78. Zemlak, T. S.,Ward, R. D., Connell, A. D., Holmes, B. H. & Hebert, P. D. N. (2009) DNA barcoding reveals overlooked marine fishes. Molecular Ecology Resources 9 (Suppl. 1): 237-242.