Phylogeny of the Gyalectales and Ostropales (Ascomycota, Fungi): Among and within order relationships based on nuclear ribosomal RNA small and large subunits

Molecular Phylogenetics and Evolution

Volumn 25, Issue 1, 2002, Pages 138-156

  Kauff, Frank ^a   Lutzoni, François ^b  

^a University of Koblenz Landau   (Germany)

^b DUKE UNIVERSITY   (United States)

Author keywords

Ascomycetes; Bayesian inference; Fungi; Gyalectales; Large subunit (LSU); Lichens; Markov chain Monte Carlo; Maximum Likelihood; Maximum Parsimony; Nuclear ribosomal DNA; Ostropales; Phylogeny; Small subunit (SSU)

Indexed keywords

ASCOMYCOTA; DNA, FUNGAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL; SEQUENCE ANALYSIS, DNA;

AGYRIACEAE; ASCOMYCOTA; BAEOMYCETACEAE; COENOGONIUM; DIMERELLA; FUNGI; GYALECTA; GYALECTALES; OSTROPALES; PETRACTIS;

EID: 0036395692     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(02)00214-2     Document Type: Article

References (61)

1. Alfaro, M.E., Zoller, S., Lutzoni, F., in press. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in accessing phylogentic confidence. Mol. Biol. Evol.
2. Barr, M.E., 1983. The Ascomycete connection. Mycologia 75 (1), 1-13.
3. Berbee, M.L., 1996. Loculoascomycete origins and evolution of filamentous ascomycete morphology based on 18S rRNA gene sequence data. Mol. Biol. Evol. 13 (3), 462-470.
4. Berbee, M.L., Carmean, D.A., Winka, K., 2000. Ribosomal DNA and resolution of branching order among the Ascomycota: How many nucleotides are enough? Mol. Phylogenet. Evol. 17, 337-344.
5. Berbee, M.L., Taylor, J.W., 1995. From 18S ribosomal sequence data to evolution of morphology among the fungi. Can. J. Bot. 73 (Suppl. 1), S677-S683.
6. Bhattacharya, D., Lutzoni, F., Reeb, V., Simon, D., Fernandez, F., 2000. Widespread occurrence of spliceosomal introns in the rDNA genes of Ascomycetes. Mol. Biol. Evol. 17 (12), 1971-1984.
7. Cunningham, C.W., 1997. Can three incongruence tests predict when data should be combined? Mol. Biol. Evol 14 (7), 733-740.
8. Eriksson, O.E., 1981. The families of bitunicate Ascomycetes. Opera Bot. 60, 1-220.
9. Eriksson, O.E., 1982. Outline of the Ascomycetes - 1982. Mycotaxon 15, 203-248.
10. Eriksson, O.E., Hawksworth, D.L., 1993. Outline of the Ascomycetes - 1993. Syst. Asc. 12 (1-2), 51-257.
11. Eriksson, O.E., Hawksworth, D.L., 1998. Outline of the Ascomycetes - 1998. Syst. Asc. 16, 83-298.
12. Felsenstein, J., 1981. A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biol. J. Linn. Socs. 16, 183-196.
13. Felsenstein, J., 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (4), 783-791.
14. Gargas, A., Taylor, J.W., 1992. Polymerase chain reaction (PCR) primers for amplifying and sequencing nuclear 18S rDNA from lichenized fungi. Mycologia 84 (4), 589-592.
15. Gilenstam, G., 1969. Studies in the lichen genus Conotrema. Arkiv för Botanik 7 (2), 149-179.
16. Hafellner, J., 1988. Principles of classification and main taxonomic groups. In: Galun, M. (Ed.), CRC Handbook of Lichenology, 3. CRC Press, Boca Raton, FL, pp. 41-52.
17. Hall, T.A., 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. 41, 95-98.
18. Hawksworth, D.L., 1985. Problems and prospects in the systematics of the Ascomycotina. Proc. Indian Acad. Sci. Plant Sci. 94, 319-339.
19. Hawksworth, D.L., Sutton, B.C., Ainsworth, G.C., 1983. Ainsworth and Bisby's Dictionary of the Fungi, seventh ed. CMI, Kew.
20. Hawksworth, D.L., Hill, D.J., 1984. The Lichen-forming Fungi. Chapman & Hall, New York.
21. Hawksworth, D.L., Eriksson, O.E., 1986. The names of accepted orders of ascomycetes. Syst. Asc. 5, 175-184.
22. Hawksworth, D.L., Kirk, P.M., Sutton, B.C., Pegler, D.N. (Eds.), 1995. Ainsworth & Bisby's Dictionary of the Fungi, eighth ed. CAB International, Wallingford, UK.
23. Henssen, A., Jahns, H.M., 1974. Lichenes. Georg Thieme Verlag, Stuttgart.
24. Honegger, R., 1996. Mycobionts. In: Nash III, T.H. (Ed.), Lichen Biology. Cambridge University Press, Cambridge, pp. 24-36.
25. Huelsenbeck, J.P., 2000. MrBayes: Bayesian inference of phylogeny, Distributed by the author (http://morphbank.ebc.uu.se/mrbayes/), University of Rochester, USA.
26. Kauff, F., Büdel, B., in prep. Ascoma ontogeny and apothecia antomy of Coenogonium (Coenogoniaceae, Ostropales, lichenized Ascomycetes).
27. Lapeyre, B., Michot, B., Feliu, J., Bachellerie, J.P., 1993. Nucleotide sequence of the Schizosaccharomyces pombe 25S ribosomal RNA and its phylogenetic implications. Nucl. Acids Res. 21, 3322.
28. Larget, B., Simon, D.L., 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16 (6), 750-759.
29. Li, S., 1996. Phylogenetic tree construction using Markov chain Monte Carlo. Ph.D. Dissertation, Ohio State University, Columbus, USA.
