Taylor Lab

321 Koshland Hall
Department of Plant and Microbial Biology
University of California at Berkeley
For an introduction to the Taylor Lab click here.

Lab Personnel	Former Post Docs and Grad Students	Other Emeritus Personnel
Chris Ellison Betty Gilbert David Jacobson Tom Sharpton Jason Stajich John Taylor Elizabeth Turner Christopher Villalta Emily Whiston	Chris Bentis Mary Berbee Austin Burt Jeremy Dettman Mat Fisher Andrea Gargas David Geiser Deb Greene Hanna Johannesson Vasso Koupoufanou Scott Kroken Steve Lee Kathy Lobuglio Georgiana May Jess Morgan Teresa Pawlowska Jamie Platt Anne Pringle Greg Saenz Eric Swann Jeff Townsend Rachel Whitaker	Erlend Aa Rachel Adams David Baker Dee Carter Diana Chen Andy Chiang Michael Cruse Briane Daniels Bryan Dechairo Joelle Dupont Thomas Gallagher Fred Harbinski Takao Kasuga Brian King Tonya Lang Thomas Lee Juan McEwen	Dave McLaughlin Tom Mitchell Danielle Nichols Hiromi Nishida Rod Olarte Don Reynolds Ray Salcedo Crystal Sau Ken Takeoka Anders Tehler Robin Telerant Kwan Teoh Eze Uzosike Howard Whisler

Tour the Taylor Lab

Your virtual tour of the Taylor Lab should start at the beginning. However, you may jump start the tour by viewing the many pieces of shared equipment, by looking at some sample results or viewing the fruitful results of the annual Mendocino mushroom foray.

Most Recent Publications:

