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Our lab pursues diverse projects in fungal evolution, ecology, and functional biology, with a focus on Agaricomycetes (mushroom-forming Fungi). A common thread uniting all of our work is a phylogenetic perspective, which is derived from analyses of molecular sequences. We take an integrative approach to fungal biology, combining fieldwork and specimen-based studies with lab-based and computational studies of molecular evolution, development, and comparative genomics. Our laboratory has facilities for molecular biology, as well as culturing and anatomical study, and we maintain a small herbarium containing specimens that members of the lab have collected locally and overseas.
The research synopses below outline the major foci of our research so far and the references section provides a guide to representative publications in each area. However, not every project has been mentioned. To learn more about our work, go to the People pages and browse our list of Publications. To get a sense of the day-to-day activities of our lab, visit our lab blog.
Major research themes of our lab include:
1. Diversity and evolution of nutritional modes in Agaricomycetes, including decay biology and mycorrhizal symbioses
2. Morphological and developmental evolution in Agaricomycetes
3. Systematics and phyloinformatics: translating trees and sequence data into taxonomy
4. Phylogenetic diversity and evolution in fungi and specific clades of Agaricomycetes, including:
• Polyporales and Gloeophyllales
• Agaricomycetidae
• Lentinoid fungi, including shiitake mushrooms
• Cyphelloid and marine Agaricomycetes
Agaricomycetes include the major concentration of wood decay fungi, as well as ectomycorrhizal (ECM) symbionts of trees such as oaks, birches, willows, pines, eucalypts, and dipterocarps. Wood decay in Agaricomycetes involves two major mechanisms, termed “white rot” (in which all components of woody plant cell walls are degraded, including the recalcitrant lignin fraction) and “brown rot” (in which cellulose is rapidly decayed, but lignin is left largely intact). Through their functioning as wood decayers and ECM symbionts, Agaricomycetes have profound impacts on forest health, timber-based industries, and the carbon cycle. Lignocelluloytic enzymes of Agaricomycetes are under investigation for potential applications in biofuel production and other green technologies.
A general goal of our research is to understand the evolution of nutritional modes in Agaricomycetes, and their impact on the evolution of terrestrial ecosystems. Our earlier work in this area made use of phylogenies derived from PCR-amplified molecular markers, which we used to reconstruct the historical patterns of transitions between decayer and ECM nutritional modes, and switches between white rot and brown rot decay chemistries. We also used phylogenetic comparative methods to address correlations between decay types and substrate ranges, as well as reversibility of “mutualistic” ECM associations.
Our molecular phylogenetic studies provided an essential comparative context for our current research in this area, which emphasizes comparative genomics. Phylogenomic analyses have provided macroevolutionary insights that have extended, or in some cases contradicted, inferences based solely on phylogenies. For example, phylogenomic analyses confirmed our prior findings that “white rot” is plesiomorphic in Agaricomycetes. However, comparative genomic studies (and molecular clock analyses) suggest that it is unlikely that there have been widespread reversals from ECM symbioses to decayer nutritional modes, as we had concluded earlier based on phylogenetic analyses.
Combined with molecular clock analyses and the paleomycological record, comparative fungal genomics provides insight into the evolution of terrestrial ecosystems and the carbon cycle over geologic time. Based on an analysis of 31 fungal genomes, we found that the origin of class II fungal peroxidases, which represent a major class of lignin-degrading enzymes, roughly coincided with the decline in carbon sequestration (leading to coal formation) at the end of the Permo-Carboniferous. Lignin is a major precursor of coal. Thus, the evolution of white rot may have had a large impact on formation of a major fossil fuel resource. In ongoing research with new genomes we are trying to refine our understanding of the origin and diversification of class II fungal peroxidases and other enzymes that are involved in white rot. We are also using the existing genomes as a resource to enable comparative transcriptomic studies of different species of wood decay fungi as they decay different wood species. In this way, we hope to gain insight into the genetic bases of substrate specificity and substrate switching in wood decaying Agaricomycetes.
