Systematics

Through AFTOL and other projects, members of our lab have studied phylogenetic relationships of Fungi as whole, as well as in specific groups within Agaricomycotina. These are some of the groups that have interested us:

Polyporales and Gloeophyllales: These clades include major concentrations of wood-decay fungi in Agaricomycetes, including both white rot and brown rot species. Most members of both groups are polypores (including massive, perennial “bracket fungi”) or resupinate fungi, but each clade also includes agarics (with a cap and gills), and some forms that defy easy definition (e.g., the “cauliflower fungus”, Sparassis).

Agaricomycetidae: This clade contains the Boletales, Agaricales, and several smaller groups. Boletales includes mostly ectomycorrhizal species, such as the edible porcini, but also contains brown-rot wood decayers. Our lab’s work on Boletales has been conducted in collaboration with Manfred Binder and Roy Halling. Agaricales is the largest clade in the Agaricomycetes (about 13,000 species), mostly gilled mushrooms, with diverse nutritional modes. P. Brandon Matheny was a post-doc in our lab who did pioneering research on phylogenetics of Agaricales and other basidiomycetes. The other groups include Atheliales and Amylocorticiales, two relatively obscure clades of mostly resupinate forms.

Lentinoid fungi, including shiitake mushrooms: This is a polyphyletic assemblage of taxa in Polyporales (Lentinus, Panus), Gloeophyllales (Neolentinus, Heliocybe), and Agaricales (Pleurotus, Lentinula) that have all been classified at one time or another in the genus Lentinus. Previously, we conducted phylogenetic studies on shiitake mushrooms, which are in Lentinula. Recently, we have launched a new project on comparative genomics of shiitake mushrooms, with support from the JGI Community Science Program.

Cyphelloid and marine Agaricomycetes: Cyphelloid fungi are basidiomycetes that produce minute, cup-shaped fruiting bodies that can easily be confused with small ascomycete fruiting bodies. They are taxonomically obscure and polyphyletic. Intriguingly, some cyphelloid lineages are closely related to Agaricomycetes that occur in intertidal (mangrove) or completely submerged marine habitats.

Representative publications (out of date! See the publication list for recent work in this area):

General fungal phylogenetics, emphasizing Agaricomycetes:

Hibbett, D.S. and R.G. Thorn. 2001. Basidiomycota: Homobasidiomycetes. The Mycota VII Part B. Systematics and Evolution. McLaughlin/McLaughlin/Lemke (Eds.) Springer-Verlag, Berlin Heidelberg. PDF

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

Lutzoni, F., F. Kauff, C. J. Cox, D. McLaughlin, G. Celio, B. Dentinger, M. Padamsee, D. Hibbett, T. Y. James, E. Baloch, M. Grube, V. Reeb, V. Hofstetter, C. Schoch, A. E. Arnold, J. Miadlikowska, J. Spatafora, D. Johnson, S.Hambleton, M. Crockett, R. Shoemaker, G.-H. Sung, R. Lücking, T. Lumbsch, K. O’Donnell, M. Binder, P. Diederich, D. Ertz, C. Gueidan, K. Hansen, R. C. Harris, K. Hosaka, Y.-W. Lim, B. Matheny, H. Nishida, D. Pfister, J. Rogers, A. Rossman, I. Schmitt, H. Sipman, J. Stone, J. Sugiyama, R. Yahr, R. Vilgalys. 2004. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. American Journal of Botany 91: 1446-1480. PDF

Hibbett, D. S. 2006. A phylogenetic overview of the Agaricomycotina. Mycologia 98: 917-925. PDF

James, T. Y., F. Kauff, C. Schoch, P. B. Matheny, V. Hofstetter, C. Cox, G. Celio, C. Gueidan, E. Fraker, J. Miadlikowska, H. T. Lumbsch, A. Rauhut, V. Reeb, A. E. Arnold, A. Amtoft, J. E. Stajich, K. Hosaka, G.-H. Sung, D. Johnson, B. O’Rourke, M. Crockett, M. Binder, J. M. Curtis, J. C. Slot, Z. Wang, A. W. Wilson, A. Schüßler, J. E. Longcore, K. O’Donnell, S. Mozley-Standridge, D. Porter, P. M. Letcher, M. J. Powell, J. W. Taylor, M. M. White, G. W. Griffith, D. R. Davies, R. A. Humber, J. B. Morton, J. Sugiyama, A. Y. Rossman, J. D. Rogers, D. H. Pfister, D. Hewitt, K. Hansen, S. Hambleton, R. A. Shoemaker, J. Kohlmeyer, B. Volkmann-Kohlmeyer, R. A. Spotts, M. Serdani, P. W. Crous, K. W. Hughes, K. Matsuura, E. Langer, G. Langer, W. A. Untereiner, R. Lücking, B. Büdel, D. M. Geiser, A. Aptroot, P. Diederich, I. Schmitt, M. Schultz, R. Yahr, D. Hibbett, F Lutzoni, D. McLaughlin, J. Spatafora, and R. Vilgalys. 2006. Reconstructing the early evolution of the fungi using a six gene phylogeny. Nature 443: 818-822. PDF

