Landmark papers in fungal phylogeny


 
This is a selected list of recent and other significant references dealing with basidiomycete phylogeny. Please inform me (fungi@duke.edu) of any serious ommissions, which I would be happy to include.

 
sections:
"Big picture" phylogeny of fungi and other eukaryotes
Glomalean (VAM) fungi
Chytrids and Zygomycetes
Basidiomycetes
Ascomycetes
Stramenopiles (oomycetes, labyrinthulids, thraustochytrids)
Mycetozoans (slime molds)

 
Big picture phylogeny of the fungi

Baldauf, S. L. 1999. A search for the origins of animals and fungi: Comparing and combining molecular data. American Natruralist 154:S178-S188, Suppl.

Baldauf, S. L., A. J. Roger, I. Wnek-Siefert, and W. F. Doolittle. 2000. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290: 972-977.

Baldauf, S. L., and J. D. Palmer. 1993. Animal and fungi are each other's closest relatives: Congruent evidence from multiple proteins. PNAS 90: 11558-11562.

Berbee, M. L., and J. W. Taylor. 2001. Fungal molecular evolution: Gene trees and geologic time. pp 229-245 in: The Mycota VIIB Systematics and Evolution (D. J. McLaughlin, E. G. McLaughlin, and P. A. Lemke, eds). Springer-Verlag, Berlin.

Berbee, M.and J. W. Taylor. 1993. Dating the divergences of the major lineages of the Eumycota. Can. J. Bot. 71: 1114-1127.

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

Borchiellini, C., N. Boury-Esnault, J. Vacelet, and Y. L. Parco. 1998. Phylogenetic analysis of the Hsp70 sequences reveals the monophyly of Metazoa and specific phylogenetic relationships between animals and fungi. Mol Biol Evol 15: 647-655.

Bruns, T. D., R. Vilgalys, S. M. Barns, D. Gonzalez, D. S. Hibbett, D. J. Lane, L. Simon, S. Stickel, T. M. Szaro, and et al. 1992. Evolutionary relationships within the fungi: Analyses of nuclear small subunit rRNA sequences. Molec. Phylog. Evol. 1: 231-241.

Bruns, T., T. White, and J. Taylor. 1991. Fungal molecular systematics. Annu. Rev. Ecol. Syst. 22: 525-564.

Doolittle, R. F., D. F. Feng, S. Tsang, G. Cho, and E. Little. 1996. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271: 470-477.

Edgell, D., S. Malik, and W. Doolittle. 1998. Evidence of independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Mol Biol Evol 15: 1207-1217.

Edman, J. C., J. A. Kovacs, H. Masur, D. V. Santi, H. J. Elwood, and M. L. Sogin. 1988. Ribosomal RNA sequence shows Pneumocystis carinii to be a member of the fungi. Nature 334: 519-522.

Gupta, RS. 1995. Phylogenetic analysis of the 90 kD heat shock family of protein sequences and an examination of the relationship among animals, plants, and fungi species. Molecular Biology and Evolution 12: 1063-1073.

Heckman, D. S., D. M. Geiser, B. R. Eidell, R. L. Stauffer, N. L. Kardos and S. B. Hedges. 2001. Molecular evidence for the early colonization of land by fungi and plants. Science 293: 1129-1133.

Hibbett, D. S. 1992. Ribosomal RNA and fungal systematics. Trans. Mycol. Soc. Japan. 33: 533-556.

Hirt, R. P., J. John M. Logsdon, B. Healy, M. W. Dorey, W. F. Doolittle, and T. M. Embley. 1999. Microsporidia are related to Fungi: Evidence from the largest subunit of RNA polymerase II and other proteins. Proc. Natl. Acad. Sci., U. S. A. 96: 580-585.

Janbon, G; Rustchenko, EP; Klug, S; Scherer, S; Sherman, F. 1997. Phylogenetic relationships of fungal cytochromes c. Yeast 13: 985-990, Aug 1997

Keeling, P. J., M. A. Luker, and J. D. Palmer. 2000. Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi. Mol. Biol. Evol. 17:23-31.

Keeling, P. J., M. A. Luker, and J. D. Palmer. 2000. Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi. Mol. Biol. Evol. 17: 23-31.