Fungi represent an independent origin of multicellularity in eukaryotes, and the most complex, developmentally integrated forms in the fungi are fruiting bodies of Agaricomycetes. Examples include gilled mushrooms (agarics), polypores, coral fungi, crustlike “resupinate” fungi, and diverse gasteroid forms (which produce their spores internally, such as puffballs, stinkhorns, birds nest fungi, etc). As in our studies of nutritional modes, we have used molecular phylogenies to reconstruct patterns of morphological evolution in Agaricomycetes, and we have used phylogenetic comparative methods to address trends in morphological evolution. General inferences from these analyses are that (1) resupinate forms may represent a plesiomorphic and paraphyletic assemblage, from which more complex forms have evolved repeatedly (although there have also been reversals to resupinate forms); (2) coralloid forms may be evolutionarily labile; (3) evolution of gasteroid forms is irreversible; and (4) agaricoid forms have evolved repeatedly in diverse lineages, and may be “stable attractors” in morphospace. The latter inference is consistent with the presence of a gilled mushroom in the Cretaceous, which we described from New Jersey amber and named Archaeomarasmius leggeti, because of its similarity to the extant genera Marasmius and Marasmiellus (Agaricales). The discovery of A. leggeti suggests that the gilled mushroom morphology has been conserved for 90-100 million years in at least one clade of Agaricomycetes.
To understand the mechanisms of morphological evolution it is necessary to describe the changes in developmental programs that underlie morphological transformations. During a post-doc, at the Tottori Mycological Institute in Japan, I studied comparative developmental morphology in “lentinoid” fungi, which are gilled mushrooms that have anatomical similarities to certain polypores. Prior phylogenetic analyses as a graduate student had suggested that lentinoid fungi are polyphyletic, and that gilled forms had evolved repetedly from poroid ancestors. Developmental analyses using scanning electron microscopy revealed basic developmental differences among the independently-derived gills and provided clues into the developmental shifts involved in transformations between gills and pores. I also studied the heritability and development of a gasteromycete-like “secotioid” variant of the gilled mushroom Lentinus tigrinus, confirming earlier (and only partially documented) reports that the secotioid form is conferred by a recessive allele of a single locus.
We are continuing to study morphological evolution using phylogenetic comparative analyses and genome-enabled studies in fungal evolutionary developmental biology (evo-devo). Our evo-devo analyses continue to focus on lentinoid fungi, and are centered on Lentinus tigrinus, including the secotioid form. By studying the genetic and developmental bases of the secotioid form in L. tigrinus we hope to gain insight into the evolution of gasteromycetes. In the course of this work, we found that blue light is required for normal formation of a pileus (mushroom cap) in L. tigrinus; without blue light a coralloid fruiting body is formed. We are now using transcriptomic approaches to understand light-induced pileus formation, (a form of developmental plasticity), which we speculate could provide clues to the mechanisms of evolutionary transformations between coralloid and pileate forms.
The third major focus of my research involves translating knowledge from phylogenetic trees and comparative sequence analyses into formal classifications. Taxonomy may not be the most glamorous of biological disciplines, but it provides an essential underpinning of comparative biology, and enables communication among basic and applied scientists, educators, students, and the general public. I have focused on the relationship between phylogeny and classification at the level of species and entire clades.
At the species level, I have written on the use of sequence data for describing species, with or without physical specimens, and I have been tangentially involved in the debate over “one name one fungus” (which concerns the transition from a dual system of nomenclature for sexual and asexual morphs for the same species, to a system of unitary nomenclature). At the level of whole clades, I have considered the utility of rank-free taxonomy for translating phylogenies into classifications, and, with the assistance of some talented biology and computer science students, I developed an early (2005) prototype for automated phylogenetic reconstruction and tree-based classification. In addition to these arguably esoteric contributions, I also led the effort to create a consensus higher-level phylogenetic classification for all fungi as part of the collaborative Assembling the Fungal Tree of Life (AFTOL) project. The “AFTOL classification” was published in 2007 and remains a standard, if somewhat out of date, taxonomy for fungi.
Currently, I am collaborating as part of the Open Tree of Life project to synthesize phylogenetic trees and taxonomy to construct a comprehensive phylogeny and classification for fungi (and all of life). Open Tree has provided a proof-of-concept model for integration of phylogenies and taxonomy, but it is far from complete. In the near future, we plan to contribute more phylogenies to Open Tree, and use those data to prepare a much-needed update of the 2007 AFTOL classification.
Through AFTOL and other projects, our lab has studied phylogenetic relationships of Fungi as whole, and specific groups within Agaricomycotina.
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.