Matheny, P. B., Z. Wang, M. Binder, J. M. Curtis, Y. W. Lim, R. H. Nilsson, K. W. Hughes, V. Hofstetter, J. F. Ammirati, C. Schoch, G. E. Langer, D. J. McLaughlin, A. W. Wilson, T. Frøslev, Z. W. Ge, R. W. Kerrigan, J. C. Slot, E. C. Vellinga, Z. L. Liang, T. J. Baroni, M. Fischer, K. Hosaka, K. Matsuura, M. T. Seidl, J. Vaura, and D. S. Hibbett. 2007. Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Molecular Phylogenetics and Evolution 43: 430-451. PDF

Staijch, J., M. L. Berbee, M. Blackwell, D.S.Hibbett, T.Y.James, J.Spatafora, and J.W.Taylor. 2009. The Fungi.Current Biology 19: R840-R845. PDF

McLaughlin,D.J.,D.S.Hibbett, F.Lutzoni, J.Spatafora, and R.Vilgalys. 2009. The search for the fungal tree of life. Trends in Microbiology doi:10:1016/j.tim.2009.08.001 PDF

Hibbett, D. D., R. Bauer, M. Binder, A.J. Giachini, K. Hosaka, A. Justo, E. Larsson, K.H. Larsson, J.D. Lawrey, O. Miettinen, L. Nagy, R.H. Nilsson, M. Weiss, and R.G. Thorn. 2014. Agaricomycetes. Pp. 373-429 In: The Mycota, vol. VII, Second Ed., Part A. Systematics and Evolution (D. J. McLaughlin and J. W. Spatafora, eds.). Springer Verlag. PDF(chapter)

Polyporales and Gloeophyllales

Hibbett, D. S., and R. Vilgalys. 1991. Evolutionary relationships of Lentinus to the Polyporaceae: evidence from restriction analysis of enzymatically amplified ribosomal DNA. Mycologia 83: 425-439. PDF 

Hibbett, D. S., and M. J. Donoghue. 1995. Progress toward a phylogenetic classification of the Polyporaceae through parsimony analyses of ribosomal DNA sequences. Canadian Journal of Botany 73(Suppl. 1): S853-S861. PDF

Garcia-Sandoval, R., Z. Wang, M. Binder, and D. S. Hibbett. 2010. Molecular phylogenetics of the Gloeophyllales and relative ages of clades of Agaricomycotina producing a brown rot. Mycologia DOI: 10.3852/10-209. PDF

Justo, A., and D. S. Hibbett. 2011. Phylogenetic classification of Trametes (Basidiomycota, Polyporales) based on a five-marker dataset. Taxon 60: 1567-1583. PDF

Ortiz-Santana, B., Lindner, D. L., Miettinen, O., Justo, A. & Hibbett, D. S. A phylogenetic overview of the antrodia clade (Basidiomycota, Polyporales). Mycologia 105, 1391-1411, doi:10.3852/13-051 (2013). PDF

Binder, Manfred, Alfredo Justo, Robert Riley, Asaf Salamov, Francesc Lopez-Giraldez, Elisabet Sjökvist, Alex Copeland, Brian Foster, Hui Sun, Ellen Larsson, Karl-Henrik Larsson, Jeffrey Townsend, Igor V. Grigoriev, and David S. Hibbett. Phylogenetic and phylogenomic overview of the Polyporales. Mycologia 105, 1350-1373, doi:10.3852/13-003 (2013). PDF 

Carlson, A., A. Justo, and D. S. Hibbett. 2014. Species delimitation in Trametes (Polyporales, Basidiomycota): a comparison of ITS, TEF-1, RPB1 and RPB2 phylogenies. Mycologia 106: Early Edition: doi: 10.3852/13-275. (2014). PDF

Floudas, D., and D. S. Hibbett. 2015. Revisiting the taxonomy of Phanerochaete (Polyporales, Basidiomycota) using a four-gene dataset and extensive ITS sampling. Fungal Biology 119: 679-719. PDF

Agaricomycetidae

Binder, M., and D. S. Hibbett. 2006. Molecular systematics and biological diversification of Boletales. Mycologia 98: 971-981. PDF

Matheny, P. B., J. M. Curtis, V. Hofstetter, M. C. Aime, J.-M. Moncalvo, Z. W. Ge, Z. L. Yang, J. C. Slot, J. F. Ammirati, T. J. Baroni, N. L. Bougher, K. W. Hughes, D. J. Lodge, R. W. Kerrigan, M. T. Seidl, D. K. Aanen, M. DeNitis, G. M. Daniele, D. E. Desjardin, B. R. Kropp, L. L. Norvell, A. Parker, E. C. Vellinga, R. Vilgalys. and D. S. Hibbett. 2006. Major clades of Agaricales: a multi-locus phylogenetic overview. Mycologia 98: 982-995. PDF

Louzan, R., Wilson, A. W., Binder, M., and D. S. Hibbett. 2007. Phylogenetic placement of Diplocystis wrightii in the Sclerodermatineae (Boletales) based on nuclear ribosomal large subunit DNA sequences. Mycoscience 48: 66-69. PDF