Thomas J. Sharpton, Daniel E. Neafsey, James E. Galagan and John W. Taylor. 2008. Mechanisms of intron gain and loss in Cryptococcus. Genome Biology 2008, 9:R24 (doi:10.1186/gb-2008-9-1-r24).
Morgan, J.A.T., Vredenburg,V.T., Rachowicz, L.J., Knapp, R.A., Stice, M.J., Tunstall, T., Bingham, R.E., Parker, J.M., Longcore, J.E., Moritz, C., Briggs, C.J., Taylor, J.W. 2007. Enigmatic amphibian declines and emerging infectious disease: population genetics of the frog killing fungus Batrachochytrium dendrobatidis. PNAS 104:13845-13850.
Mary L. Berbee, John W. Taylor. 2007. Rhynie chert: a window into a lost world of complex plant-fungus interactions. New Phytologist 174(3): 475–479. doi:10.1111/j.1469-8137.2007.02080.x
Taylor, J.W., Turner, E., Pringle, A., Dettman, J., Johannesson, H. 2007. Fungal species: thoughts on their recognition, maintenance and selection. Pp. 313-339, In 'Fungi in the Environment'. (British Mycological Society Symposia No. 25) eds. G.M. Gadd, S.C. Watkinson and P.S. Dyer. Cambridge: Cambridge University Press.
John W. Taylor & Mary L. Berbee. 2006. Dating divergences in the Fungal Tree of Life: review and new analyses. Mycologia 2006 98: 838-849.
Meredith Blackwell, David S. Hibbett, John W. Taylor & Joseph W. Spatafora. 2006. Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha). Mycologia 2006 98: 829-837.
Taylor, John W.; Turner, Elizabeth; Townsend, Jeffrey P.; Dettman, Jeremy R.; Jacobson, David. 2006. Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi. Philosophical Transactions of the Royal Society of London B Biological Sciences 361(1475): 1947-1963.
James TY, Kauff F, Schoch C, Matheny PB, Hofstetter V, Cox CJ, Celio G, Gueidan D, Fraker E, Miadlikowska J, Lumbsch HT, Rauhut A, Reeb V, Arnold AE, Amtoft A, Stajich JE, Hosaka K, Sung G, Johnson D, O'Rourke B, Crockett M, Binder M, Curtis JH, Slot JC, Wang Z, Wilson AW, Schussler A, Longcore JE, O'Donnell K, Mozley-Standridge S, Porter D, Letcher PM, Powell MJ, Taylor JW, White MM, Griffith GW, Davies DR, Humber RA, Morton JB, Sugiyama J, Rossman AY, Rogers JD, Pfister DH, Hewitt D, Hansen K, Hambleton S, Shoemaker RA, Kohlmeyer J, Volkmann-Kohlmeyer B, Spotts RA, Serdani M, Crous PW, Hughes KW, Matsuura K, Langer E, Langer G, Untereiner WA, Lucking R, Budel B, Geiser DM, Aptroot A, Diederich P, Schmitt I, Schultz M, Yahr R, Hibbett DS, Lutzoni F, McLaughlin DJ, Spatafora JW, and Vilgalys R. 2006. Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature 443:818-822. doi: 10.1038/nature05110
David J. Jacobson, Jeremy R. Dettman, Rachel I. Adams, Cornelia Boesl, Shahana Sultana, Till Roenneberg, Martha Merrow, Margarida Duarte, Isabel Marques, Alexandra Ushakova, Patrícia Carneiro, Arnaldo Videira, Laura Navarro-Sampedro, María Olmedo, Luis M. Corrochano and John W. Taylor. 2006. New findings of Neurospora in Europe and comparisons of diversity in temperate climates on continental scales. Mycologia 98(4): 550-559.
Jeremey R. Dettman, David J. Jacobson and John W. Taylor. 2006. Multilocus sequence data reveal extensive phylogenetic species diversity within the Neurospora discreta complex. Mycologia 98(3): 436–446.
Matute, D.R., Sepulveda, V.E., Quesada, L.M., Goldman, G.H., Taylor, J.W., Restrepo, A., McEwen, J.G. 2006. Microsatellite analysis of three phylogenetic species of Paracoccidioides brasiliensis. J. Clinical Microbiology 44: 2153-2157.
H. Johannesson, T. Kasuga, R.A. Schaller, B. Good, M.J. Gardner, J.P. Townsend, G.T. Cole and J.W. Taylor. 2006. Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii. Fungal Genetics and Biology 43(8): 545-559.
Taylor, J.W. 2006. Evolution of human-pathogenic fungi: Phylogenies and species. Pp. 113-132 and Color Plate 5. In: Molecular Principles of Fungal Pathogenesis, J. Heitman et al. (eds). ASM Press, Washington, D.C.
Aa, E., Townsend, J. P., Adams, R. I., Nielsen, K. M., Taylor, J. W. 2006. Population structure and gene evolution in Saccharomyces cerevisiae. FEMS Yeast Research 6(5): 702-715.
