Genetic distances within and among species in monophyletic lineages of Parmeliaceae (Ascomycota) as a tool for taxon delimitation

Molecular Phylogenetics and Evolution

Volumn 56, Issue 1, 2010, Pages 125-133

  Del Prado, Ruth ^a   Cubas, Paloma ^a   Lumbsch, H Thorsten ^b   Divakar, Pradeep K ^a   Blanco, Oscar ^c   de Paz, Guillermo Amo ^a   Molina, M Carmen ^d   Crespo, Ana ^a  

^a UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

^b FIELD MUSEUM OF NATURAL HISTORY   (United States)

^c Instituto Nacional del Consumo   (Spain)

^d UNIVERSIDAD REY JUAN CARLOS   (Spain)

Author keywords

Genetic distance threshold; Interspecific distances; Intraspecific distances; Parmelioid genera; Taxon delimitation

Indexed keywords

FUNGAL DNA; RIBOSOMAL SPACER DNA;

ARTICLE; ASCOMYCETES; CLASSIFICATION; DNA SEQUENCE; GENETICS; HAPLOTYPE; MOLECULAR EVOLUTION; PHYLOGENY; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; STATISTICAL MODEL;

ASCOMYCOTA; DNA, FUNGAL; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; HAPLOTYPES; LIKELIHOOD FUNCTIONS; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

ASCOMYCOTA; FUNGI; PARMELIACEAE;

EID: 77953598029     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.04.014     Document Type: Article

References (69)