Keeling, P.and W. Doolittle. 1996. Alpha-tubulin from early-diverging eukaryotic lineages and the evolution of the tubulin family. Mol Biol Evol 13: 1297-1305.

Nagahama, T., H. Sato, M. Shimuzu, and J. Sugiyama. 1995. Phylogenetic divergence of the entomorphthoralean fungi: evidence from nuclear 18S ribosomal RNA gene sequences. Mycologia 87: 203-209.

Paquin, B., M.-J. Laforest, L. Forget, I. Roewer, W. Zhang, J. Longcore, and B. F. Lang. 1997. The Fungal Mitochondrial Genome Project: evolution of fungal mitochondrial genomes and their gene expression. Curr. Genet. 31: 380-395.

Radford, A. 1993. A fungal phylogeny based upon orotidine-5'-monophosphate decarboxylase. J. Mol. Evol. 36: 389-395.

Ragan, M. A., C. L. Goggin, R. J. Cawthorn, L. Cerenius, A. V. C. Jamieson, S. M. Plourd, T. G. Rand, K. Soderhall, R. R. Gutell.1996 A novel clade of protistan parasites near the animal-fungal divergence PNAS 93: 11907-11912.

Sugiyama, J. 1998. Relatedness, phylogeny, and evolution of the fungi. Mycoscience 39:487-511.

Tehler, A., J.S. Farris, D.L. Lipscomb, and M. Källersjo.  2000.  Phylogenetic analyses of the fungi based on large rDNA data sets.  Mycologia 92: 459-474.

Vandenkoornhuyse, P., S. L. Baldauf, C. Leyval, J. Straczek, and J. P W. Young. 2002. Extensive fungal diversity in plant roots. Science 295: 2051.

Wainright, P. O., G. Hinkle, M. L. Sogin, and S. K. Stickel. 1993. Monophyletic origins of the metazoa: an evolutionary link with fungi. Science 260: 340-342.

Glomalean (VAM) fungi phylogeny

Gehrig, H., A. Schuessler, and M. Kluge. 1996. Geosiphon pyriforme, a fungus forming endocytobiosis with Nostoc (Cyanobacteria) is an ancestral member of the glomales: Evidence by SSU rRNA analysis. Journal of Molecular Evolution. 43: 71-81.

Redecker, D., J. B. Morton, and T. D. Bruns. 2000. Ancestral lineages of arbuscular mycorrhizal fungi (Glomales). Molecular Phylogenetics and Evolution. 14: 276-284.

Redecker, D., R. Kodner, L. E. Graham.  2000. Glomalean fungi from the Ordivician.  Science 289:1920-1921.

Schuessler, A. 1999. Glomales SSU rRNA gene diversity. New Phytologist. 144: 205-207.

Schuessler, A., D. Schwarzott, and C. Walker. 2001. A new fungal phylum, the Glomeromycota: Phylogeny and evolution. Mycological Research. 105: 1413-1421.

Schuessler, A., H. Gehrig, D. Schwarzott, and C. Walker. 2001. Analysis of partial Glomales SSU rRNA gene sequences: Implications for primer design and phylogeny. Mycological Research. 105: 5-15.

Simon, L., L. Bousquet, R. C. Levesque, and M. Lalonde. 1993. Origin and diversification of endomycorrhizal fungi and coincidence with vascular plants. Nature 363: 67-69.

Chytrid and Zygomycete Phylogeny

Benny, G. L., and K. OíDonnell. 2000. Amoebidium parasiticum is a protozoan, not a Trichomycete. Mycologia 92:1133-1137.

James, T. Y., D. Porter, C. A. Leander, R. Vilgalys, and J. E. Longcore 2000. Molecular phylogenetics of the Chytridiomycota support the utility of ultrastructural data in chytrid systematics. Canad. J. Bot. 78: 336-350.

Jensen, A. B., A. Gargas, J. Eilenberg, and S. Rosendahl. 1998. Relationships of the insect-pathogenic order Entomophtorales (Zygomycota, Fungi) based on phylogenetic analyses of nuclear small subunit ribosomal DNA sequences (SSU rDNA). Fungal Genet. Biol. 24:325-334.

Nagahama, T., H. Sato, M. Shimazu, and J. Sugiyama. 1995. Phylogenetic divergence of the entomophthoralean fungi: Evidence from nuclear 18S ribosomal RNA gene sequences. Mycologia 87: 203-209.