Matute, D.R., McEwen, J.G., Montes, B.A., San-Blas, G., Bagagli, E., Rauscher, J.T., Restrepo, A., Morais, F., Nino-Vega, G., Taylor, J.W. 2006. Cryptic speciation and recombination in the fungus Paracoccidioides brasiliensis as revealed by gene genealogies. Molecular Biology and Evolution 23: 65-73.
Takao Kasuga, Jeffrey P. Townsend, Chaoguang Tian, Luz B. Gilbert, Gertrud Mannhaupt, John W. Taylor and N. Louise Glass. 2005. Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Research 33(20): 6469–6485.
Rachowicz, L. J., Hero, J.-M., Alford, R. A., Taylor, J. W., Morgan, J. A. T., Vredenberg, V. T., Collins, J. P. and C. J. Briggs. 2005. The novel and endemic pathogen hypotheses: Competing explanations for the origin of emerging infectious diseases of wildlife. Conservation Biology 19:1441-1447.
Rachel J. Whitaker, Dennis W. Grogan and John W. Taylor. 2005. Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus ‘islandicus’. Molecular Biology and Evolution 22(12): 2354-2361; doi:10.1093/molbev/msi233
Johannesson, H., J.P. Townsend, C.-Y. Hung, G.T. Cole, J.W. Taylor. 2005. Concerted evolution of the repeats of an immunomodulating cell surface protein, SOWgp, of the human pathogenic fungi Coccidioides immitis and C. posadasii. Genetics 171:109-117.
Pringle, A., D.M. Baker, J.L. Platt, J.P. Wares, J.P. Latge and J.W. Taylor. 2005. Cryptic speciation in the cosmopolitan and clonal human pathogenic fungus Aspergillus fumigatus. Evolution 59(9): 1886-1899.
Pawlowska, T.E. and J.W. Taylor. 2005. Arbuscular mycorrhizal fungi: Hyphal fusion and multigenomic structure (reply). Nature 433(7022): E4 (doi: 10.1038/nature03295).
Jeffrey P. Townsend and John W. Taylor. 2005. Designing experiments using spotted microarrays to detect gene regulation differences within and among Species. Methods in Enzymology 395: 597-617.
Nascimento, T., Martinez, R., Lopes, A. R., Bernardes, L. A. D., Barco, C. P., Goldman, M. H. S., Taylor, J. W., McEwen, J. G., Nobrega, M. P., Nobrega, F. G. and Goldman, G. H. 2004. Detection and selection of microsatellites in the genome of Paracoccidioides brasiliensis as molecular markers for clinical and epidemiological studies. Journal of Clinical Microbiology 42: 5007-5014.
Dettman, J.R. and Taylor, J.W. 2004. Mutation and evolution of microsatellite loci in Neurospora. Genetics 168: 1231-1248.
John W. Taylor, Joseph Spatafora, Kerry O'Donnell, Francois Lutzoni, Timothy James, David S. Hibbett, David Geiser, Thomas D. Bruns and Meredith Blackwell. 2004. The Fungi. In: Assembling the tree of life. Edited by Joel Cracraft and Michael J. Donoghue. Oxford University Press, pp. 171 - 194. (download large file: 13mb)
Johannesson, H., Vidal, P., Guarro, J., Herr, R. A., Cole, G. T., John W. Taylor. 2004. Positive directional selection in the proline-rich antigen (PRA) gene among the human pathogenic fungi Coccidioides immitis, C. posadasii and their closest relatives. Molecular Biology and Evolution 21(6):1134-1145.
Pawlowska, T. E. and Taylor, J. W. 2004. Organization of genetic variation in individuals of arbuscular mycorrhizal fungi. Nature 427(6976): 733-737.
David J. Jacobson, Amy J. Powell, Jeremy R. Dettman, Gregory S. Saenz, Magdalen M. Barton, Megan D. Hiltz, William H. Dvorachek, Jr., N. Louise Glass, John W. Taylor and Donald O. Natvig. 2004. Neurospora in temperate forests of western North America. Mycologia 96(1): 66-74.
Medina, M., Collins, A.G., Taylor, J.W., Valentine, J.W., Lipps, J.H., Amaral-Zettler, L., and M. L. Sogin. 2003. Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa. International Journal of Astrobiology 2 (3) : 203–211.
Birgitte Andersen, Kristian F. Nielsen, Ulf Thrane, Tim Szaro, John Taylor and Bruce B. Jarvis. 2003. Molecular and phenotypic descriptions of Stachybotrys chlorohalonata sp. nov. and two chemotypes of Stachybotrys chartarum found in water-damaged buildings. Mycologia 95: 1227-1238.
S. Kroken, N. L. Glass, J. W. Taylor, O. C. Yoder, B. G. Turgeon. 2003. Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes. Proceedings of the National Academy of Sciences of the United States of America 100(26): 15670-15675.