1. Argüello A., Del-Prado R., Cubas P., and Crespo A. Parmelina quercina (Parmeliaceae, Lecanorales) includes four phylogenetically supported morphospecies. Biological Journal of the Linnean Society 91 (2007) 455-467
2. Avise J.C., and Aquadro C.F. A comparative summary of genetic distances in the vertebrates - patterns and correlations. Evolutionary Biology 15 (1982) 151-185
3. Baloch E., and Grube M. Pronounced genetic diversity in tropical epiphyllous lichen fungi. Molecular Ecology 18 (2009) 2185-2197
4. Blanco O., Crespo A., Elix J.A., Hawksworth D.L., and Lumbsch H.T. A molecular phylogeny and a new classification of parmelioid lichens containing Xanthoparmelia-type lichenan (Ascomycota: Lecanorales). Taxon 53 (2004) 959-975
5. Blanco O., Crespo A., Divakar P.K., Esslinger T.L., Hawksworth D.L., and Lumbsch H.T. Melanelixia and Melanohalea, two new genera segregated from Melanelia (Parmeliaceae) based on molecular and morphological data. Mycological Research 108 (2004) 873-884
6. Blanco O., Crespo A., Divakar P.K., Elix J.A., and Lumbsch H.T. Molecular phylogeny of parmotremoid lichens (Ascomycotina, Parmeliaceae). Mycologia 97 (2005) 150-159
7. Blanco O., Crespo A., Ree R.H., and Lumbsch H.T. Major clades of parmelioid lichens (Parmeliaceae, Ascomycota) and the evolution of their morphological and chemical diversity. Molecular Phylogenetics and Evolution 39 (2006) 52-69
8. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17 (2000) 540-552
9. Castresana J. Cytochrome b phylogeny and the taxonomy of great apes and mammals. Molecular Biology and Evolution 18 (2001) 465-471
10. Clauzade G., and Roux C. Likenoj de Okcidenta Europo. Ilustrita Determinlibro. - Bulletin de la Societe Botanique du Centre-Ouest, Nouvelle Serie, Numero Special 7 (1985), Royan, France
11. Crespo A., Blanco O., and Hawksworth D.L. The potential of mitochondrial DNA for establishing phylogeny and stabilising generic concepts in the parmelioid lichens. Taxon 50 (2001) 807-819
12. Crespo A., Molina M.C., Blanco O., Schroeter B., Sancho L.G., and Hawksworth D.L. rDNA ITS and β-tubulin gene sequence analyses reveal two monophyletic groups within the cosmopolitan lichen Parmelia saxatilis. Mycological Research 106 (2002) 788-795
13. Crespo A., Divakar P.K., Argüello A., Gasca C., and Hawksworth D.L. Molecular studies on Punctelia species of the Iberian Peninsula, with an emphasis on specimens newly colonizing Madrid. Lichenologist 36 (2004) 299-308
14. Crespo A., Lumbsch H.T., Mattsson J.E., Blanco O., Divakar P.K., Articus K., Wiklund E., Bawingan P.A., and Wedin M. Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene. Molecular Phylogenetics and Evolution 44 (2007) 812-824
15. Crespo A., and Pérez-Ortega S. 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 Suppl.1 (2009) 71-81
16. Crespo A., Ferencova Z., Pérez-Ortega S., Argüello A., Elix J.A., and Divakar P.K. Austroparmelina, a new Australasian lineage in parmelioid lichens (Parmeliaceae, Ascomycota): a multigene and morphological approach. Systematics and Biodiversity 8 (2010) 10·1080/14772001003738320
17. Del-Prado R., Schmitt I., Kautz S., Palice Z., Lücking R., and Lumbsch H.T. Molecular data place Trypetheliaceae in Dothideomycetes. Mycological Research 110 (2006) 511-520
18. DePriest P.T. Development of Mason E. Hale's list of epithets in the parmelioid genera (lichen-forming Ascomycotina): a bibliographic review. Bryologist 102 (1999) 442-461
19. Divakar P.K., Molina M.C., Lumbsch H.T., and Crespo A. Parmelia barrenoae, a new lichen species related to Parmelia sulcata (Parmeliaceae) based on molecular and morphological data. Lichenologist 37 (2005) 37-46
20. Divakar P.K., Blanco O., Hawksworth D.L., and Crespo A. Molecular phylogenetic studies on the Parmotrema reticulatum (syn. Rimelia reticulata) complex, including the confirmation of P. pseudoreticulatum as a distinct species. Lichenologist 37 (2005) 55-65
21. Divakar, P.K., Figueras, G., Hladun, N.L., Crespo. A., 2010. Morphological versus phylogenetic species: an example from Melanelixia glabra (Parmeliaceae, Ascomycota). Fungal Diversity, doi: 10·1007/513225-010-0027-3.
22. Elix J.A. Progress in the generic delimitation of Parmelia sensu lato lichens (Ascomycotina: Parmeliaceae) and a synoptic key to the Parmeliaceae. Bryologist 96 (1993) 359-383
23. Ellstrand N., and Roose M.L. Patterns of genotypic diversity in clonal plant species. American Journal of Botany 76 (1987) 123-131
24. Eriksson O.E., and Hawksworth D.L. Outline of the ascomycetes. Systema Ascomycetum 16 (1998) 83-301
25. Fazekas A.J., Kesanakurti P.R., Burgess K.S., Percy D.M., Graham S.W., Barrett S.C.H., Newmaster S.G., Hajibabaei M., and Husband B.C. Are plant species inherently harder to discriminate than animal species using DNA barcoding markers?. Molecular Ecology Resources 9 (2009) 130-139
26. Fuerer T., and Thell A. Parmelia ernstiae: a new macrolichen from Germany. Mitteilungen aus dem Institut für Allgemeine Botanik Hamburg 30-32 (2002) 49-60
27. Gardes M., and Bruns T.D. ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Molecular Ecology 2 (1993) 113-118
28. Gaya E., Navarro-Rosines P., Llimona X., Hladun N., and Lutzoni F. Phylogenetic reassessment of the Teloschistaceae (lichen-forming Ascomycota, Lecanoromycetes). Mycological Research 112 (2008) 528-546
29. Geml J., Laursen G.A., O'Neill K., Nusbaum H.C., and Taylor D.L. Beringian origins and cryptic speciation events in the fly agaric (Amanita muscaria). Molecular Ecology 15 (2006) 225-239
30. Giraud T., Refregier G., Le Gac M., de Vienne D.M., and Hood M.E. Speciation in fungi. Fungal Genetics and Biology 45 (2008) 791-802
31. Grube M., and Kroken S. Molecular approaches and the concept of species and species complexes in lichenized fungi. Mycological Research 104 (2000) 1284-1294
32. Hale Jr. M.E. Bulbothrix, Parmelina, Relicina, and Xanthoparmelia, four new genera in the Parmeliaceae. Phytologia 28 (1974) 479-490
33. Hale Jr. M.E. A monograph of the lichen genus Karoowia Hale (Ascomycotina: Parmeliaceae). Mycotaxon 35 (1989) 177-198
