Phylogenetic analyses of the fungi based on large rDNA data sets

LITERATURE CITED

• Alexopoulos CJ, Mims CW. 1979. Introductory mycology. New York: J. Wiley and Sons. 632 p.
   Google Scholar
• Alexopoulos CJ, Mims CW., Blackwell M. 1996. Introductory mycology. 4th ed. New York: J. Wiley and Sons. 868 p.
   Google Scholar
• Barr DJS. 1983. The zoosporic grouping of fungi-entity or nonentity. In: Buczacki ST, ed. Zoosporic plant pathogens—a modern perspective. London: Academic Press. p 43–83.
   Google Scholar
• Barr DJS.. 1992. Evolution and kingdoms of organisms from the perspective of a mycologist. Mycologia 84: 1–11.
   Web of Science ®Google Scholar
• Bessey EA. 1942. Some problems in fungus phylogeny. Mycologia 34: 355–379.
   Google Scholar
• Brims TD, Vilgalys R, Barns SM, Gonzalez D, Hibett DS, Lane JD, Simon L, Stickel S, Szaro TM, Weisburg WG, Sogin ML. 1992. Evolutionary relationships within the Fungi: analyses of nuclear small subunit rRNA sequences. Mol Phyl Evol 1: 231–241.
   Web of Science ®Google Scholar
• Brims TD, Vilgalys R, Barns SM, Gonzalez D, Hibett DS, Lane JD, Simon L, Stickel S, Szaro TM, Weisburg WG, Sogin ML., White TJ, Taylor JW. 1991. Fungal molecular systematics. Annu Rev Ecol Syst 22: 525–564.
   Google Scholar
• Carpenter JM. 1996. Uninformative bootstrapping. Cladistics 12: 177–180.
   PubMed Web of Science ®Google Scholar
• Cavalier-Smith T. 1987. The origin of fungi and pseudofungi. In: Rayner ADM, Brasier CN, Moore D, eds. Evolutionary biology of the fungi. Cambridge: Cambridge Univ. Press. p 339–353.
   Google Scholar
• Cavalier-Smith T.. 1991. Archamobae: the ancestral eukaryotes? BioSystems 25: 25–38.
   Web of Science ®Google Scholar
• Celerin M, Ray JM, Schisler NJ, Day AW, Stetler-Stevenson WG, Laudenbach DE. 1996. Fungal fimbriae are composed of collagen. EMBOJ 15: 4445–4453.
   PubMed Web of Science ®Google Scholar
• Curry KJ. 1985. Ascosporogenesis in Dipodascopsis tothii (Hemiascomycetidae). Mycologia 77: 401–411.
   Web of Science ®Google Scholar
• Donoghue MJ, Doyle JA 1989. Phylogenetic analysis of seed plants and angiosperms based on morphological characters. In: Fernholm B, Bremer K, Jörnvall H, eds. The hierarchy of life. Amsterdam: Elsevier Science Publishers. p 181–195.
   Google Scholar
• Eriksson O. 1981. The families of bitunicate Ascomycetes. Opera Bot 60: 1–220.
   Google Scholar
• Eriksson O., Winka K. 1997. Supraordinal taxa of Ascomycota. Myconet 1: 1–16.
   Google Scholar
• Eriksson O., Winka K.. 1998. Families and higher taxa of Ascomycota. Myconet 1: 17–24.
   Google Scholar
• Farris JS. 1995. Jac: Parsimony Jackknifer. Version 4.2. Stockholm: Molekylärsystematiska laboratoriet, Naturhistoriska riksmuseet.
   Google Scholar
• Farris JS.. 1997. Xac: Parsimony Jackknifer. Stockholm: Molekylärsystematiska laboratoriet, Naturhistoriska riksmuseet.
   Google Scholar
• Farris JS.. 1999. Likelihood and inconsistency. Cladistics 15: 199–204.
   Web of Science ®Google Scholar
• Farris JS., Albert VA, Källersjö M, Lipscomb D, Kluge AG. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12: 99–124.
   PubMed Web of Science ®Google Scholar
• Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27: 401–410.
   Google Scholar
• Felsenstein J.. 1985. Confidence limits on phylogenetics: an approach using the bootstrap. Evolution 39: 783–791.
   PubMed Web of Science ®Google Scholar
• Gargas A, DePriest PT, Grube M, Tehler A. 1995. Multiple origins of lichen symbiosis in fungi suggested by SSU rDNA phylogeny. Science 268: 1492–1495.
   PubMed Web of Science ®Google Scholar
• Gargas A, DePriest PT, Grube M, Tehler A., Taylor JW. 1995. Phylogeny of Discomycetes and early radiations of the apothecial Ascomycotina inferred from SSU rDNA sequence data. Exp Mycol 19: 7–15.