Takao Kasuga, Thomas J. White, Gina Koenig, Juan McEwen, Angela Restrepo, Elizabetha Castañeda, Carlos da Silva Lacaz, Elisabeth M. Heins-Vaccari, Roseli S. de Freitas, Rosely M. Zancopé-Oliveira, Zhenyu Qin, Ricardo Negroni, Deidre A. Carter, Yuzuru Mikami, Miki Tamura, María Lucía Taylor, Georgina F. Miller, Natteewan Poonwan and John W Taylor. 2003. Phylogeography of the fungal pathogen Histoplasma capsulatum. Molecular Ecology 12: 3383-3401.
Dettman, J. R., D. J. Jacobson, Taylor, J. W. 2003. A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora. Evolution 57(12): 2703-2720.
Dettman, J. R., Jacobson, D. J., Turner, E., Pringle, A., Taylor, J. W. 2003. Reproductive isolation and phylogenetic divergence in Neurospora: Comparing methods of species recognition in a model eukaryote. Evolution 57(12): 2721-2741.
Rachel J. Whitaker, Dennis W. Grogan and John W. Taylor. 2003. Geographic barriers isolate endemic populations of hyperthermophilic Archaea. Science Aug 15 2003: 976-978, published online July 24, 2003. (10.1126/science.1086909)
Taylor, J. W. and M. C. Fisher. 2003. Fungal multilocus sequence typing - it's not just for bacteria [Review]. Current Opinion in Microbiology 6(4): 351-356.
Pringle, A., D. Chen and J. W. Taylor. 2003. Sexual fecundity is correlated to size in the lichenized fungus Xanthoparmelia cumberlandia. Bryologist 106(2): 221-225.
T. Kasuga, T. J. White and J. W. Taylor 2002. Estimation of nucleotide substitution rates in eurotiomycete fungi. Molecular Biology and Evolution 19(12): 2318-24.
Högberg, Nils, Kroken, Scott, Thor, Göran & Taylor, John W. 2002. Reproductive mode and genetic variation suggest a North American origin of European Letharia vulpina. Molecular Ecology 11 (7): 1191-1196.
Katherine F. LoBuglio and John W. Taylor. 2002. Recombination and genetic differentiation in the mycorrhizal fungus Cenococcum geophilum Fr. Mycologia 94(5): 772-780.
Michael Cruse, Robin Telerant, Thomas Gallagher, Thomas Lee & John W. Taylor. 2002. Cryptic species in Stachybotrys chartarum. Mycologia 94(5): 814-822.
Anne Pringle and John W. Taylor. 2002. The fitness of filamentous fungi. Trends in Microbiology. 10(10): 474-481.
Leonel Mendoza, John W. Taylor and Libero Ajello. 2002. The class mesomycetozoea: a heterogeneous group of microorganisms at the animal-fungal boundary. Annual Review of Microbiology 56: 315-344.
Matthew C. Fisher, Bruce Rannala, Vishnu Chaturvedi, and John W. Taylor. 2002. Disease surveillance in recombining pathogens: Multilocus genotypes identify sources of human Coccidioides infections Proc. Natl. Acad. Sci. USA. 99: 9067-9071.
Matthew C. Fisher, Gina L. Koenig, Thomas J. White and John W. Taylor. 2002. Molecular and phenotypic description of Coccidioides posadasii sp. nov., previously recognized as the non-California population of Coccidioides immitis. Mycologia 94(1): 73-84.
Scott Kroken and John W. Taylor. 2001. Outcrossing and recombination in the lichenized fungus Letharia. Fungal Genetics and Biology 34(2): 83-92.
Scott Kroken and John W. Taylor. 2001. A gene genealogical approach to recognize phylogenetic species boundaries in the lichenized fungus Letharia. Mycologia 93: 38–53.
Jeremy R. Dettman, Fred M. Harbinski, John W. Taylor. 2001. Ascospore morphology is a poor predictor of the phylogenetic relationships of Neurospora and Gelasinospora. Fungal Genetics and Biology 34(1): 44-61.
D. A. Carter, J. W. Taylor, B. Dechairo, A. Burt, G. L. Koenig, T. J. White. 2001. Amplified Single-Nucleotide Polymorphisms and a (GA)_n Microsatellite Marker Reveal Genetic Differentiation between Populations of Histoplasma capsulatum from the Americas. Fungal Genetics and Biology 34(1): 37-48.
Vassiliki Koufopanou, Austin Burt, Timothy Szaro and John W. Taylor. 2001. Gene Genealogies, Cryptic Species, and Molecular Evolution in the Human Pathogen Coccidioides immitis and Relatives (Ascomycota, Onygenales). Molecular Biology and Evolution 18: 1246-1258.
Matthew C. Fisher, Gina L. Koenig, Thomas J. White, Gioconda San-Blas, Ricardo Negroni, Bodo Wanke, Gutierrez Alvarez and John W. Taylor. 2001. Biogeographic range expansion into South America by Coccidioides immitis mirrors New World patterns of Human migration. Proc. Natl. Acad. Sci. USA. 98(8): 4558–4562.
