John W Taylor

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Dating divergences in the Fungal Tree of Life: review and new analyses
    John W Taylor
    Department of Plant and Microbial Biology, University of California, Berkeley 94720 3102, USA
    Mycologia 98:838-49. 2006
  2. pmc Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi
    John W Taylor
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Philos Trans R Soc Lond B Biol Sci 361:1947-63. 2006
  3. ncbi request reprint Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus
    Rachel J Whitaker
    Department of Plant and Microbial Biology, University of California, Berkeley, USA
    Mol Biol Evol 22:2354-61. 2005
  4. ncbi request reprint Reproductive isolation and phylogenetic divergence in Neurospora: comparing methods of species recognition in a model eukaryote
    Jeremy R Dettman
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 3102, USA
    Evolution 57:2721-41. 2003
  5. pmc Population genomics and local adaptation in wild isolates of a model microbial eukaryote
    Christopher E Ellison
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Proc Natl Acad Sci U S A 108:2831-6. 2011
  6. ncbi request reprint Positive directional selection in the proline-rich antigen (PRA) gene among the human pathogenic fungi Coccidioides immitis, C. posadasii and their closest relatives
    Hanna Johannesson
    Department of Plant and Microbial Biology, University of California, Berkeley, USA
    Mol Biol Evol 21:1134-45. 2004
  7. ncbi request reprint Multilocus sequence data reveal extensive phylogenetic species diversity within the Neurospora discreta complex
    Jeremy R Dettman
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Mycologia 98:436-46. 2006
  8. pmc Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination
    Takao Kasuga
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Nucleic Acids Res 33:6469-85. 2005
  9. ncbi request reprint Three new phylogenetic and biological Neurospora species: N. hispaniola, N. metzenbergii and N. perkinsii
    Christopher F Villalta
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 3102, USA
    Mycologia 101:777-89. 2009
  10. pmc Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives
    Thomas J Sharpton
    Department of Plant and Microbial Biology, University of California, Berkeley, 94720, USA
    Genome Res 19:1722-31. 2009

Detail Information

Publications47

  1. ncbi request reprint Dating divergences in the Fungal Tree of Life: review and new analyses
    John W Taylor
    Department of Plant and Microbial Biology, University of California, Berkeley 94720 3102, USA
    Mycologia 98:838-49. 2006
    ..The most useful calibration is likely to depend on the discovery and description of continuous records of fossil fungi, or their spores, that show recognizable shifts in morphology...
  2. pmc Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi
    John W Taylor
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Philos Trans R Soc Lond B Biol Sci 361:1947-63. 2006
    ..The final step in speciation, reproductive isolation, also follows genetic isolation and may precede morphological change...
  3. ncbi request reprint Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus
    Rachel J Whitaker
    Department of Plant and Microbial Biology, University of California, Berkeley, USA
    Mol Biol Evol 22:2354-61. 2005
    ..We propose instead that frequent recombination among closely related individuals prevents periodic selection from purging diversity and provides a fundamental cohesive mechanism within this and perhaps other archaeal species...
  4. ncbi request reprint Reproductive isolation and phylogenetic divergence in Neurospora: comparing methods of species recognition in a model eukaryote
    Jeremy R Dettman
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 3102, USA
    Evolution 57:2721-41. 2003
    ..We also observed sympatry-associated sexual dysfunction in interspecific crosses, which was consistent with the existence of reinforcement mechanisms...
  5. pmc Population genomics and local adaptation in wild isolates of a model microbial eukaryote
    Christopher E Ellison
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Proc Natl Acad Sci U S A 108:2831-6. 2011
    ..4°-10.6° difference in latitude between the populations may be another important environmental parameter...
  6. ncbi request reprint Positive directional selection in the proline-rich antigen (PRA) gene among the human pathogenic fungi Coccidioides immitis, C. posadasii and their closest relatives
    Hanna Johannesson
    Department of Plant and Microbial Biology, University of California, Berkeley, USA
    Mol Biol Evol 21:1134-45. 2004
    ..Instead, we suggest that positive selection act on PRA as a consequence of spore cell-wall morphogenesis unique to each species...
  7. ncbi request reprint Multilocus sequence data reveal extensive phylogenetic species diversity within the Neurospora discreta complex
    Jeremy R Dettman
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Mycologia 98:436-46. 2006
    ....
