Research Expertise and Interest

evolution, fungi, phylogenomics, mycology, population genomics, ecology

Research Description

Some recent publications from the lab:

Valley Fever or coccidioidomycosis

  • Taylor, J. W., & Barker, B. M. (2019). The endozoan, small-mammal reservoir hypothesis and the life cycle of Coccidioides species. Medical mycology57(Supplement_1), S16-S20.
  • Taylor, J.W., Hann-Soden, C., Branco, S., Sylvain, I., Ellison, C.E.  2015. Clonal reproduction in fungi. Proceedings of the National Academy of Science 112(29): 8901-8908.
  • Whiston, E. and J. W. Taylor. 2016. Comparative phylogenomics of pathogenic and non-pathogenic species. G3: Genes, Genomes, Genetics 6:235-244
  • Taylor, J. W. 2015. Evolutionary perspectives on human fungal pathogens. Pp 23-40, In: Casadevall, A., Mitchell, A., Berman, J., Kwon-Chung, K., Perfect, J., Heitman, J. (eds), Human Fungal Pathogens, Cold Spring Harbor Perspectives in Medicine, CSHL Press, Cold Spring Harbor, NY. DOI: 10.1101/cshperspect.a019588
  • Thompson, G. R., Stevens, D. A., Clemons, K. V, Fierer, Johnson, R. H., Sykes, J. Rutherford, M. Peterson, J. W. Taylor and V. Chaturvedi (2015). "Call for a California Coccidioidomycosis Consortium to Face the Top Ten Challenges Posed by a Recalcitrant Regional Disease." Mycopathologia 179: 1-9.
  • Whiston, E., Taylor, J.W., 2014. Genomics in Coccidioides: Insights into evolution, ecology, and pathogenesis. Medical Mycology. 52, 149-155.
  • Wise, H-Z, Hung, C-Y, Whiston, E, Taylor, JW, Cole GT. 2013. Extracellular ammonia at sites of pulmonary infection with Coccidioides posadasii contributes to severity of the respiratory disease. Microbial Pathogenesis 59-60: 19-28.
  • Whiston, E., Wise, H.-Z., Jui, G., Sharpton, T. J., Cole, G. T., J. W. Taylor. 2012. Comparative transcriptomics of the saprobic and parasitic growth phases in Coccidioides spp. PLoS One 7: e41034.
  • Neafsey, D. E., B. M. Barker, Sharpton, T.J., Stajich, J. E., Park, D. J., Whiston, E. Taylor, J.W., Rounsley, S. D. (2010). Population genomic sequencing of Coccidioides fungi reveals recent hybridization and a novel form of transposon control. Genome Research 20:938-946. 10.1101/gr.103911.109
  • Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, Maiti R, Kodira CD, Neafsey DE, Zeng Q, Hung C-Y, McMahan C, Muszewska A, Grynberg M, Mandel MA, Kellner EM, Barker BM, Galgiani JN, Orbach MJ, Kirkland TN, Cole GT, Henn MR, Birren BW, and JW Taylor. 2009. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Research 19 1722-1731. 10.1101/gr.087551.108
  • Johannesson, H. Kasuga, T., Schaller, R.A, Good, B. Gardner, M.J., Townsend, J.P., Cole, G.T., and J. W. Taylor. 2006. Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii. Fungal Genetics and Biology 43:545-559.
  • Johannesson, H., Townsend, J.P., Hung, C.-Y., Cole, G.T., and J.W. Taylor. 2005.  Concerted evolution in the repeats of an immunomodulating cell surface protein, SOWgp, of the human pathogenic fungi Coccidioides immitis and C. posadasii.  Genetics 171: 109-117. 10.1534/genetics.105.040923
  • Johannesson, H., Vidal, P., Guarro, J., Herr, R.A., Cole, G.T., and J. W. Taylor. 2004. Positive directional selection in the proline-rich-antigen (PRA) gene among the human pathogenic fungi Coccidioides immitisCoccidioides posadasii and their closest relatives. Molecular Biology and Evolution 21:1134-1145.
  • Fisher, M.C., Ranalla, B., Chaturvedi, V. and J. W. Taylor. 2002. Disease surveillance in recombining pathogens: multilocus genotypes identify sources of human Coccidioides infections.  Proc. Natl. Acad. Sci. (USA) 99:9067-9071.
  • Fisher, M. C., Koenig, G. L., White, T. J., and J. W. Taylor. 2002. Molecular and phenotypic description of Coccidioides posadasii sp. nov., previously recognized as the non-California population of Coccidioides immitis.  Mycologia 94:73-84.
  • Koufopanou, V., Burt, A., Szaro, T., and Taylor, J. W. 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.
  • Fisher, M. C., Koenig, G. L., White, T. J., San-Blas, G., Negroni, R., Gutierrez Alvarez, I., Wanke, B., and J. W. Taylor. 2001. Biogeographic range expansion into South America by Coccidioides immitis mirrors New World patterns of human migration. Proc. Natl. Acad. Sci. (USA) 98:4558-4562.
  • McEwen, J.G., Taylor, J.W., Carter, D., Xu J., Felipe, M.S.S., Vilgalys, R., Mitchell, T.G., Kasuga, T., White, T. and C.M.S. Soares. 2000. Molecular typing of pathogenic fungi. Medical Mycology 38 (Supplement 1): 189-97.
  • 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.
  • Fisher, M.C., Koenig, G., White, T.W., Taylor, J.W. 2000. A test for concordance between the multilocus genealogies of genes and microsatellites in the pathogenic fungus Coccidioides immitis.  Molec. Biol. Evol. 17:1164-1174.
  • Fisher, M.C., Koenig, G.L., White, T.J. and J.W. Taylor.  2000.  Pathogenic clones versus environmentally driven population increase: analysis of an epidemic of the human fungal pathogen Coccidioides immitis.  J. Clin. Microbiol. 38:807-813.
  • Greene, D. R. and Taylor, J. W. 2000.  Soil isolation and molecular identification of Coccidioides immitis.  Mycologia 92: 406-410.