O'Donnell, K., E. Cigelnik, and G. L. Benny. 1998. Phylogenetic relationships among the Harpellales (Trichomycetes) and Kickxellales (Zygomycetes), two orders of Zygomycota that form regularly septate hyphae. Mycologia 90: 624-639.

O'Donnell, K., F. M. Lutzoni, T. J. Ward, and G. L. Benny . 2001. Evolutionary relationships among mucoralean fungi (Zygomycota): Evidence for family polyphyly on a large scale. Mycologia 93:286-296.

Tanabe Y, O'Donnell K, Saikawa M, Sugiyama J. 2000. Molecular Phylogeny of Parasitic Zygomycota (Dimargaritales, Zoopagales) Based on Nuclear Small Subunit Ribosomal DNA Sequences. Mol Phylogenet Evol. 2000 Aug;16(2):253-262.

Van Dover CL, and RW Lichtwardt. 1986. A new trichomycete commensal with a galatheid squat lobster from deep-sea hydrothermal vents. Biol. Bull. 171:461-468.

Basidiomycete phylogeny

Bauer, R., D. Begerow, F. Oberwinkler, M. Piepenbring, and M. L. Berbee. 2001. Ustilaginomycetes. pp 57-84 in: The MycotaVIIB, Systematics and Evolution (D. J. McLaughlin, E. G. McLaughlin, and P. A. Lemke, eds).  Springer-Verlag, Berlin.

Bauer, R., Oberwinkler, F., Vánky, K. 1997. Ultrastructural markers and systematics in smut fungi and allied taxa. Can. J. Bot. 75: 1273-1314

Begerow, D; Bauer, R; Oberwinkler, F. 1997. Phylogenetic studies on nuclear large subunit ribosomal DNA sequences of smut fungi and related taxa. 1997. Canadian Journal of Botany 75: 2045-2056.

Berres, M. E., L. J. Szabo, and D. J. McLaughlin. 1995. Phylogenetic relationship in auriculariaceous basidiomycetes based on 25S ribosomal DNA sequences. Mycologia 87: 821-840.

Binder, M., and D. S. Hibbett. 2002. Higher level phylogenetic relationships of homobasidiomycetes inferred from four rDNA regions. Molecular Phylogenetics and Evolution 22:76-90.

Blanz, P.A., and M. Gottschalk. 1986. Systematic position of Septobasidium, Graphiola and other basidiomycetes as deduced on the basis of their 5S ribosomal RNA nucleotide sequences. System. Appl. Microbiol. 8: 121-127.

Boidin, J., J. Mugnier, and R. Canales. 1998. Taxonomie moleculaire des Aphyllophorales. Mycotaxon 66: 445-491.

Hibbett, D. S., and R. G. Thorn. 2001. Basidiomycota: Homobasidiomycetes. Pp. 121-168 in: The Mycota, vol. VII part B, Systematics and Evolution (D. J. McLaughlin, E. G. McLaughlin, and P. A. Lemke, eds.). Springer Verlag.

Hibbett, D. S., E. M. Pine, E. Langer, G. Langer, and M. J. Donoghue. 1997. Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences. Proc. Natl. Acad.  Sci. USA 94:12002-12006.

Hibbett, D. S.and R. G. Thorne.  2000.  Basidiomycota: Homobasidiomycetes. Pp. in press In: The Mycota VII: Systematics and Evolution, ed. McLaughlin, D. S.

Matheny, P.B., Yajuan J. Liu, Joseph F. Ammirati, and Benjamin D. Hall. 2002. Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales). Am. J. Bot. 89:688-698.

McLaughlin, D.J., M.E. Berres and L.J. Szabo.  1995a.  Molecules and morphology in basidiomycete phylogeny.  Can. J. Bot. 73 (Suppl. 1):S684-S692.

Moncalvo, J. M., F. M. Lutzoni, S. A. Rehner, J. Johnson, and R. Vilgalys. 2000. Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. Syst. Biol. 49: 278-305.

Moncalvo, J. M., R. Vilgalys, S. A. Redhead, J. E. Johnson, T. Y. James, M. C. Aime, V. Hofstetter, S. J. W. Verduin, E. Larsson, T. J. Baroni, R. G. Thorn, S. Jacobsson, H. Clémençon, and O. K. Miller Jr. 2002. One hundred and seventeen clades of Euagarics. Mol. Phyl. Evol. In press.