34. Hale Jr. M.E. A synopsis of the lichen genus Xanthoparmelia (Vainio) Hale (Ascomycotina, Parmeliaceae). Smithsonian Contributions to Botany 74 (1990) 1-250
35. Hale B.W., and DePriest P.T. Mason E. Hale's list of epithets in the parmelioid genera. Bryologist 102 (1999) 462-544
36. Hasegawa M., Kishino H., and Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22 (1985) 160-174
37. Hebert P.D.N., Ratnasingham S., and deWaard J.R. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London Series B, Biological Sciences 270 (2003) S96-S99
38. Hebert P.D.N., Stoeckle M.Y., Zemlak T.S., and Francis C.M. Identification of birds through DNA barcodes. PLoS Biology 3 (2004) e422
39. Huelsenbeck J.P., and Ronquist F. MrBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
40. Johns G.C., and Avise J.C. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Molecular Biology and Evolution 15 (1998) 1481-1490
41. Kauserud H., Stensrud O., Decock C., Shalchian-Tabrizi K., and Schumacher T. Multiple gene genealogies and AFLPs suggest cryptic speciation and long-distance dispersal in the basidiomycete Serpula himantioides (Boletales). Molecular Ecology 15 (2006) 421-431
42. Kress W.J., Wurdack K.J., Zimmer E.A., Weigt L.A., and Janzen D.H. Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America 102 (2005) 8369-8374
43. Krog H. Punctelia, a new lichen genus in the Parmeliaceae. Nordic Journal of Botany 2 (1982) 287-292
44. Kroken S., and Taylor J.W. A gene genealogical approach to recognize phylogenetic species boundaries in the lichenizaed fungus Letharia. Mycologia 93 (2001) 38-53
45. Lefébure T., Douady C.J., Gouy M., and Gibert J. Relationship between morphological taxonomy and molecular divergence within Crustacea: proposal of a molecular threshold to help species delimitation. Molecular Phylogenetics and Evolution 40 (2006) 435-447
46. Llimona X., and Hladun N.L. Checklist of the lichens and lichenicolous fungi of the Iberian Peninsula and Balearic Islands. Bocconea 14 (2001) 1-581
47. Lohtander K., Myllys L., Sundin R., Källersjö M., and Tehler A. The species pair concept in the lichen Dendrographa leucophaea (Arthoniales): analyses based on ITS sequences. Bryologist 101 (1998) 404-411
48. Lumbsch H.T. How objective are genera in euascomycetes? Perspectives in Plant Ecology. Evolution and Systematics 5 (2002) 91-101
49. Lumbsch H.T., Hipp A.L., Divakar P.K., Blanco O., and Crespo A. Accelerated evolutionary rates in tropical and oceanic parmelioid lichens (Ascomycota). BMC Evolutionary Biology 8 (2008) 257
50. Matute D.R., McEwen J.G., Montes B.A., San-Blas G., Bagagli E., Rauscher J.T., Restrepo A., Morais F., Nino-Vega G., and Taylor J.W. Cryptic speciation and recombination in the fungus Paracoccidioides brasiliensis as revealed by gene genealogies. Molecular Biology and Evolution 23 (2006) 65-73
51. Meyer C.P., and Paulay G. DNA barcoding: error rates based on comprehensive sampling. PLoS Biology 3 (2005) e422
52. Molina M.D., Crespo A., Blanco O., Lumbsch H.T., and Hawksworth D.L. Phylogenetic relationships and species concepts in Parmelia s.str. (Parmeliaceae) inferred from nuclear ITS rDNA and beta-tubulin sequences. Lichenologist 36 (2004) 37-54
53. Moritz C., and Cicero C. DNA barcoding: promise and pitfalls. PLoS Biology 2 (2004) 1529-1531
54. Myllys L., Lohtander K., Källersjö M., and Tehler A. Sequence insertions and ITS data provide congruent information on Roccella canariensis and R. tuberculata (Arthoniales, Euascomycetes) phylogeny. Molecular Phylogenetics and Evolution 12 (1999) 295-309
55. Nimis P.L. The Lichens of Italy (1993), Museo Regionale di Scienze Naturali, Torino
56. Nimis P.L. A critical appraisal of modern generic concepts in lichenology. Lichenologist 30 (1998) 427-438
57. Pringle A., Baker D.M., Platt J.L., Wares J.P., Latge J.P., and Taylor J.W. Cryptic speciation in the cosmopolitan and clonal human pathogenic fungus Aspergillus fumigatus. Evolution 59 (2005) 1886-1899
58. Seifert K.A. Progress towards DNA barcoding of fungi. Molecular Ecology Resources 9 (2009) 83-89
59. Seifert K.A., Samson R.A., deWaard J.R., Houbraken J., Levesque C.A., Moncalvo J.-M., Louis-Seize G., and Hebert P.D.N. 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 (2007) 3901-3906
60. Stuessy T.F. Plant Taxonomy. The Systematic Evaluation of Comparative Data (2009), Columbia University Press, New York
61. Strimmer K., and von Haeseler A. Puzzle. Maximum Likelihood Analysis for Nucleotide, Amino Acid, and two-state Data. Version 4.0 (1997), University of München, München
62. Summerbell R.C., Moore M.K., Starink-Willemse M., and Van Iperen A. ITS barcodes for Trichophyton tonsurans and T. equinum. Medical Mycology 45 (2007) 193-200
63. Taylor J.W., Jacobson D.J., Kroken S., Kasuga T., Geiser D.M., Hibbett D.S., and Fisher M.C. Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology 31 (2000) 21-32
64. Templeton A.R. Using phylogeographic analyses of gene trees to test species status and processes. Molecular Ecology 10 (2001) 779-791
65. Thell A., Feuerer T., Elix J.A., and Kärnefelt I. A contribution to the phylogeny and taxonomy of Xanthoparmelia (Ascomycota, Parmeliaceae). Journal of the Hattori Botanical Laboratory 100 (2006) 797-807
66. Thell A., Elix J.A., Feuerer T., Hansen E.S., Kärnefelt E.I., Schüler N., and Westberg M. Notes on the systematics, chemistry and distribution of European Parmelia and Punctelia species (lichenized ascomycetes). Sauteria 15 (2008) 545-559
67. Thompson J.D., Higgins D.G., and Gibson T.J. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22 (1994) 4673-4680
68. White T.J., Bruns T., Lee S., and Taylor J.W. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M.A., Gelfand D.H., Sninsky J.J., and White T.J. (Eds). PCR Protocols: A Guide to Methods and Applications (1990), New York Academic Press, Inc., New York 315-322
69. Wirtz N., Printzen C., and Lumbsch H.T. 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 (2008) 472-484