   PubMedGoogle Scholar
• Gauthier J, Kluge AG, Rowe T. 1988. Amniote phylogeny and the importance of fossils. Cladistics 4: 105–209.
   PubMed Web of Science ®Google Scholar
• Hawksworth DL. 1991. The fungal dimension of biodiversity: magnitude, significance, and conservation. Mycol Res 95: 641–655.
   Web of Science ®Google Scholar
• Hawksworth DL., Kirk PM, Sutton BC, Pegler DN. 1995. Ainsworth's & Bisby's dictionary of the fungi. 8th ed. Cambridge: University Press. 616 p.
   Google Scholar
• Hawksworth DL., Kirk PM, Sutton BC, Pegler DN., Sutton BC, Ainsworth GC. 1983. Ainsworth's & Bisby's dictionary of the fungi. 7th ed. Kew, UK: Commonwealth Mycological Institute. 445 p.
   Google Scholar
• Hibett DS, Pine EM, Langer E, Langer G, Donoghue MJ. 1997. Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences. Proc Natl Acad Sci USA 94: 12002–12006.
   Web of Science ®Google Scholar
• Huelsenbeck JP. 1998. Systematic bias in phylogenetic analysis: Is the Strepsiptera problem solved? Syst Biol 47: 519–537.
   Web of Science ®Google Scholar
• Jahn TL. 1949. How to know the Protozoa. Dubuque, Iowa: William C. Bown. 234 p.
   Google Scholar
• Klein RM, Cronquist A. 1967. A consideration of the evolutionary and taxonomic significance of some biochemical, micromorphological, and physiological characters in the Thallophytes. Quart Rev Biol 42: 105–296.
   PubMed Web of Science ®Google Scholar
• Källersjö M, Farris JS, Chase M, Bremer B, Fay M, Humphries C, Pedersen G, Seberg O, Bremer K. 1998. Simultaneous parsimony jackknife analysis of 2538 rbcl DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants. Pl Syst Evol 213: 259–287.
   Web of Science ®Google Scholar
• Lipscomb DL. 1989. Relationships among the eukaryotes. In: Fernholm B, Bremer Kr, Jörnvall H, eds. The hierarchy of life. Amsterdam: Elsevier Science Publishers B.V. p 161–178.
   Google Scholar
• Lipscomb DL.. 1991. The kingdoms and the protozoa. In: Kreier JP, Baker JR, eds. Parasitic protozoa. 2nd ed. New York: Academic Press. p 81–136.
   Google Scholar
• Lipscomb DL., Farris JS, Källersjö M, Tehler A. 1998. Support, ribosomal sequences, and the phylogeny of the eukaryotes. Cladistics 14: 303–338.
   Web of Science ®Google Scholar
• Luttrell ES. 1951. Taxonomy of the Pyrenomycetes. Univ Missouri Stud 24: 1–120.
   Google Scholar
• Maidak BL, Cole JR, Parker CT, Garrity GMJ, Larsen N, Li B, Lilburn TG, McCaughey MJ, Olsen GJ, Overbeek R, et al. 1999. A new version of the RDP (Ribosomal Database Project). Nucl Acids Res 27: 171–173.
   PubMed Web of Science ®Google Scholar
• Maidak BL, Cole JR, Parker CT, Garrity GMJ, Larsen N, Li B, Lilburn TG, McCaughey MJ, Olsen GJ, Overbeek R, et al., Olsen GJ, Larsen N, Overbeek R, McCaughey M, Woese C. 1997. The RDP (ribosomal database project). Nucl Acids Res 25: 109–111.
   PubMed Web of Science ®Google Scholar
• Nannfeldt JA. 1932. Studien über die Morphologie und Systematik der nicht-lichenisierten inoperculaten Discomyceten. Nova Acta Regiae Soc Sci Ups 8: 1–368.
   Google Scholar
• Nishida H, Sugiyama J. 1994. Archiascomycetes: detection of a major new lineage within the Ascomycota. Myco-science 35: 361–366.
   Google Scholar
• Novacek MJ. 1992. Fossils, topologies, missing data, and higher level phylogeny of eutherian mammals. Syst Biol 41: 58–73.
   Web of Science ®Google Scholar
• Patterson DJ. 1989. Stramenopila: Chromophytes from a protistan perspective. In: Green JC, Leadbeater BSC, Diver WL, eds. The chromophyte algae: problems and perspectives. Oxford: Systematics Association. p 357–379.