Nakase, T., S. O. Suh, and M. Hamamoto.  1995.  Molecular systematic of ballistoconidium-forming yeasts.  Studies in Mycology 163-173.

Suh, S. O.and J. Sugiyama. 1994. Phylogeny among the basidiomycetous yeasts as inferred from molecular data. Nippon Nogeikagaku Kaishi 68: 67-71.

Swann, E. C.and J. W. Taylor. 1993. Higher taxa of basidiomycetes: an 18S rRNA gene perspective. Mycologia 85: 923-936.

Swann, E. C.and J. W. Taylor. 1995. Phylogenetic diversity of yeast-producing basidiomycetes. Mycol. Res. 99: 1205-1210.

Swann, E. C.and J. W. Taylor. 1995. Phylogenetic perspectives on basidiomycete systematics: Evidence from the 18S rRNA gene. Can. J. Bot. 73: S862-S868.

Swann, E. C.and J. W. Taylor. 1995. Toward a phylogenetic systematics of the basidiomycota: Integrating yeasts and filamentous basidiomycetes using 18S RRNA gene sequences. Studies in Mycology 147-161.

Swann, E.C., E.M. Frieders, and D.J. McLaughlin. 2001. Urediniomycetes. In McLaughlin, D.J., E.G. McLaughlin, and P.A. Lemke (eds.). The Mycota. VIIB. Systematics and Evolution. Springer Verlag. Pp. 37-56.

Walker, W. F.and W. F. Doolittle. 1982. Redividing the Basidiomycetes on the basis of 5S rRNA sequences. Nature 299: 723-724.

Ascomycete phylogeny

Berbee, M. L.and J. W. Taylor. 1992. Convergence in ascospore discharge mechanism among pyrenomycete fungi based on 18S ribosomal RNA gene sequence. Molec. Phylog. Evol. 1: 59-71.

Berbee, M. L.and J. W. Taylor. 1992. Two ascomycete classes based on fruiting-body characters and ribosomal DNA sequence. Mol. Biol. Evol. 9: 278-284.

Berbee, M.L. 1998.  Loculoascomycete origins and evolution of filamentous ascomycete morphology based on 18S rRNA gene sequence data.  Molec. Biol. Evol. 13: 462-470.

Bowman, B. H., J. W. Taylor, and T. J. White. 1992. Molecular evolution of the fungi: Human pathogens. Mol. Biol. Evol. 9: 893-904.

Bowman, B. H., T. J. White, and J. W. Taylor. 1996. Human pathogenic fungi and their close nonpathogenic relatives. Molec. Phylog. Evol. 6: 89-96.

Eriksson, O.E., H.-O. Baral, R.S. Currah, K. Hansen, C.P. Kurtzman, G. Rambold, and T. Laessøe. 2001. pp 1-88: in Outline of Fungi ? 2001.  Myconet Umeå, Umeå, University Sweden. http://www.umu.se/myconet/Myconet.html.

Gargas, A., P. T. Depriest, M. Grube, and A. Tehler. 1995. Multiple origins of lichen symbioses in fungi suggested by SSU rDNA phylogeny. Science 268: 1492-1495.

Gargas, A.and J. W. Taylor. 1995. Phylogeny of discomycetes and early radiations of the apothecial ascomycotina inferred from SSU rDNA sequence data. Exp. Mycol. 19: 7-15.

Gernandt, D.S., J.L. Platt, J.K. Stone, J.W. Spatafora, A. Holst-Jensen, R.C. Hamelin, and L.M. Kohn.  2001.  Phylogenetics of Helotiales and Rhytismatales based on partial small subunit nuclear ribosomal DNA sequences.  Mycologia 93: 915-933.

Holst-Jensen, A., L.M. Kohn, and T. Schumacher.  1997.  Nuclear rDNA phylogeny of the Sclerotiniaceae.  Mycologia 89: 885-899.

Kauff, F. and Lutzoni, F.  2002. 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 (in press).

Liu, Y.J., S. Whelen, and B.D. Hall. 1999. Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit.  Mol Biol Evol 16: 1799-1808.

