Thomas J. White and John W. Taylor began their collaboration on fungal molecular evolution in 1982 when Taylor invited White to an informal seminar in the Botany Department on the Berkeley campus to present his Cetus Corporation research on fungal enzymes that convert plant cell walls to sugar. Following that meeting, they used a cloned fungal ribosomal DNA to show that fungi were not close relatives of red algae (Kwok et al. 1986); a modest accomplishment, but one of the first efforts to apply molecular evolution to fungi.
In 1988, White took a sabbatical from Cetus to work in Taylor’s lab, where he introduced Berkeley mycologists to the polymerase chain reaction (PCR), a technique that was just becoming practical due to the availability of thermocyclers and a recombinant form of thermostable Taq polymerase. Working with postdoc Tom Bruns and graduate student Steve Lee, they developed an approach to rapidly PCR amplify and sequence fungal rDNA for evolutionary comparisons (White et al. 1990), which has been cited over 11,000 times to date. The application of PCR to questions in fungal evolution led to the first publication on the topic (Bruns et al. 1989), and an influential review on fungal molecular evolution (Bruns et al. 1991).
The potential of PCR led National Institutes of Helath to support research on the evolutionary relationships of human pathogenic fungi in a series of joint projects between Roche Molecular Systems in Alameda, California, where White had begun his second career in the biotech industry, and the new Plant and Microbial Biology Department at Berkeley, to which Taylor had migrated.
White and postdoc Barbara Bowman initially focused their efforts on a survey of fungal pathogens in humans (Bowman et al. 1992), and then Dee Carter and Takao Kasuga worked on the systemic, human pathogen Histoplasma capsulatum. Taylor and postdocs Austin Burt, Vassiliki Koufopanou, Deb Greene and Mat Fisher focused their efforts on the systemic, human pathogen, Coccidioides immitis. Among the accomplishments of the group was the first population genetic demonstration that fungi were recombining in nature, even those fungi for which sex had never been observed (Burt et al. 1996, Carter et al. 1996), the discovery that morphological species were composed of two to several genetically isolated species (Koufopanou et al. 1997; Carter et al. 2001), inferences about the role of humans in the evolutionary history of pathogenic fungi (Kasuga et al. 2003, Fisher et al. 2001), the first description of new fungal species solely on DNA sequence variation (Fisher et al. 2002), and what remains the only estimation of the nucleotide substitution rate in filamentous fungi (Kasuga et al. 2002).
Training the Next Generation
Perhaps the most lasting accomplishment was the training of the next generation of mycologists. Tom Bruns is now Professor and former Division Chair of Plant and Microbial Biology at Berkeley, Steve Lee is now Professor at San Jose State University; Barbara Bowman is now Associate Professor at Mills College; Dee Carter is now Professor and Chair of Microbiology at Sydney University; Austin Burt is now Professor and Head of the Division of Ecology and Evolution at Imperial College; Vassiliki Koufopanou is now Research Associate at Imperial College; Takao Kasuga is now Research Molecular Geneticist at University of California, Davis; Mat Fisher is now Reader, Imperial College, London. Taylor continues to work at Berkeley with Coccidioides species and has applied his experience with pathogens to the model fungus, Neurospora, most recently with population genomics. White is now retired from a third career with Celera Diagnostics, where he researched medical aspects of human genomics, and has begun a fourth career that allows him to advise and support the Human Rights Center and the SAGE Scholar’s programs, as well as serving on the Advisory Board of the College of Natural Resources, all at Berkeley.
See the video of the recent Regents Lecture on Genomic Medicine featuring Tom White, with an introduction by John Taylor. Download the powerpoint presentation from the lecture which has been split into Part One and Part Two.
Collaborative Publications, 1996-2003
Kwok, S., White, T.J. and Taylor, J.W., (1986). Evolutionary relationships between fungi, red algae, and other simple eucaryotes inferred from total DNA hybridizations to a cloned basidiomycete ribosomal DNA. Experimental Mycology, 10:196-204.