Drought, fungi and Sorghum

  • Gao, Cheng, Liliam Montoya, Ling Xu, Mary Madera, Joy Hollingsworth, Elizabeth Purdom, Vasanth Singan, John Vogel, Robert B. Hutmacher, Jeffery A. Dahlberg, Devin Coleman-Derr, Peggy G. Lemaux, John W. Taylor. 2020. Fungal community assembly in drought stressed sorghum shows stochasticity, selection, and universal ecological dynamics. Nature Communications (in press).
  • Nelle Varoquaux, Benjamin Cole, Cheng Gao, Grady Pierroz, Christopher R. Baker, Dhruv Patel, Mary Madera, Tim Jeffers, Joy Hollingsworth, Julie Sievert, Yuko Yoshinaga, Judith A. Owiti, Vasanth R. Singan, Stephanie DeGraaf, Ling Xu, Matthew J. Blow, Maria J. Harrison, Axel Visel, Christer Jansson, Krishna K. Niyogi, Robert Hutmacher, Devin Coleman-Derr, Ronan C. O’Malley, John W. Taylor, Jeffery Dahlberg, John P. Vogel, Peggy G. Lemaux, and Elizabeth Purdom. 2019. Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses. Proc Natl Acad Sci USA first published December 5, 2019.
  • Gao, C., Montoya, L., Xu, L., Madera, M., Hollingsworth, J., Purdom, E., Hutmacher, R.B., Dahlberg, J.A., Coleman-Derr, D., Lemaux, P.G. and Taylor, J.W., 2019. Strong succession in arbuscular mycorrhizal fungal communities. The ISME journal13:214-226
  • Ling Xu, Dan Naylor, Zhaobin Dong, Tuesday Simmons, Grady Pierroz, Kim K. Hixson, Young-Mo Kim, Erika M. Zink, Kristin M. Engbrecht, Yi Wang, Cheng Gao, Stephanie DeGraaf, Mary A. Madera, Julie A. Sievert, Joy Hollingsworth, Devon Birdseye, Henrik V. Scheller, Robert Hutmacher, Jeffery Dahlberg, Christer Jansson, John W. Taylor, Peggy G. Lemaux, and Devin Coleman-Derr (2018). Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proceedings of the National Academy of Sciences, 115(18), E4284-E4293.

Indoor air, fungi and water intrusion

  • Sylvain IA, Adams RI, Taylor JW (2019) A different suite: The assemblage of distinct fungal communities in water-damaged units of a poorly-maintained public housing building. PLOS ONE 14(3): e0213355.
  • Adams, R. I., Lymperopoulou, D. S., Misztal, P. K., Pessotti, R. D., Behie, S. W., Tian, Y. L., Goldstein, A. H., Lindow, S. E., Nazaroff, W. W., Taylor, J. W., Traxler, M. F., Bruns, T. D., 2017. Microbes and associated soluble and volatile chemicals on periodically wet household surfaces. Microbiome. 5, Article number 128,
  • Adams, Rachel I.,  Yilin Tian, John W. Taylor, Thomas D. Bruns, Anne Hyvärinen, Martin Täubel. 2015. Passive dust collectors for assessing airborne microbial material. Microbiome 3(1):46.
  • Adams, Rachel I.,  Seema Bhangar, Wilmer Pasut, Edward A. Arens , John W. Taylor, Steven E. Lindow, William W. Nazaroff, Thomas D. Bruns. 2015. Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes. PLoS ONE 10(5):e0128022.
  • Adams, R. I., Miletto, M., Lindow, S. E., Taylor, J. W., Bruns, T. D., 2013b. Airborne bacterial communities in residences: Similarities and differences with fungi. Plos One. 9: e91283.
  • Adams, R. I., Miletto, M., Taylor, J. W., Bruns, T. D., 2013b. The Diversity and Distribution of Fungi on Residential Surfaces. Plos One. 8(11) e78866.
  • Adams, R.I., Amend, A.S., Taylor, J.W., Bruns, T.D. 2013. A unique signal distorts the perception of species richness and composition in high-throughput sequencing surveys of microbial communities: A case study of fungi in indoor dust. Microbial. Ecol. 66:735-741
  • Adams RI, Miletto M, Taylor JW, Bruns TD. 2013. Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME J 7:1262-1273, 21 February 2013;

In the News

Bread mold genomes demo 'reverse-ecology'

In a demonstration of “reverse-ecology,” UC Berkeley biologists have shown that one can determine an organism’s adaptive traits by looking first at its genome and checking for variations across a population. The study offers a powerful new tool in evolutionary genetics research, one that could be used to help monitor the effects of climate change and habitat destruction.

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