  8. pmc Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination
    Takao Kasuga
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Nucleic Acids Res 33:6469-85. 2005
    ....
  9. ncbi request reprint Three new phylogenetic and biological Neurospora species: N. hispaniola, N. metzenbergii and N. perkinsii
    Christopher F Villalta
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 3102, USA
    Mycologia 101:777-89. 2009
    ..hispaniola (PS1), N. metzenbergii (PS2) and N. perkinsii (PS3)...
  10. pmc Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives
    Thomas J Sharpton
    Department of Plant and Microbial Biology, University of California, Berkeley, 94720, USA
    Genome Res 19:1722-31. 2009
    ....
  11. ncbi request reprint A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora
    Jeremy R Dettman
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 3102, USA
    Evolution 57:2703-20. 2003
    ..Although species-level clades were strongly supported, the phylogenetic relationships among species remained difficult to resolve, perhaps due to conflicting signals resulting from differential lineage sorting...
  12. ncbi request reprint Organization of genetic variation in individuals of arbuscular mycorrhizal fungi
    Teresa E Pawlowska
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 3102, USA
    Nature 427:733-7. 2004
    ..Polyploid organization of glomeromycotan genomes could accommodate intranuclear rDNA polymorphism and buffer these apparently asexual organisms against the effects of accumulating mutations...
  13. ncbi request reprint Reproductive mode and genetic variation suggest a North American origin of European Letharia vulpina
    Nils Högberg
    Department of Plant and Microbial Biology, University of California, Berkeley CA, 94720 3102, USA
    Mol Ecol 11:1191-6. 2002
    ....
  14. pmc Genome wide association identifies novel loci involved in fungal communication
    Javier Palma-Guerrero
    Department of Plant and Microbial Biology, University of California, Berkeley, USA
    PLoS Genet 9:e1003669. 2013
    ..Our study demonstrates the power of population-genetic analyses for the rapid identification of genes contributing to complex traits in microbial species. ..
  15. pmc Comparative transcriptomics of the saprobic and parasitic growth phases in Coccidioides spp
    Emily Whiston
    Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
    PLoS ONE 7:e41034. 2012
    ..These observations will impact priorities for future genetics-based studies in Coccidioides and provide context for studies in other fungal pathogens...
  16. pmc Genetic architecture of a reinforced, postmating, reproductive isolation barrier between Neurospora species indicates evolution via natural selection
    Elizabeth Turner
    Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
    PLoS Genet 7:e1002204. 2011
    ..Our results strongly support a role for natural selection in the evolution of reinforced postmating isolation in N. crassa...
  17. ncbi request reprint Phylogeography of the fungal pathogen Histoplasma capsulatum
    Takao Kasuga
    Department of Plant and Microbial Biology, 321 Koshland Hall, University of California, Berkeley, CA 94720, USA
    Mol Ecol 12:3383-401. 2003
    ..Combining DNA substitution rates of protein-coding genes with the phylogeny suggests that the radiation of Histoplasma started between 3 and 13 million years ago in Latin America...
  18. pmc Mechanisms of intron gain and loss in Cryptococcus
    Thomas J Sharpton
    Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720, USA
    Genome Biol 9:R24. 2008
    ..To ascertain mechanisms of intron gain and loss, we compared five relatively closely related genomes from the yeast Cryptococcus...
  19. doi request reprint Airborne bacterial communities in residences: similarities and differences with fungi
    Rachel I Adams
    Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
    PLoS ONE 9:e91283. 2014
    ..These data show that while the outdoor source for indoor bacteria and fungi varies in both space and time, humans provide a strong and homogenizing effect on indoor bacterial bioaerosols, a pattern not observed in fungi. ..
  20. pmc The diversity and distribution of fungi on residential surfaces
    Rachel I Adams
    Plant and Microbial Biology, University of California, Berkeley, California, United States of America
    PLoS ONE 8:e78866. 2013
    ....
  21. pmc Mutation and evolution of microsatellite loci in Neurospora
    Jeremy R Dettman
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Genetics 168:1231-48. 2004
    ..To test if the observed patterns of microsatellite variation and mutation could be generalized, an additional eight microsatellite loci were characterized and sequenced from a subset of the same Neurospora individuals...