30. Lücking, R., Kalb, K., 2000. Foliikole Flechten aus Brasilien (vornehmlich Amazonien), inklusive einer Checkliste und Bemerkungen zu Coenogonium und Dimerella (Gyalectaceae). Bot. Jahrb. Syst. 122 (1), 1-61.
31. Lumbsch, H.T., Schmitt, I., Döring, H., Wedin, M., 2001. Molecular systematics supports the recognition of an additional order of Ascomycota: the Agyriales. Mycol. Res. 105 (1), 16-23.
32. Luttrell, E.S., 1951. Taxonomy of the pyrenomycetes. Univ. Missouri Studies 24, 1-120.
33. Lutzoni, F., Pagel, M., Reeb, V., 2001. Major fungal lineages are derived from lichen symbiotic ancestors. Nature 411, 937-940.
34. Lutzoni, F., Wagner, P., Reeb, V., Zoller, S., 2000. Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violationg positional homology. Syst. Biol. 49 (4), 628-651.
35. Mankin, A.S., Skryabin, K.G., Rubtsov, P.M., 1986. Identification of ten additional nucleotides in the primary structure of yeast 18S rRNA. Gene 44, 143-145.
36. Mau, B., 1996. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Ph.D. Dissertation, University of Wisconsin, Madison, USA.
37. Mau, B., Newton, M., 1997. Phylogenetic inference for binary data on dendrograms using Markov chain Monte Carlo. J. Comput. Graph. Stat. 6, 122-131.
38. Mau, B., Newton, M., Larget, B., 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo. Biometrics 55, 1-12.
39. Miadlikowska, J., Lutzoni, F., 2000. Phylogenetic revision of the genus Peltigera (lichen-forming Ascomycota) based on morphological, chemical and large subunit nuclear ribosomal RNA data. Int. J. Plant Sci. 161 (6), 925-958.
40. Miadlikowska, J., McCune, B., Lutzoni, F., 2001. Pseudocyphellaria perpetua, a new lichen from western North America. The Bryologist (in press).
41. Müller-Argoviensis, J., 1881. Lichenologische Beiträge XII. Flora 64, 100-112.
42. Nannfeldt, J.A., 1932. Studien über die Morphologie und Systematik der nicht-lichenisierten inoperculaten Discomyceten. Almqvist & Wiksells, Uppsala.
43. Platt, J.L., Spatafora, J.W., 2000. Evolutionary relationships of nonsexual lichenized fungi: molecular phylogenetic hypotheses for the genera Siphula and Thamnolia from SSU and LSU rDNA. Mycologia 92, 475-487.
44. Posada, D., Crandall, K.A., 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (9), 817-818.
45. Rannala, B., Yang, Z., 1994. Probability distribution of molecular biodiversity trees: a new method of phylogenetic inference. J. Mol. Evol. 3, 240-247.
46. Rehner, S.A., Samuels, G.J., 1994. Taxonomy and phylogeny of Gliocladium analysed from nuclear large subunit ribosomal DNA sequences. Mycol. Res. 98 (6), 625-634.
47. Sanderson, M.K., 1995. Objections to bootstrapping phylogenies: a critique. Syst. Biol. 44 (3), 299-320.
48. Sanderson, M.J., Wojciechowski, M.F., 2000. Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae). Syst. Biol. 49 (4), 671-685.
49. Sherwood, M.A., 1977. The ostropalean fungi. Mycotaxon 5, 1-255.
50. Spatafora, J.W., 1995. Ascomal evolution of filamentous ascomycetes: evidence from molecular data. Can. J. Bot. 73 (Suppl. 1), S811-S815.
51. Spatafora, J.W., Mitchell, T.G., Vilgalys, R., 1995. Analysis of genes coding for small-subunit rRNA sequences in studying phylogenetics of dematiaceous fungal pathogens. J. Clin. Microbiol. 33 (5), 1322-1326.
52. Suh, S.-G., Blackwell, M., 1999. Molecular phylogeny of the cleistothecial fungi placed in Cephalothecaceae and Pseudeurotiaceae. Mycologia 91, 836-848.
53. Swofford, D.L., 1998-2001. PAUP*: Phylogenetic Analysis Using Parsimony* and other methods, Version 4. Sinauer Associates, Sunderland, MA.
54. Tamura, K., Nei, M., 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512-526.
55. Tehler, A., 1996. Systematics, phylogeny and classification. In: Nash III, T.H. (Ed.), Lichen Biology. University Press, Cambridge, pp. 217-239.
56. Vêzda, A., 1965. Flechtensystematische Studien I. Die Gattung Petractis Fr. Preslia 37, 127-143.
57. Vilgalys, R., Hester, M., 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J. Bacteriol. 172 (8), 4238-4246.
58. Wheeler, W., 1990. Combinatorial weights in phylogenetic analysis: a statistical parsimony procedure. Cladistics 6, 269-275.
59. White, T.J., Bruns, S.L., Taylor, J.W., 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, M.A., Gelfand, D.H., Sninsky, J.J., White, T.J. (Eds.), PCR protocols: A Guide to Methods and Applications. Academic Press, New York, pp. 315-322.
60. Winka, K., Ahlberg, C., Eriksson, O.E., 1998. Are there lichenized Ostropales? Lichenologist 30 (4-5), 455-462.
61. Zahlbruc 3 kner, A., 1924. Catalogus lichenum universalis. 2. Gebr. Borutraeger, Leipzig.