Mendoza, L., L. Ajello, J.W. Taylor. 2001. The taxonomic status of Lacazia loboi and Rhinosporidium seeberi has been finally resolved with the use of molecular tools. Revista Iberoamericana de Micologia 18(3): 95-98.
Roger A. Herr, Eric J. Tarcha, Paulo R. Taborda, John W. Taylor, Libero Ajello and Leonel Mendoza. 2001. Phylogenetic analysis of Lacazia loboi places this previously uncharacterized pathogen within the dimorphic Onygenales. Journal of Clinical Microbiology 39(1): 309-314.
Mary L. Berbee and John W. Taylor. 2001. Fungal Molecular Evolution: Gene Trees and Geologic Time. The Mycota: a comprehensive treatise on fungi as experimental systems for basic and applied research. Volume VII: Systematics and Evolution, Part B, pp.229-245. (published in 2000, labeled 2001 by Springer)
David M. Geiser, Joe W. Dorner, Bruce W. Horn and John W. Taylor. 2000. The phylogenetics of mycotoxin and sclerotium production in Aspergillus flavus and Aspergillus oryzae. Fungal Genetics and Biology 31(1): 169-179.
J. G. McEwen, J. W. Taylor, D. Carter, J. Xu, M. S. Felipe, R. Vilgalys, T. G. Mitchell, T. Kasuga, T. White, T. Bui and C. M. Soares. 2000. Molecular typing of pathogenic fungi. Medical Mycology 38: 189-197.
Geiser, D. M., F. M. Harbinski and J. W. Taylor. 2000. Molecular and analytical tools for characterizing Aspergillus and Penicillium species at the intra- and interspecific levels. Pp 179-188. In: Integration of modern taxonomic methods for Penicillium and Aspergillus classification (R. A. Samson and J. I. Pitt, eds.). Harwood Academic Publishers, Gordon and Breach Publishing Group, Amsterdam. ISBN 90-5823-159-3.
Skouboe, P, Taylor, J.W., Frisvad, J.C., Lauritsen, D, Larsen, L., Albaek, Cl, Boysen, M, and L. Rossen. 2000. Molecular methods for differentiation of closely related Penicillium species. Pp 381-394. In: Integration of modern taxonomic methods for Penicillium and Aspergillus classification (R. A. Samson and J. I. Pitt, eds.). Harwood Academic Publishers, Gordon and Breach Publishing Group, Amsterdam. ISBN 90-5823-159-3.
Kroken, S. and Taylor, J. W. 2000. Phylogenetic species, reproductive mode, and specificity of the green alga Trebouxia forming lichens with the fungal genus Letharia. Bryologist V103, 645-660.
John W. Taylor, David J. Jacobson, Scott Kroken, Takao Kasuga, David M. Geiser, David S. Hibbett and Matthew C. Fisher. 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology, Vol. 31(1): pp. 21-32.
Burt, A., Koufopanou, V., Taylor, J.W. 2000. Population genetics of human-pathogenic fungi. Pp. 229-244 In: Molecular Epidemiology of Infectious Diseases, R.C.A. Thompson (ed.). Arnold, London.
M. C. Fisher, G. Koenig, T. J. White J. W. Taylor. 2000. A test for concordance between the multilocus genealogies of genes and microsatellites in the pathogenic fungus Coccidioides immitis. Molecular Biology and Evolution 17: 1164-1174.
Fisher MC, Koenig GL, White TJ, Taylor JW. 2000. Pathogenic clones versus environmentally driven population increase: analysis of an epidemic of the human fungal pathogen Coccidioides immitis. Journal of Clinical Microbiology 38(2):807-13.
Deborah R. Greene, Gina Koenig, Matthew C. Fisher, John W. Taylor. 2000. Soil isolation and molecular identification of Coccidioides immitis. Mycologia: Vol. 92, No. 3, pages 406-410.

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Photographs of the Berkeley Campus by Ansel Adams

UCR/CMP Ansel Adams Fiat Lux Database
West from the "Big C", 1965.
Plaza North of Student Union, 1966.
Memorial Stadium from Southeast, 1966.
View from "Big C" Hill, Eucalyptus Grove, 1965.

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Acknowledgment and Disclaimer:

Some of the material found on this website is based upon work supported by the National Science Foundation. Any opinions, findings and conclusions or recomendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF).

Last updated: April 15 2008

Author: Tim Szaro