Hibbett, D. S., Luz-Beatriz Gilbert, and Michael J. Donoghue. 2000. Evolutionary instability of ectomycorrhizal symbioses in basidiomycetes. Nature 407: 506-508. PDF
Hibbett, D. S., and M. J. Donoghue. 2001. Analysis of correlations among wood decay mechanisms, mating systems, and substrate ranges in homobasidiomycetes. Systematic Biology 50: 215-242. PDF
Hibbett, D. S., and P. B. Matheny. 2009. Relative ages of ectomycorrhizal mushrooms and their plant hosts. BMC Biology 7:13 http://www.biomedcentral.com/1741-7007/7/13
Martinez, D., J. Challacombe, I. Morgenstern, D. Hibbett, M. Schmoll, C. P. Kubicek, P. Ferreira, F. J. Ruiz-Duenas, A. T. Martinez, P. Kersten, K. E. Hammel, A. Vanden Wymelenberg, J. Gaskell, E. Lindquist, G. Sabat, S. Splinter Bondurant, L. F. Larrondo, P. Canessa, R. Vicuna, J. Yadav, H. Doddapaneni, V. Subramanian, A. G. Pisabarro, J. L. Lavín, J. A. Oguiza, E. Master, B. Henrissat, P. M. Coutinho, P. Harris, J. K. Magnuson, S. Baker, K. Bruno, W. Kenealy, P. J. Hoegger, U. Kues, P. Ramiaiya, S. Lucas, A. Salamov, H. Shapiro, H. Tu, C. L. Chee, M. Misra, G. Xie, S. Teter, D. Yaver, T. James, M. Mokrejs, M. Popisek, I. Grigoriev, T. Brettin, D. Rokhsar, R. Berka and D. Cullen. 2009. Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proceedings of the National Academy of Sciences, U.S.A. 106: 1954-1959. PDF
Eastwood, D. C., D. Floudas, M. Binder, A. Majcherczyk, P. Schneider, A. Aerts, F. O. Asiegbu, S. E. Baker, K. Barry, M. Blumentritt, P. M. Coutinho, D. Cullen, R. P. De Vries, A. Gathman, B. Goodell, B. Henrissat, K. Ihrmark, H. Kauserud, A. Kohler, K. LaButti, A. Lapidus, J. L. Lavin, Y.-H. Lee, E. Lindquist, W. Lilly, S. Lucas, E. Morin, C. Murat, J. A. Oguiza, J. Park, A. G. Pisabarro, R. Riley, A. Rosling, A. Salamov, O. Schmidt, J. Schmutz, I. Skrede, J. Stenlid, A. Wiebenga, X. Xie, U. Kües, D. S. Hibbett, D. Hoffmeister, N. Högberg, F. Martin, I., V. Grigoriev, S. C. Watkinson. 2011. Evolution of plant cell wall degrading machinery underlies the functional diversity of forest fungi. Science 333: 762-765. PDF
Floudas, D., M. Binder, R, Riley, K. Barry, R. A. Blanchette, B. Henrissat, A. T. Martínez, R. Otillar, J. W. Spatafora, J. S. Yadav, A. Aerts, I. Benoit,, A. Boyd, A. Carlson, A. Copeland, P. M. Coutinho, R. P. de Vries,, P. Ferreira, K. Findley, B. Foster, J. Gaskell, D. Glotzer, P. Górecki, J. Heitman, C. Hesse, C. Hori, K. Igarashi, J. A. Jurgens, N. Kallen, P. Kersten, A. Kohler, U. Kües, T. K. A. Kumar, A. Kuo, K. LaButti, L. F. Larrondo, E. Lindquist, A. Ling, V. Lombard, S. Lucas, T. Lundell, R. Martin, D. J. McLaughlin, I. Morgenstern, E. Morin, C. Murat, M. Nolan, R. A. Ohm, A. Patyshakuliyeva, A. Rokas, F. J. Ruiz-Dueñas, G. Sabat, A. Salamov, M. Samejima, J. Schmutz, J. C. Slot, F. St. John, J. Stenlid, H. Sun, S. Sun, K. Syed, A. Tsang, A. Wiebenga, D. Young, A. Pisabarro, D. C. Eastwood, F. Martin, D. Cullen, I. V. Grigoriev, and D. S. Hibbett. 2012. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336: 1715-1719. PDF
Ruiz-Dueñas, Francisco J., Taina Lundell, Dimitrios Floudas, Laszlo G. Nagy, José M. Barrasa, David S. Hibbett, and Angel T. Martínez. 2013. Lignin-degrading peroxidases in Polyporales: an evolutionary survey based on 10 sequenced genomes. Mycologia 105, 1428-1444, doi: 10.3852/13-059. PDF