Bruns, T., Fogel, R., White, T., Palmer, J., (1989). Accelerated evolution of a false-truffle from a mushroom ancestor. Nature. 339, 140-142.
White, T.J., Bruns, T., Lee, S. and Taylor, J., (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Chapter 38. Pages 315-322. In: PCR Protocols: a Guide to Methods and Applications (M. Innis, D. Gelfand, J. Sninsky and T. White, eds.). Academic Press, Orlando, Florida.
Lee, S.B. and Taylor, J.W. 1990. Isolation of DNA from fungal mycelia and single spores. Chapter 34. In: PCR Protocols: A Guide to Methods and Applications (M. Innis, D. Gelfand, J. Sninsky and T. White , eds.). Academic Press, Orlando, Florida.
Bruns, T.D., White, T.J. and Taylor, J.E., (1991). Fungal Molecular Systematics. Annual Review of Ecology and Systematics, 22:525-564.
Gardes, M., White, T.J., Fortin, J.A., Bruns, T.D., and Taylor, J.W., (1991). Identification of indigenous and introduced symbiotic fungi in ectomycorrhizae by amplification of nuclear and mitochondrial ribosomal DNA, Canadian J. Botany, 69:180-190.
Mitchell, T.G., White, T.J., and Taylor, J.W. (1992) Comparison of 5.8S Ribosomal DNA Sequences among the Basidiomycetous Yeast Genera Cystofilobasidium, Filobasidium and Filobasidiella. J. Med. & Vet. Mycology, 30:207-218.
Bowman, B., Taylor, J.W. and White, T.J., (1992) Molecular evolution of the human pathogenic fungi. Molecular Biology and Evolution, 9:893-904.
Taylor, J.W., Bowman, B., Berbee, M.L., and White, T.J., (1993). Fungal model organisms: phylogenetics of Saccharomyces, Aspergillus and Neurospora. Systematic Biology 42(4):440-457.
Lee, S.B., White, T.J., Taylor, J.W. (1993) Detection of Phytophthora by oligonucleotide hybridization to amplified ribosomal DNA spacers. Phytopathology 83:177-181.
Mitchell, T.G., Freedman, E.Z., Meyer, W., White, T.J., and Taylor, J.W., (1993) PCR identification of Cryptococcus neoformans. pp. 431-436 in: Diagnostic Molecular Microbiology: Principles and Applications, D.H. Persing, T.F. Smith, F.C. Tenover, and T.J. White (eds.), American Society for Microbiology, Washington.
Mitchell, T.J., Freedman, E.Z., White, T.J., and Taylor, J.W. (1994) Unique oligonucleotide primers for the polymerase chain reaction to identify Cryptococcus neoformans. J. Clin. Microb. 32:253-255.
Burt, A., Carter, D.A., White, T.J., and Taylor, J.W. (1994) DNA sequencing with arbitrary primer pairs (SWAPP). Molecular Ecology 3:523-525.
Burt, A., Carter, D.A., Koenig, G.L., White, T.J., and Taylor, J.W. (1995) A safe method of extracting DNA from Coccidiodes immitis. Fungal Genetics Newsletter: 42:23.
Carter, D.A., Burt, A., and Taylor, J.W. (1995). Direct analysis of specific bands from arbitrarily primed PCR reactions. Pp. 325-332 In: PCR Strategies. M.A. Innis, D.H. Gelfand and J.J. Sninsky (eds.) Academic Press.
Carter, D., Reynolds, R., Fildes, N. and White, T.J. (1996) Future applications of PCR to conservation biology in Molecular Genetic Approaches in Conservation, T. Smith and R.K. Wayne, eds. Chp. 19, pp 314-326 Oxford University Press, 483 pages.
Burt, A., Carter, D.A., Koenig, G.L., White, T.J. and Taylor, J.W. (1996) Molecular markers reveal cryptic sex in the human pathogen Cocciodioides immitis. Proc. Natl. Acad. Sci. USA 93:770-773.
Bowman, B.H., White, T.J., and Taylor, J.W. (1996). Human Pathogenic fungi and their close non-pathogenic relatives. Molecular Phylogenetics and Evolution 6:89-96.