Lumbsch, H. T., N. Wirtz, R. Lindemuth, I. Schmitt.  2002.  Higher level phylogenetic relationships of euascomycetes (Pezizomycotina) inferred from a combined analysis of nuclear and mitochondrial sequence data.  Mycological Progress 1:57-70.

Lutzoni, F., Pagel, M., Reeb, V.  2001.  Major fungal lineages are derived from lichen symbiotic ancestors.  Nature 411:937-940.

Nishida, H., and J Sugiyama. 1993. Phylogenetic relationships among Taphrina, Saitoella, and other higher fungi. Mol Biol Evol 1993 10: 431-436.

Nishida, H., and J. Sygiyama. 1994. Archiascomycetes: Detection of a major new lineage within the ascomycota. Mycoscience 35: 361-366.

O'Donnell, K., E. Cigelnik, N. S. Weber, and J. M. Trappe. 1997. Phylogenetic relationships among ascomycetous truffles and the true and false morels inferred from 18S and 28S ribosomal DNA sequence analysis. Mycologia 89: 48-65.

Spatafora, J. W. 1995. Ascomal evolution among filamentous ascomycetes: evidence from molecular data. Canad. J. Bot. 73: S811-S815.

Spatafora, J. W., B. Volkmann-Kohlmeyer, and J. Kohlmeyer.  1998.  Independent  terrestrial origins of the Halosphaeriales (marine Ascomycota).  Am. J. Bot. 85: 1569-1580.Spatafora, J. W.and M. Blackwell. 1994. The polyphyletic origins of ophiostomatoid fungi. Mycol. Res. 98: 1-9

Spatafora, J. W.and M. Blackwell. 1993. Molecular systematics of unitunicate perithecial ascomycetes: The Clavicipitales-Hypocreales connection. Mycologia 85: 912-922.

Taylor, J. W. 1995. Making the Deuteromycota redundant: A practical integration of mitosporic and meiosporic fungi. Can. J. Bot. 73: S754-S759.

YJ Liu, S Whelen, and BD Hall. 1999. Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit. Mol Biol Evol 1999 16: 1799-1808.

Phylogeny of the Stramenopiles

Cavalier-Smith, T., MTEP Allsop, and E.E. Chao. 1994. Thraustochytrids are chromists, not fungi: 18S rRNA signatures of heterokonta. Philos. Trans. Roy. Soc. Lond. Ser. B 339: 139-146.

Förster, H., M. D. Coffey, H. Elwood, and M. L. Sogin. 1990. Sequence analysis of the small subunit ribosomal RNA of three zoosporic fungi and implications for fungal evolution. Mycologia 82: 306-312.

G Van der Auwera, R De Baere, Y Van de Peer, P De Rijk, I Van den Broeck, and R De Wachter. 1995. The phylogeny of the Hyphochytriomycota as deduced from ribosomal RNA sequences of Hyphochytrium catenoides. Mol Biol Evol 1995 12: 671-678

Hausner G. Belkhiri A. Klassen GR. 2000. Phylogenetic analysis of the small subunit ribosomal RNA gene of the hyphochytrid Rhizidiomyces apophysatus. Canadian Journal of Botany. 78:124-128.

Honda D; Yokochi T; Nakahara T; Raghukumar S; Nakagiri A; Schaumann K; Higashihara T. 1999. Molecular phylogeny of labyrinthulids and thraustochytrids based on the sequencing of 18S ribosomal RNA gene. J Eukaryot Microbiol. 46:637-47

Leipe, D. D., P. Wainright, J. H. Gunderson, D. Porter, D. J. Patterson, F. Valois, S. Himmerich, and M. L. Sogin. 1994. The stramenopiles from a molecular perspective: 16S like rRNA sequences from Labyrinthuloides minuta and Cafeteria roenbergensis. Phycologia 33: 369-377.

Saunders, G. W., D. Potter, and R. A. Anderson. 1997. Phylogenetic affinities of the Sarcinochrysidales and Chysomeridales (Heterokonta) based on analyses of molecular and combined data. J. Phycol. 33: 310318.

Mycetozoan phylogeny

Baldauf, S. L.and W. F. Doolittle. 1997. Origin and evolution of the slime molds (Mycetozoa). Proc. Natl. Acad. Sci., U. S. A. 94: 12007-12012.