Hori, Chiaki, Jill Gaskell, Kiyohiko Igarashi, Masahiro Samejima, David Hibbett, Bernard Henrissat, and Dan Cullen. 2013. Genomewide analysis of polysaccharides degrading enzymes in 11 white- and brown-rot Polyporales provides insight into mechanisms of wood decay. Mycologia 105, 1412-1427, doi:10.3852/13-072. PDF
Riley, Robert W., Asaf A. Salamov, Daren W. Brown, Laszlo G Nagy, Dimitrios Floudas, Benjamin W Held, Anthony Levasseur, Vincent Lombard, Emmanuelle Morin, Robert Otillar, Erika A Lindquist, Hui Sun, Kurt M. LaButti, Jeremy Schmutz, Dina Jabbour, Hong Luo, Scott E Baker, Antonio G Pisabarro, Jonathan D Walton, Robert A Blanchette, Bernard Henrissat, Francis Martin, Dan Cullen, David S. Hibbett, and Igor V. Grigoriev. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white rot/brown rot paradigm for wood decay fungi. 2014. Proceedings of the National Academy of Science USA 111: Early Edition doi: 10.1073/pnas.1400592111 (2014). PDF
Kohler, A. A. Kuo, L. G. Nagy, E. Morin, K. W. Barry, F. Buscot, B. Canbäck, C Choi, N. Cichocki, A. Clum, J.Colpaert, A. Copeland, M. D. Costa, J. Doré, D. Floudas, G. Gay, M. Gardes, M. Girlanda, G. Grelet, H. Gryta, B. Henrissat, S. Herrmann, J Hess, N Högberg, P Jargat, T Johansson, H.-R. Khouja, K. LaButti, U. Lahrmann, A. Levasseur, E. A. Lindquist, A. Lipzen, R. Marmeisse, E. Martino, C. Murat, C.Y. Ngan, U. Nehls, M. Peter, J.M. Plett, A. Pringle, R. Ohm, S Perotto, R. Riley, F. Rineau, J. Ruytinx, A. Salamov, F. Shah, H. Sun, M Tarkka, A. Tritt, C. Veneault-Fourrey, S Zimmermann, A Zuccaro, A. Tunlid, I. V. Grigoriev, D. S. Hibbett*, F. Martin*. 2015. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nature Genetics 47: 410-415. doi:10.1038/ng.3223 PDF *corresponding authors
Floudas, Dimitrios, Laszlo G. Nagy, Benjamin W. Held, Robert Riley, Robin A. Ohm, Robert A. Blanchette, Ursula Kües, Igor V. Grigoriev, Robert E. Minto, David S. Hibbett. 2015. Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii. Fungal Genetics and Biology 76: 78-92. doi:10.1016/j.fgb.2015.02.002. PDF
Nagy, L. G., R. Riley, A. Tritt, C. Adam, C. Daum, D. Floudas, H. Sun, J. S. Yadav, J. Pangilinan, K.-H. Larsson, K. Matsuura, K. Barry, K. LaButti, R. Kuo, R. Ohm, S. S. Bhattacharya, T. Shirouzu, Y. Yoshinaga, F. M. Martin, I. V. Grigoriev, and D. S. Hibbett. Comparative genomics of early-diverging mushroom-forming fungi provides insights into the origins of lignocellulose decay capabilities. Molecular Biology and Evolution (in review).
Hibbett, D. S., S. Murakami, and A. Tsuneda. 1993. Sporocarp ontogeny in Panus: evolution and classification. American Journal of Botany 80: 1336-1348. PDF
Hibbett, D. S., S. Murakami, and A. Tsuneda. 1993. Hymenophore development and evolution in Lentinus. Mycologia 85: 428-443. PDF
Hibbett, D. S., A. Tsuneda, and S. Murakami. 1994. The secotioid form of Lentinus tigrinus: genetics and development of a fungal morphological innovation. American Journal of Botany 81: 466-478. PDF
Hibbett, D. S., D. Grimaldi, and M. J. Donoghue. 1995. Cretaceous mushrooms in amber. Nature 377: 487.