Carter, D.A., Burt, A., Taylor, J.W., Koenig, G.L. and White, T.J. (1996). Clinical isolates of Histoplasma capsulatum from Indianapolis have a recombining population structure J. Clin. Micro. 34:2577-2584.
Carter, D.A., Burt, A., Taylor, J.W., Koenig, G.L., Dechairio, B. and White, T.J. (1997) A set of electrophoretic molecular markers for strain typing and population genetic studies of Histoplasma capsulatum. Electrophoresis 18:1047-1053.
Carter, D.A., Burt, A., Taylor, J.W., Koenig, G.L. and White, T.J. (1997) Development of molecular markers from arbitrarily amplified DNA fragments for the analysis of fungal populations in Methods in Molecular Medical Mycology, ed. K. Haynes. Humana Press.
Koufopanou, V., Burt, A. and J.W. Taylor. (1997). Concordance of gene geneologies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis. Proc. Natl. Acad. Sci. 94:5478-5482.
Burt, A., Dechairo, B. M., Koenig, G. L., Carter, D. A., White, T.J., and Taylor, J.W. (1997) Molecular markers reveal differentiation among Cocciodiodes immitis from California, Arizona and Texas. Molecular Ecology 6:781-786.
Kasuga, T, Taylor, J.W., and White, T.J. (1999) Phylogenetic relationships of varieties and geographical groups of the human pathogenic fungus Histoplasma capsulatum Darling. J .Clin. Micro. 37:653-663.
Fisher, M., White, T., and Taylor, J.W. (1999) Primers for genotyping single nucleotide polymorphisms and microsatellites in the pathogenic fungus Coccidioides immitis. Molecular Ecology 6:1082-1084
Fisher, M., Koenig, G.L., White, T.J., and Taylor, J.W. (2000) Pathogenic Clones versus Environmentally Driven Population Increase: Analysis of an Epidemic of the Human Fungal Pathogen Coccidioides immitis. J. Clin. Micro. 38(2): 807-813.
Fisher, M.C., Koenig, G., White, T.J., 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(8): 1164-1174.
McEwen, J.G., Taylor, J.W., Carter, D., Xu J., Felipe, M.S.S., Vilgalys, R., Mitchell, T.G., Kasuga, T., White, T.J. and C.M.S. Soares (2000). Molecular typing of pathogenic fungi. Medical Mycology 38: 189-97.
Greene, D. R. and Taylor, J. W. (2000). Soil isolation and molecular identification of Coccidioides immitis. Mycologia 92: 406-410.
Carter, D.A., Taylor, J. W., Dechairo, B. Burt, A., Koenig, G. L. and White, T.J. (2001). Amplified Single Nucleotide Polymorphisms and a (GA)n microsatellite marker reveal genetic differentiation between populations of Histoplasma capsulatum from the Americas. Fungal Genet. Biol. 34:37-48.
Fisher, M. C., Koenig, G. L., White, T. J., San-Blas, G., Negroni, R., Gutierrez Alvarez, I., Wanke, B., and Taylor, J.W. (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.
Kasuga, T., White, T. J., Taylor, J.W. (2002). Estimation of nucleotide substitution rates in Eurotiomycete fungi. Molecular Biology and Evolution 19:2318-2324.
Fisher, M. C., Koenig, G. L., White, T. J., and Taylor, J.W. (2002). Molecular and phenotypic description of Coccidioides posadasii sp. nov., previously recognized as the non-California population of Coccidioides immitis. Mycologia 94:73-84.
Kasuga, T., White, T. J., Koenig, G., McEwen, J., Restrepo, A., Castaneda, E., Lacaz, C. de S., Heins-Vaccari, M., Freitas, R.S. de, Zancope-Oliveira, R.M., Qin, Z., Negroni, R., Carter, D.A., Mikami, Y., Tamura, M., Taylor, M.L., Miller, G.F., Poonwan N., and Taylor, J.W. (2003). Phylogeography of the fungal pathogen Histoplasma capsulatum. Molecular Ecology 12:3383-3401.