  22. pmc Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma
    Christopher E Ellison
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 3102, USA
    Genetics 189:55-69. 2011
    ..In addition, we show that the N. tetrasperma mat a mating-type region appears to be accumulating deleterious substitutions at a faster rate than the other mating type (mat A) and thus may be in the early stages of degeneration...
  23. pmc Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances
    Rachel I Adams
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    ISME J 7:1262-73. 2013
    ....
  24. pmc 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
    Rachel I Adams
    Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
    Microb Ecol 66:735-41. 2013
    ..Lastly, aerobiology of indoor fungi is discussed. ..
  25. pmc Nuclear and genome dynamics in multinucleate ascomycete fungi
    Marcus Roper
    Department of Mathematics, University of California, Berkeley, USA
    Curr Biol 21:R786-93. 2011
    ....
  26. pmc Systematic search for cultivatable fungi that best deconstruct cell walls of Miscanthus and sugarcane in the field
    Prachand Shrestha
    Energy Biosciences Institute, University of California, Berkeley, California 94720, USA
    Appl Environ Microbiol 77:5490-504. 2011
    ..This is the first systematic, high-throughput, isolation and biodegradation assessment of fungi isolated from decaying bioenergy grasses...
  27. ncbi request reprint Designing experiments using spotted microarrays to detect gene regulation differences within and among species
    Jeffrey P Townsend
    Plant and Microbial Biology Department, University of California, Berkeley, California 94720, USA
    Methods Enzymol 395:597-617. 2005
    ..We conclude with a discussion of experimental protocols that are designed for investigations of differential gene expression and their pitfalls...
  28. pmc Population genetics of the frog-killing fungus Batrachochytrium dendrobatidis
    Jess A T Morgan
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 104:13845-50. 2007
    ..Recombination raises the possibility of resistant sporangia and a mechanism for rapid spread as well as persistence that could greatly complicate global control of the pathogen...
  29. doi request reprint Genomics in Coccidioides: Insights into evolution, ecology, and pathogenesis
    Emily Whiston
    University of California Berkeley, Department of Plant and Microbial Biology, Berkeley, California, USA
    Med Mycol 52:149-55. 2014
    ....
  30. ncbi request reprint Fungal multilocus sequence typing--it's not just for bacteria
    John W Taylor
    Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 3102, USA
    Curr Opin Microbiol 6:351-6. 2003
    ..mode can help answer questions common to all emerging diseases: is the disease due to the recent spread of a pathogen, to the emergence of a virulent strain of an existing pathogen, or to a change in the environment that promotes disease?..
  31. ncbi request reprint Geographic barriers isolate endemic populations of hyperthermophilic archaea
    Rachel J Whitaker
    Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA
    Science 301:976-8. 2003
    ..The identification of a biogeographic pattern in the archaeon Sulfolobus challenges the current model of microbial biodiversity in which unrestricted dispersal constrains the development of global species richness...
  32. pmc Disease surveillance in recombining pathogens: multilocus genotypes identify sources of human Coccidioides infections
    Matthew C Fisher
    The Institute of Zoology, Regent s Park, London NW1 4RY, United Kingdom
    Proc Natl Acad Sci U S A 99:9067-71. 2002
    ..the etiological agents of human coccidioidomycosis, but with a travel history including visits to one or more endemic areas...
  33. ncbi request reprint The class mesomycetozoea: a heterogeneous group of microorganisms at the animal-fungal boundary
    Leonel Mendoza
    Medical Technology Program, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing 48824 1030, USA
    Annu Rev Microbiol 56:315-44. 2002
    ..This review provides descriptions of the genera that comprise the class Mesomycetozoea and highlights their morphological features, pathogenic roles, and phylogenetic relationships...
  34. ncbi request reprint Estimation of nucleotide substitution rates in Eurotiomycete fungi
    Takao Kasuga
    Mol Biol Evol 19:2318-24. 2002
  35. ncbi request reprint Cryptic speciation and recombination in the fungus Paracoccidioides brasiliensis as revealed by gene genealogies
    Daniel R Matute
    Corporacion para Investigaciones Biologicas, Medellin, Colombia
    Mol Biol Evol 23:65-73. 2006
    ..Our study provides the first evidence for possible sexual reproduction in P. brasiliensis S1, but does not rule it out in the other two species...
