Karen Hughes


1972 – Ph.D., University of Utah

Research Interests

My interests are in fungal (agaric) speciation patterns and biogeography.  Phylogenies based on DNA sequences are used to answer the following questions.

  • Do agaric  “species” have a global distribution indicating widespread gene flow via airborne spore distribution or are they partitioned into geographic sub-areas?  If partitioned, what factors act to prevent gene flow between populations and how did populations migrate to present-day distributions?
  • Are current distribution patterns within species a consequence of vicariance events or more recent quaternary migrations?

Together with Ron Petersen and many other mycological experts, we are examining agaric biodiversity in the Great Smoky Mountains National Park (GSMNP) with a grant from NSF. This is in conjunction with the All Taxa Biodiversity Inventory that is taking place.  We wish to answer the following questions:

  • What factors contribute to the unusually high diversity of fungi found in the Smokies? Is diversity partitioned?
  • What factors contribute to the unusually high rates of heterozygosity observed in fungi from the Smokies and are there limits to the observed heterozygosity.
  • How has biodiversity changed over a 50 year period?  Can the effects of climate change be detected?

A third interest is in modernizing biological collections.  The fungal herbarium at Tennessee  holds over 60,000 specimens.  An NSF grant has been awarded to digitize the collection and make it available through GBIF.  Funds are available for undergraduate and graduate students who are interested in collections to work on this project.