Hibbett, D. S., D. Grimaldi, and M. J. Donoghue. 1997. Fossil mushrooms from Cretaceous and Miocene ambers and the evolution of homobasidiomycetes. American Journal of Botany 84: 981-991. PDF
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. Proceedings of the National Academy of Sciences, U.S.A. 94: 12002-12006. PDF
Hibbett, D. S., and M. Binder. 2002. Evolution of complex fruiting body morphologies in homobasidiomycetes. Proceedings of the Royal Society of London Series B. 269: 1963-1969. PDF
Hibbett, D. S. 2004. Trends in morphological evolution in homobasidiomycetes. Systematic Biology 53: 889-903. PDF
Binder, M., D. S. Hibbett, K.-H. Larsson, E. Larsson, and E. Langer. 2005. The phylogenetic distribution of resupinate forms in the homobasidiomycetes. Systematics and Biodiversity 3: 113-157. PDF
Hibbett, D. S. 2007. After the gold rush, or before the flood? Evolutionary morphology of mushroom-forming fungi (Agaricomycetes) in the early 21st century. Mycological Research 111: 1001-1018. PDF
Wilson, A., M. Binder, and D. S. Hibbett. 2011. Effects of fruiting body morphology on diversification rates in three independent clades of fungi estimated using binary state speciation and extinction analysis. Evolution doi:10.1111/j.1558-5646.2010.01214.x. PDF
Hibbett, D. S., and M. J. Donoghue. 1998. Integrating phylogenetic analysis and classification in fungi. Mycologia 90:347-356. PDF
Taylor J. W., D. J. Jacobson, S. Kroken, T. Kasuga, D. M. Geiser, D. S. Hibbett, and M. C. Fisher. 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology 31: 21-32. PDF
Hibbett, D. S., R. H. Nilsson, M. Snyder, M. Fonseca, J. Costanzo, and M. Shonfeld. 2005. Automated Phylogenetic Taxonomy: An Example in the Homobasidiomycetes (Mushroom-Forming Fungi). Systematic Biology 54: 660-668. PDF
Hibbett, D. S., M. Binder, J. F. Bischoff, M. Blackwell, P. F. Cannon, O. E. Eriksson, S. Huhndorf, T. James, P. M. Kirk, R. Lücking, T. Lumbsch, F. Lutzoni, P. B. Matheny, D. J. Mclaughlin, M. J. Powell, S. Redhead, C. L. Schoch, J. W. Spatafora, J. A. Stalpers, R. Vilgalys, M. C. Aime, A. Aptroot, R. Bauer, D. Begerow, G. L. Benny, L. A. Castlebury, P. W. Crous, Y.-C. Dai, W. Gams, D. M. Geiser, G. W. Griffith, C. Gueidan, D. L. Hawksworth, G. Hestmark, K. Hosaka, R. A. Humber, K. Hyde, J. E. Ironside, U. Kõljalg, C. P. Kurtzman, K.-H. Larsson, R. Lichtwardt, J. Longcore, J. Miądlikowska, A. Miller, J.-M. Moncalvo, S. Mozley-Standridge, F. Oberwinkler, E. Parmasto, V. Reeb, J. D. Rogers, C. Roux, L. Ryvarden, J. P. Sampaio, A. Schüßler, J. Sugiyama, R. G. Thorn, L. Tibell, W. A. Untereiner, C. Walker, Z. Wang, A. Weir, M. Weiß, M. M. White, K. Winka, Y.-J. Yao, N. Zhang. 2007. A higher-level phylogenetic classification of the Fungi. Mycological Research 111: 509-547. PDF
Hibbett, D. S., A. Ohman, D. Glotzer, M. Nuhn, P. M. Kirk, and R. H. Nilsson. 2011. Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences. Fungal Biology Reviews 25: 38-47. PDF
Hibbett, D. S., and D. Glotzer. 2011. Where are all the undocumented fungal species? A study of Mortierella demonstrates the need for sequence-based classification. New Phytologist 191: 592-596.PDF
Hibbett, D. S., and J. W. Taylor. 2013. Fungal systematics: is a new age of enlightenment at hand? Nature Reviews Microbiology doi:10.1038/nrmicro2942. PDF
Drew, B.T., R. Gazis, P. Cabezas, K.S. Swithers, J. Deng, R. Rodriguez, L.A. Katz, K.A. Crandall, D.S. Hibbett, D.E. Soltis. 2013. Lost branches on the tree of life. PLOS Biology 11:e1001636. PDF
Hinchcliff, C. E., S. A. Smith, J. F. Allman, G. Burleigh, R. Chaudury, L. Coghill, K. A. Crandall, J. Deng, B. Drew, R. Gazis, K. Gude, D. S. Hibbett, L. A. Katz, H. D. Laughinghouse IV, E. J. McTavish, P. E. Midford, C. L. Owen, R. H. Ree, J. A. Rees, D. E. Soltis, T. Williams, and K. A. Cranston. 2015. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences, U.S.A. doi: 10.1073/pnas.1423041112 PDF
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