  36. pmc Concerted evolution in the repeats of an immunomodulating cell surface protein, SOWgp, of the human pathogenic fungi Coccidioides immitis and C. posadasii
    Hanna Johannesson
    Department of Evolution, Genomics and Systematics, Evolutionary Biology Centre, Uppsala University, Sweden
    Genetics 171:109-17. 2005
    ....
  37. pmc Microsatellite analysis of three phylogenetic species of Paracoccidioides brasiliensis
    Daniel R Matute
    Corporacion para Investigaciones Biologicas CIB, Medellin, Colombia
    J Clin Microbiol 44:2153-7. 2006
    ..brasiliensis. In addition, this system provides an unambiguous tool for strain discrimination between two (S1 and PS2) of the three phylogenetic species...
  38. ncbi request reprint Population structure and gene evolution in Saccharomyces cerevisiae
    Erlend Aa
    Department of Pharmacy, University of Tromsø, Tromsø, Norway
    FEMS Yeast Res 6:702-15. 2006
    ..cerevisiae, is the first study to demonstrate population structure within S. cerevisiae, and the first study to detect historical selection on a locus important to the natural history of wine yeast...
  39. ncbi request reprint Rhynie chert: a window into a lost world of complex plant-fungus interactions
    Mary L Berbee
    Department of Botany, The University of British Columbia, Vancouver BC, V6T 1Z4, Canada
    New Phytol 174:475-9. 2007
  40. ncbi request reprint New findings of Neurospora in Europe and comparisons of diversity in temperate climates on continental scales
    David J Jacobson
    Department of Biological Sciences, Stanford University, Stanford, California 94305 5020, USA
    Mycologia 98:550-9. 2006
    ..The differences in regional diversity, reported here, can form the basis of testable hypotheses. Questions of phylogeography and adaptations can be addressed specifically by studying Neurospora in nature...
  41. ncbi request reprint Reconstructing the early evolution of Fungi using a six-gene phylogeny
    Timothy Y James
    Department of Biology, Duke University, Durham, North Carolina 27708 0338, USA
    Nature 443:818-22. 2006
    ..The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree...
  42. doi request reprint New Paracoccidioides brasiliensis isolate reveals unexpected genomic variability in this human pathogen
    Lilia L Carrero
    Instituto Venezolano de Investigaciones Cientificas, Laboratorio de Micologia, P O Box 21827, Caracas, Venezuela
    Fungal Genet Biol 45:605-12. 2008
    ..This isolate clearly separates from all other Paracoccidioides isolates in phylogenetic analyses and greatly increases the genomic variation known in this genus...
  43. ncbi request reprint Determination of the substrate specificity of tripeptidyl-peptidase I using combinatorial peptide libraries and development of improved fluorogenic substrates
    Yu Tian
    Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
    J Biol Chem 281:6559-72. 2006
    ....
  44. pmc Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes
    Scott Kroken
    Torrey Mesa Research Institute, Syngenta, 3115 Merryfield Row, San Diego, CA 92121, USA
    Proc Natl Acad Sci U S A 100:15670-5. 2003
    ..vi) The discontinuous distributions of orthologous PKSs among fungal species can be explained by gene duplication, divergence, and gene loss; horizontal gene transfer among fungi does not need to be invoked...
  45. ncbi request reprint Conformationally constrained human calcitonin (hCt) analogues reveal a critical role of sequence 17-21 for the oligomerization state and bioactivity of hCt
    Athanasios Kazantzis
    Physiological chemical Institute, Department of Physical Biochemistry, University of Tubingen, Germany
    Eur J Biochem 269:780-91. 2002
    ..These results may assist to delineate the structure-function relationships of hCt and to design novel hCt agonists for the treatment of osteoporosis and other bone-disorder-related diseases...
  46. pmc Detection and selection of microsatellites in the genome of Paracoccidioides brasiliensis as molecular markers for clinical and epidemiological studies
    Erika Nascimento
    Departamento de Ciências Farmacêuticas de Ribeirão Preto, Universidade de Sao Paulo, Brazil
    J Clin Microbiol 42:5007-14. 2004
    ..We did not observe any correlation between the clinical form of human PCM and four simple sequence repeat patterns analyzed...
  47. ncbi request reprint Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha)
    Meredith Blackwell
    Department of Biological Sciences, Louisiana State University, Baton Rouge 70803, USA
    Mycologia 98:829-37. 2006
    ....