Higher level phylogenetic relationships of euascomycetes (Pezizomycotina) inferred from a combined analysis of nuclear and mitochondrial sequence data
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Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000) GenBank. — Nucleic Acids Research 28: 15–18.
Berbee ML (1996) Loculoascomycete origins and evolution of filamentous ascomycete morphology based on 18S rRNA gene sequence data. — Molecular Biology and Evolution 13: 462–470.
Berbee ML, Taylor JW (1992) Two classes based on fruiting-body characters and ribosomal DNA sequence. — Molecular Biology and Evolution 9: 278–284.
Berbee ML, Taylor JW (1992b) Convergence in ascospore discharge mechanism among pyrenomycete fungi based on 18S ribosomal RNA gene sequence. — Molecular Phylogenetics and Evolution 1: 59–71.
Berbee ML, Taylor JW (1995) From 18S ribosomal sequence data to evolution of morphology among the fungi. — Canadian Journal of Botany 73(Suppl. 1): S677–S683.
Berbee ML, Carmean DA, Winka K (2000) Ribosomal DNA and resolution of branching order among the Ascomycota: how many nucleotides are enough? — Molecular Phylogenetics and Evolution 17: 337–344.
Bhattacharya D, Lutzoni F, Reeb V, Simon D, Nason J, Fernandez F (2000) Widespread occurrence of spliceosomal introns in the rDNA genes of ascomycetes. — Molecular Biology and Evolution 17: 1971–1984.
Bruns TD, Szaro TM (1992) Rate and mode differences between nuclear and mitochondrial small rRNA genes in mushrooms. — Molecular Biology and Evolution 9: 836–855.
Carlini DB, Reece KS, Graves JE (2000) Actin gene family evolution and the phylogeny of coleoid cephalopods (Mollusca: Cephalopoda). — Molecular Biology and Evolution 17: 1353–1370.
Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. — Molecular Biology and Evolution 17: 540–552.
Cubero OF, Crespo A, Fathei J, Bridge PD (1999) DNA extraction and PCR amplification method suitable for fresh, herbarium-stored, lichenized and other fungi. — Plant Systematics and Evolution 216: 243–249.
Cunningham CW (1997) Can three incongruence tests predict when data should be combined? — Molecular Biology and Evolution 14: 733–740.
Eriksson OE (2000) Outline of Ascomycota — 2000. Myconet [ http://www.umu.se/myconet/curr/outline.00.html ]
Eriksson OE (2000b) Notes on ascomycete systematics. Nos. 2756–2939. — Myconet 4: 1–20.
Eriksson OE, Hawksworth DL (1993) Outline of the ascomycetes — 1993. — Systema Ascomycetum 12: 51–257.
Eriksson OE, Winka K (1997) Supraordinal taxa of Ascomycota. — Myconet 1: 1–16.
Farris JS, Källersjö M, Kluge AG, Bult C (1994) Testing significance of incongruence. — Cladistics 10: 315–319.
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. — Journal of Molecular Evolution 17: 368–376.
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. — Evolution 39: 783–791.
Gargas A, Taylor JW (1995) Phylogeny of Discomycetes and early radiations of the apothecial Ascomycotina inferred from SSU rDNA sequence data. — Experimental Mycology 19: 7–15.
Geiser DM, LoBuglio KF (2001) The monophyletic Plectomycetes: Ascosphaerales, Onygenales, Eurotiales. In: McLaughlin DJ, McLaughlin EG, Lemke PA (eds): The Mycota VII Part A, Systematics and Evolution, 201–219. Springer Verlag, Berlin.
Goldman N, Anderson JP, Rodrigo AG (2000) Likelihood-based tests of topologies in phylogenetics. — Systematic Biology 49: 652–670.
Hausner G, Reid J, Klassen GR (1992) Do galeate-ascospore members of the Cephalothecaceae, Endomycetaceae and Ophiostomataceae share a common phylogeny? — Mycologia 84: 870–881.
Hibbett DS, Pine EM, Langer E, Langer G, Donoghue MJ (1997) Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences. — Proceedings of the National Academy of Sciences of the United States of America 94: 12002–12006.
Höhnel F von (1907) Fragmente zur Mykologie. III. Mitteilung, Nr. 128. — Sitzungsberichte der kaiserlichen Akademie der Wissenschaften Wien, mathematisch-naturwissenschaftliche Klasse, Abteilung I, 116: 126–129.
Hong SG, Park YD, Jeong W, Bae KS (2000) Sequence comparison of mitochondrial small subunit ribosomal DNA in Penicillium. — Journal of Microbiology 38: 62–65.
Huelsenbeck JP (2000) MrBayes: Bayesian inference of phylogeny. Distr. by the author. Dept. of Biology. University of Rochester/USA.
Huelsenbeck JP, Crandall KA (1997) Phylogeny estimation and hypothesis testing using maximum likelihood. — Annual Reviews in Ecology and Systematics 28: 437–466.
Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order of the Hominoidea. — Journal of Molecular Evolution 29: 170–179.
Kluge AG, Farris JS (1969) Quantitative phyletics and the evolution of anurans. — Systematic Zoology 18: 1–32.