  • Aldrovandi  M. S. P., O’Meara, B, Johnson, J.E., Petersen, R.H., Hughes, K.W.(2015 In press). Xeromphalina section Xeromphalina: Intercontinental Biogeography and Cryptic species.  (Mycologia)
  • Petersen, R.H., Psurtseva, N., Zmitrovich, I., Arslanov, S., Hughes, K.W. 2015. Lignomyces, a new genus of pleurotoid Agaricomycetes.  Mycologia 107(5):1045-1054. doi: 10.3852/14-355
  • Hughes KW, Reboredo-Segovia A, Morris SD (2015) Cloning of ribosomal ITS PCR products creates frequent, non-random chimeric sequences – a test involving a heterozygotes between Gymnopus dichrous taxa I and II. Mycokeys 10: 45-56  doi: 10.3897/mycokeys.10.5126.
  • Hughes KW and Petersen RH. Transatlantic disjunction in fleshy fungi III: Gymnopus confluens.  Mycokeys. doi: 10.3897/mycokeys.9.4700
  • Petersen R, Borovička J, Segovia A, Hughes K (2015) Transatlantic disjunction in fleshy fungi. II. The Sparassis spathulata – S. brevipes complex Mycological Progress 14:1-18 doi:10.1007/s11557-015-1049-8
  • Tulloss RE, Rodriguez Caycedo C, Hughes KW, Gemp J, Kudzma LV, Wolfe B, Arora D. (2015) Nomenclatural changes in Amanita. II.  Amanitaceae 1(2):1-6
  • Petersen RH, Hughes KH, Justice J. (2014) Two new species of Ramaria from Arkansas.  MycoKeys  8:19-29 doi: 10.3897/mycokeys.8.7356.  www.pensoft.net/journals/mycokeys
  • Schock et al, 2014. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database bau061, doi: 10.1093/database/bau061 (http://database.oxfordjournals.org/content/2014/bau061.full)
  • Petersen RH, Hughes KH, (2014) Cauliflower Tales. McIlvania 23 (popular journal- article about sparassis) http://www.namyco.org/publications/mcilvainea/v23/cauliflower_tales.html
  • Petersen, R.H., Hughes, K., Voitk, A. 2014. Gymnopus eneficola—species nova from Newfoundland.  Omphalina 5(5):5-12
  • Hughes KW, Aldrovandi M, Petersen RH, Voitk A. 2014. Gymnopus dryophilus-like mushrooms in Newfoundland. Omphalina 5(5): 13-15.
  • Voitk A,  Hughes KW, Aldrovandi M, 2014. Dryophilic and dryophobic clade clusters. Omphalina 5(5): 17-20.
  • Lodge DL, Padamsee M, Matheny PB, Aime MC, Cantrell SA, Boertmann D, Kovalenko A, Vizzini A, Dentinger B, Kirk P, Ainsworth M, Moncalvo J-M, Vilgalys R, Larsson E, Lücking R, Griffith G, Smith M, Norvell LL, Desjardin DE, Redhead SA, Ovrebo CL, Lickey E, Ercole E, Hughes KW, Courtecuisse R, Young A, Binder M, Minnis A, Lindner DL, Ortiz-Sanatan B, Haight J, Læssøe T, Baroni TJ, Geml J, Hattori T (2014) Molecular phyologeny, morphology, pigment chemistry and ecology in Hygrophoraceae (Agaricales). Fungal Diversity 64: 1-99. (DOI) 10.1007/s13225-013-0259-0 http://www.springerlink.com/openurl.asp?genre=article&id=doi:10.1007/s13225-013-0259-0
  • Hughes KW, Reboredo-Segovia A, Petersen RH. (2014) Transatlantic disjunction in fleshy fungi. I. The sparassis crispa complex. Mycological Progress 13(2): 407-427
  • Hughes KW, Petersen RH, Lodge DJ, Bergemann, SE, Baumgartner K, Tulloss RE, Lickey E. (2013) Evolutionary consequences of putative intra- and interspecific hybridization in agaric fungi.  Mycologia: 105 (6):1577-1594 041 doi:10.3852/13-041
  • Niskanen, T,  Liimatainen, K,  Ammirati, J. F., and  Hughes, K. (2013)  Cortinarius section Sanguinei in North America.  Mycologia. 105(2):344-56. doi: 10.3852/12-086
  • Petersen RH and Hughes KW 2013.  The concept of taxa in some non-mycorrhizal Russulales.  Scripta Botanica Belgica 51: 1-xxx
  • Joseph F Ammirati, Karen W Hughes, Kare Liimatainen, Tuula Niskanen, and P Brandon Matheny (2013) Cortinarius hesleri and related species from Europe and western North American. Mycologia. 105(2):344-56. doi: 10.3852/12-086.
  • Petersen, RH, Hughes, KW, Adamcik S, ZDENKO Tkalcec, Z., Mesic, A. (2012)  Typification of three European species epithets attributable to Strobilomyces (Boletales) Czech Mycology 64 (2): 141-163
  • Van de Putte, K., Nuytinck, J., De Crop, E., Hughes, K, Verbeken, A. (2012)  Lactifluus volemus (Russulales) in Europe:  Three species in one-revealed by a multilocus geoealogical approach, Bayesian species delimitation and morphology.  In: Hidden Diversity Exposed, A case study of Lactifluus volemus sensu lato.  Ph.D. Thesis Ghent University
  • Baumgartner K, Baker B R, Korhonen K, Zhao J, Hughes K, Bruhn J, Bowman TS, Bergemann SE. 2012 Evidence of natural hybridization among homothallic members of the basidiomycete Armillaria mellea. Fungal Biol;116(6):677-91.
  • Petersen, RH, Dunlap J. and Hughes, KH.  (2011)  Reticulate spore ornamentation in Strobilomyces.  Mycosystema 30:901-911
  • Conrad. L. Schoch1et al. 2012 The internal transcribed spacer as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. 109:6241-6246   http://www.pnas.org/content/early/2012/03/23/1117018109.full.pdf+html
  • Christoffer Bugge Harder, D. Jean Lodge, Ronald H. Petersen, Karen W. Hughes, Joaquin Cifuentes Blanco, Tobias Guldberg Frøslev and Thomas Læssøe (2011) Amyloidity is not diagnostic for species in the Mycena pearsoniana complex (Mycena section Calodontes). Mycological Progress Vol. 11 (3): 725-732. DOI: 10.1007/s11557-011-0782-x
  • Jean-Philippe SR, Franklin JA, Buckley DS, Hughes K. (2011) The effect of mercury on trees and their mycorrhizal fungi. Environ. Pollut. 159(10): 2733-9.