Binder, M., K.H.Larsson, P.B. Matheny, and D.S.Hibbett. 2010. Amylocorticiales ord. nov. and Jaapiales ord. nov.: Early diverging clades of Agaricomycetidae dominated by corticioid forms. Mycologia, 102: 865-880 PDF

Neves, M. A., M. Binder, R. Halling, D. S. Hibbett, and K. Soytong. 2012. The phylogeny of selected Phylloporus species, inferred from NUC-LSU and ITS sequences, and descriptions of new species from the Old World. Fungal Diversity DOI 10.1007/s13225-012-0154-0.PDF 

Wilson, A., M. Binder, and D. S. Hibbett. 2012. Diversity and evolution of ectomycorrhizal host associations in Sclerodermatineae (Boletales, Basidiomycota). New Phytologist 194(4): doi: 10.1111/j.1469-8137.2012.04109. PDF

Halling, R. H., M. Nuhn, N. A. Fechner, T. W. Osmundson, K. Soytong, D. S. Hibbett, and M. Binder. 2012. Sutorius: a new genus for Boletus eximius (Boletineae). Mycologia 104: 951-961. PDF

Halling, R. H., M Nuhn,T. Osmundson, N. Fechner, J.M. Trappe, K. Soytong, D. Arora, D.S. Hibbett, M. Binder. 2012. Affinities of the Boletus chromapes group to Royoungia and the description of two new genera, Harrya and Australopilus. Australian systematic Botany 25: 418–431. PDF

Nuhn, Mitchell E., M. Binder, A.F.S. Taylor, R.E. Halling and D.S. Hibbett. 2013. Phylogenetic overview of the Boletineae. Fungal Biology 117: 475-511. doi:10.1016/j.funbio.2013.04.008. PDF

Halling, R., M. Nuhn, T. Osmundson, K. Soytong, D. Arora, M. Binder, and D. S. Hibbett. 2015. Evolutionary relationships of Heimioporus and Boletellus (Boletales) with an emphasis on Australian taxa. Australian Systematic Botany 28: 1-22. PDF

Lentinoid fungi, including shiitake mushrooms (developmental studies in lentinoid fungi are referenced above)

Hibbett, D. S., and R. Vilgalys. 1991. Evolutionary relationships of Lentinus to the Polyporaceae: evidence from restriction analysis of enzymatically amplified ribosomal DNA. Mycologia 83: 425-439. PDF

Hibbett, D. S., and R. Vilgalys. 1993. Phylogenetic relationships of Lentinus (Basidiomycotina) inferred from molecular and morphological characters. Systematic Botany 18: 409-433. PDF

Hibbett, D. S., and R. G. Thorn. 1994. Nematode-trapping in Pleurotus tuberregium. Mycologia 86: 696-699. PDF

Fukuda, M. Y. Nakai, D. S. Hibbett, T. Matsumoto, and Y. Hayashi. 1994. Mitochondrial DNA restriction fragment length polymorphisms in natural populations of Lentinula edodes. Mycological Research 98: 169-175.

Hibbett, D. S., A. Tsuneda, Y. Fukumasa-Nakai, and M. J. Donoghue. 1995. Phylogenetic diversity in shiitake inferred from nuclear ribosomal DNA sequences. Mycologia 87: 618-638. PDF

Hibbett, D. S., and M. J. Donoghue. 1996. Implications of phylogenetic studies for conservation of genetic diversity in shiitake mushrooms. Conservation Biology 10: 1321-1327. PDF

Hibbett, D. S., K. Hansen, and M. J. Donoghue. 1998. Phylogeny and biogeography of Lentinula inferred from an expanded rDNA dataset. Mycological Research 102: 1041-1049. PDF

Hibbett, D. S. 2001. Shiitake mushrooms and molecular clocks: historical biogeography of Lentinula. Journal of Biogeography 28: 231-241. PDF

Seelan, J-S, L. G. Nagy, E. Grand, D. S. Hibbett. 2015. Phylogenetic relationships and morphological evolution in Lentinus, Polyporellus and Neofavolus, emphasizing Southeast Asian taxa. Mycologia. 107:XXX-XXX doi: 10.3852/14-084 in press.

Cyphelloid and marine Agaricomycetes

Hibbett, D. S. and M. Binder. 2001. Evolution of marine mushrooms. Biological Bulletin 201: 319-322. PDF

Binder, M., and D. S. Hibbett. 2001. Phylogenetic relationships of the marine gasteromycete Nia vibrissa. Mycologia 93: 679-688.

Bodensteiner, P., M. Binder, R. Agerer, J.-M. Moncalvo and D. S. Hibbett. 2004.

Phylogenetic relationships of cyphelloid homobasidiomycetes. Molecular Phylogenetics and Evolution 33: 501-515. PDF

Binder, M., D. S. Hibbett, Z. Wang, and W. Farnham. 2006. Evolutionary origins of Mycaureola dilseae, a basidiomycete pathogen of the subtidal red alga Dilsea carnosa. American Journal of Botany 93: 547-556. PDF

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