Larget B, Simon DL (1999) Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. — Molecular Biology and Evolution 16: 750–759.
Li SX, Tam YK, Hartman GL (2000) Molecular differentiation of Fusarium solani f. sp. glycines from other F. solani based on mitochondrial small subunit rDNA sequences. — Phytopathology 90: 491–497.
Lindemuth R, Wirtz N, Lumbsch HT (2001) Multi-gene analysis of nuclear and mitochondrial sequence data supports that loculoascomycetes (Ascomycota) are not monophyletic. — Mycological Research 105: 1176–1181.
Liu YJ, Whelen S, Hall BD (1999) Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. — Molecular Biology and Evolution 16: 1799–1808.
Lumbsch HT, Lindemuth R, Schmitt I (2000) Evolution of filamentous ascomycetes inferred from LSU rDNA sequence data. — Plant Biology 2: 525–529.
Lumbsch HT, Schmitt I, Messuti MI (2001) Utility of nuclear SSU and LSU rDNA data sets to discover the ordinal placement of the Coccotremataceae (Ascomycota). — Organisms, Diversity and Evolution 1: 99–112.
Lumbsch HT, Schmitt I, Döring H, Wedin W (2001) Molecular systematics supports the recognition of an additional order of Ascomycota: the Agyriales. — Mycological Research 105: 16–23.
Luttrell ES (1951) Taxonomy of the pyrenomycetes. — University of Missouri Studies 24: 1–120.
Lutzoni F, Pagel M, Reeb V (2001) Major fungal lineages are derived from lichen symbiotic ancestors. — Nature 411: 937–940.
Maddison WP, Maddison DR (1992) MacClade. Vers. 3. Sinauer, Sunderland/MA.
Nannfeldt JA (1932) Studien über die Morphologie und Systematik der nicht-lichenisierten inoperculaten Discomyceten. — Nova Acta Regiae Societatis Scientiarum Upsaliensis, series IV 8(2): 1–368.
Nikoh N, Fukatsu T (2000) Interkingdom host jumping underground: Phylogenetic analysis of entomoparasitic fungi of the genus Cordyceps. — Molecular Biology and Evolution 17: 629–638.
Page RDM (1996) Treeview: An application to display phylogenetic trees on personal computers. — Computer Applied Biosciences 12: 357–358.
Pagel M (1994) Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. — Proceedings of the Royal Society, London B 255: 37–45.
Pagel M (1999) The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. — Systematic Biology 48: 612–622.
Pine EM, Hibbett DS, Donoghue MJ (1999) Phylogenetic relationships of cantharelloid and clavarioid Homobasidiomycetes based on mitochondrial and nuclear rDNA sequences. — Mycologia 91: 944–963.
Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. — Bioinformatics 14: 817–818.
Poulsen R, Schmitt I, Søchting U, Lumbsch HT (2001) Molecular and morphological studies on the genus Orceolina (Agyriaceae). — Lichenologist 33: 323–329.
Rambaut A, Grassly NC (1997) Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. — Computer Applied Biosciences 13: 235–238.
Saenz GS, Taylor JW, Gargas A (1994) 18S rRNA gene sequences and supraordinal classification of the Erysiphales. — Mycologia 86: 212–216.
Schluter D, Price T, Mooers AØ, Ludwig D (1997) Likelihood of ancestor states in adaptive radiation. — Evolution 51: 1699–1711.
Schmitt I, Lumbsch HT (2001) Identification of the photobionts in Trapeliopsis and Pertusaria using SSU ribosomal DNA sequences obtained from PCR amplification with a non-green-algal primer. — Mycotaxon 78: 407–411.
Schmitt I, Messuti MI, Feige GB, Lumbsch HT (2001) Molecular data suggest rejection of the generic concept in the Coccotremataceae. — Lichenologist 33: 315–321.
Spatafora JW (1995) Ascomal evolution of filamentous ascomycetes: evidence from molecular data. — Canadian Journal of Botany 73(Suppl. 1): S811–S815.
Stenroos SK, dePriest PT (1998) SSU rDNA phylogeny of cladoniiform lichens. — American Journal of Botany 85: 1548–1559.
Sugiyama M, Ohara A, Mikawa T (1999) Molecular phylogeny of onygenalean fungi based on small subunit ribosomal DNA (SSU rDNA) sequences. — Mycoscience 40: 251–258.
Suh S-O, Blackwell M (1999) Molecular phylogeny of the cleistothecial fungi placed in Cephalothecaceae and Pseudoeurotiaceae. — Mycologia 91: 836–848.
Swofford D L (1998) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, MA.
Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. — Molecular Biology and Evolution 10: 512–526.
Tehler A (1995) Morphological data, molecular data, and total evidence in phylogenetic analysis. — Canadian Journal of Botany 73(Suppl. 1): S667–S676.
Tehler A, Farris JS, Lipscomb DL, Källersjö M (2000) Phylogenetic analyses of the fungi based on large rDNA data sets. — Mycologia 92: 459–474.
Thompson JD, Higgins DG, Gibson TJ (1994) 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: 4673–4680.
Winka K (2000) Phylogenetic relationships within the Ascomycota based on 18S rDNA sequences. Ph D thesis, Umeå University, Umeå.