   Google Scholar
• Prillinger H. 1982. Zur genetishen Kontrolle und Evolution der sexuellen Fortplanzung und Heterothallie der Chitinpilzen. Z Mykol 48: 297–324.
   Google Scholar
• Rice KA, Donoghue MJ, Olmstead RG. 1997. Analyzing large data sets: rbcL revisited. Syst Biol 46: 554–563.
   Web of Science ®Google Scholar
• Schlegel M. 1994. Molecular phylogeny of eukaryotes. Tree 9: 330–335.
   Web of Science ®Google Scholar
• Siddall ME. 1998. Success of parsimony in the four-taxon case: Long-branch repulsion by likelihood in the Farris Zone. Cladistics 14: 209–220.
   PubMed Web of Science ®Google Scholar
• Siddall ME., Whiting MF. 1999. Long-branch abstractions. Cladistics 15: 9–24.
   Web of Science ®Google Scholar
• Sogin ML. 1989. Evolution of eukaryotic microorganisms and their small subunit RNAs. Am Zool 29: 487–499.
   Google Scholar
• Spiegel FW, Lee SB, Rusk SA. 1995. Eumycetozoans and molecular systematics. Can J Bot 73(Suppl 1): 738–746.
   Google Scholar
• Swann EC, Taylor JW. 1995. Phylogenetic perspectives in basidiomycete systematics: evidence from the 18S rRNA gene. Can J Bot 73(Suppl 1): 862–868.
   Google Scholar
• Swofford DL. 1999. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland, Massachusetts: Sinauer Associates.
   Google Scholar
• Taylor JW. 1995. Making the Deuteromycota redundant: a practical integration of mitosporic and meiosporic fungi. Can J Bot 73(Suppl 1):754–759.
   Google Scholar
• Tehler A. 1988. A cladistic outline of the Eumycota. Cladistics 4: 227–277.
   PubMed Web of Science ®Google Scholar
• Tehler A.. 1990. A new approach to the phylogeny of Euascomycetes with a cladistic outline of Arthoniales focussing on Roccellaceae. Can J Bot 68: 2458–2492.
   Google Scholar
• Tehler A.. 1995. Morphological data, molecular data and total evidence in phylogenetic analysis. Can J Bot 73(Suppl 1): 667–676.
   Google Scholar
• Tehler A.. 1996. Systematics, Phylogeny and Classification. In: Nash T, ed. Lichen Biology. Cambridge: Cambridge University Press. p 217–239.
   Google Scholar
• Tehler A., Lipscomb DL, Farris JS, Källersjö M. 1998a. Abstract. The phylogeny of the fungi, as supported by ribosomal sequences. In: de Pinna M, ed. Hennig XVII. 17th meeting of the Willi Hennig Society: Program and abstracts. São Paulo: Universidade de São Paulo. p 82–83.
   Google Scholar
• Tehler A., Lipscomb DL, Farris JS, Källersjö M.. 1998b. Abstract. Support, ribosomal sequences and the phylogeny of the fungi. In: Kenes Congress organizers, ed. Sixth International Mycological Congress, IMC6. Abstracts. Jerusalem: Kenes Tours. p 90.
   Google Scholar
• Van de Peer Y, De Rijk P, De Wachter R, Jansen J. 1997. Database on the structure of small ribosomal subunit RNA. Nucl Acids Res 25: 111–116.
   PubMed Web of Science ®Google Scholar
• Vogel HJ. 1964. Distribution of lysine pathways among fungi: evolutionary implications. Am Naturalist 98: 435–446.
   Web of Science ®Google Scholar
• Wainright PO, Hinkle G, Sogin ML, Stickel SK. 1993. Monophyletic origins of the Metazoa: an evolutionary link with fungi. Science 260: 340–342.
   PubMed Web of Science ®Google Scholar
• Wakeley J. 1996. The excess of transitions among nucleotide substitutions: new method of estimating transition bias underscore its significance. Tree 11: 158–163.
   PubMed Web of Science ®Google Scholar
• Wedin M, Tehler A, Gargas A. 1998. Phylogenetic relationships of Sphaerophoraceae (Ascomycetes) inferred from SSU rDNA sequences. Pl Syst Evol 209: 75–83.
   Web of Science ®Google Scholar
• Wenzel JW, Siddall ME. 1999. Noise. Cladistics 15: 51–64.
   Web of Science ®Google Scholar
• Whittaker RH. 1969. New concepts of kingdoms of organisms. Science 163: 150–160.
   PubMed Web of Science ®Google Scholar
• Young TWK. 1969. Ultrastructure of aerial hyphae in Linderina pennispora. Ann Bot 33: 211–216.
   Web of Science ®Google Scholar