  • Petersen, R.H. and Hughes, K.W. 2011. The concept of “taxa” in some non-mycorrhizal Russulales. Proceedings of the Russulales Congress, Belgium.
  • Edward A. Grand, K. W. Hughes and R. H. Petersen (2011) A phylogeny of Lentinus subg. Lentinus (Polyporales, Agaricomycetes), with emphasis on sects. Lentinus and Tigrini.
  • K. W. Hughes, D. Mather (undergraduate) and R. H. Petersen (2010). A new genus to accommodate Gymnopus acervatus (Agaricales). Mycologia   102(6);1463-1478.
  • Petersen, R.H. and Hughes, K.W.  (2010) The Xerula/Oudemansiella Complex. Nova Hedwigia Beiheft 136. J. Cramer Publ. Stuttgart 625pp
  • Soňa Ripková, Karen Hughes, Slavomír Adamčík, Viktor Kučera and Katarína Adamčíková (2010) The delimitation of Flammulina fennae. Mycological progress 9(4):46-484. DOI: 10.1007/s11557-009-0654-9. My contribution was the molecular part of this paper.  The remainder of the authors contributed a morphological analysis and PCA analysis. http://www.springerlink.com/content/806532ww14354565/fulltext.pdf
  • Petersen, R.H. and K. W. Hughes (2009) Names, Names, Names:  When nomenclature meets molecules.  McIlvainea 18 (1): 22-28
  • Hughes, K.W., R. H. Petersen and E. B. Lickey (2009) Using heterozygosity to estimate a percent DNA sequence similarity for environmental species delimitation across basidiomycete fungi. New Phytologist 182:795-798
  • Bidartondo, M.I. et al. (250 Authors) Preserving accuracy in GenBank.   Science 319:1616 (2008).  [Letter to Science concerning incorrectly named sequences in GenBank]
  • Ronald H. Petersen, Karen W. Hughes, Edgar B. Lickey, Alexander E. Kovalenko, Olga V. Morozova and Nadezhda V. Psurtseva  (2008) A new genus, Cruentomycena, with Mycena viscidocruenta as type species.  Mycotaxon 105:119-136.
  • Petersen, R.H. and Hughes, K.W.  (2007) Some agaric distributions involving Pacific landmasses and Pacific Rim. Mycoscience 48(1):1-14.
  • Hughes, K.W. and Petersen, R.H. (2007 ) Relationships among Collybia s. str. from Greenland, North America and Eurasia.p 99-105 In:  Meddelelser om Gronland, Bioscience: Arctic and Alpine Mycology 9: Eds  D. Boertmann and H. Knudsen. 161pp.
  • Lickey, E.B., Tieken, S., Hughes, K. W. and Petersen, R.H. (2007) The mushroom TWIG: A marvelous mycological menagerie in the Mountains.  Southeastern Naturalist Special Issue 1:73-82
  • Spatafora, J.W., Hughes, K.W. and Blackwell, M.B., Eds. 2006. A Phylogeny of Kingdom Fungi: Deep Hypha Issue.  Mycologia 98 (6): 1105pp.
  • Badalyan, S.M., Hughes, K.W., Sakeyan, C.Z. and Helmbrecht, E. (2006)  Morphology, growth characteristics and genetic variability of the edible medicinal mushroom Flammulina velutipes (W. Curt.: Fr.) Singer collections.  Int. J. Med. Mushrooms 8:263-278.
  • Mata, J. L., Hughes, K.W. and Petersen, R.H. (2007) An investigation of omphalotaceae (Fungi: Euagarics) with emphasis on the genus Gymnopus.  Sydowia: 59(2) 181-289.
  • Matheny P.B., Zheng Wang, Manfred Binder, Judd M. Curtis, Young Woon Lim, R. Henrik Nilsson, Karen W. Hughes, Valérie Hofstetter, Joseph F. Ammirati, Conrad L. Schoch, Ewald Langer, Gitta Langer, David J. McLaughlin, Andrew W. Wilson, Tobias Frøslev, Zai-Wei Ge,Richard W. Kerrigan, Jason C. Slot, Zhu-Liang Yang, Timothy J. Baroni, Michael Fischer, Kentaro Hosaka Kenji Matsuura, Michelle T. Seidl, Jukka Vauras and David S. Hibbett (2006) Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi) Molecular Phylogenetics and Evolution: 430-451
  • 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, D.S. Hibbett (2006) Major clades of Agaricales: a multi-locus phylogenetic overview.  Mycologia 98:984-997.
  • James T. Y., Frank Kauff’, Conrad L. Schoch, P. Brandon Matheny,  Valerie Hofstetter, Cymon J. Coxlt, Gail Cel, Cecile Gueidan, Emily Fraker, Jolanta Miadlikowska, H. Thorsten Lumbsch, Alexandra Rauhut, Valerie Reeb, A. Elizabeth Arnoldl, Anja Amtotf, Jason E. Stajich, Kentaro Hosaka, Gi-Ho Sung, Desiree Johnson, Ben O’Rourke, Michael Crockett,    Manfred Binder, Judd M. Curtis, Jason C. Slot, Zheng Wang, Andrew W. Wilson, Arthur Sch?ler, Joyce E. Longcore, Kerry O’Donnell, Sharon Mozley-Standridge , David Porter, Peter M. Letcher , Martha J. Powell, John W. Taylor, Merlin M. White, Gareth W. Griffith, David R. Davies, Richard A. Humber, Joseph B. Morton, Junta Sugiyama, Amy Y. Rossman, Jack D. Rogers, Don H. Pfister, David Hewitt, Karen Hansen, Sarah Hambleton, Robert A. Shoemaker, Jan Kohlmeyer , Brigitte Volkmann-Kohimeyer, Robert A.  Spotts, Maryna Serdani, Pedro W. Crous, Karen W. Hughes, Kenji Matsuura, Ewald Langer , Gitta Langer, Wendy A. Untereiner, Robert Lucking, Burkhard Budel, David M. Geiser, Andre Aptroot, Paul Diederich, lmke Schmitt, Matthias Schultz, Rebecca Yahr, David S. Hibbett, Francois Lutzoni, David J. McLaughlin, Joseph W. Spatafora & Rytas Vilgalys (2006) Reconstructing the early evolution of Fungi using a six gene phylogeny.  Nature 443:818-822.
  • Kruger, D., Petersen, R.H. and Hughes, K. W. (2006) Molecular phylogenies and mating study data in Polyporus with special emphasis on group’ Melanopus’ (Basidiomycota).  Mycological Progress 5:185-206.