Research Topics
| John W TaylorSummaryAffiliation: University of California Country: USA Publications
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Detail Information
Publications
Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom FungiJohn 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...
Dating divergences in the Fungal Tree of Life: review and new analysesJohn 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...- Reproductive isolation and phylogenetic divergence in Neurospora: comparing methods of species recognition in a model eukaryoteJeremy 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... - Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicusRachel 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... - Population genomics and local adaptation in wild isolates of a model microbial eukaryoteChristopher 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... - Positive directional selection in the proline-rich antigen (PRA) gene among the human pathogenic fungi Coccidioides immitis, C. posadasii and their closest relativesHanna 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... - Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germinationTakao Kasuga
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720-3102, USA
Nucleic Acids Res 33:6469-85. 2005.... - Comparative genomic analyses of the human fungal pathogens Coccidioides and their relativesThomas J Sharpton
Department of Plant and Microbial Biology, University of California, Berkeley, 94720, USA
Genome Res 19:1722-31. 2009.... - Multilocus sequence data reveal extensive phylogenetic species diversity within the Neurospora discreta complexJeremy R Dettman
Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
Mycologia 98:436-46. 2006.... - Three new phylogenetic and biological Neurospora species: N. hispaniola, N. metzenbergii and N. perkinsiiChristopher 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)... - A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote NeurosporaJeremy 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... - Organization of genetic variation in individuals of arbuscular mycorrhizal fungiTeresa 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... - Reproductive mode and genetic variation suggest a North American origin of European Letharia vulpinaNils Högberg
Department of Plant and Microbial Biology, University of California, Berkeley CA, 94720 3102, USA
Mol Ecol 11:1191-6. 2002.... - Genetic architecture of a reinforced, postmating, reproductive isolation barrier between Neurospora species indicates evolution via natural selectionElizabeth 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... - Phylogeography of the fungal pathogen Histoplasma capsulatumTakao 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... - Mechanisms of intron gain and loss in CryptococcusThomas 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... - Mutation and evolution of microsatellite loci in NeurosporaJeremy 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... - Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetraspermaChristopher 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... - Comparative transcriptomics of the saprobic and parasitic growth phases in Coccidioides sppEmily 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... - Systematic search for cultivatable fungi that best deconstruct cell walls of Miscanthus and sugarcane in the fieldPrachand 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... - Nuclear and genome dynamics in multinucleate ascomycete fungiMarcus Roper
Department of Mathematics, University of California, Berkeley, USA
Curr Biol 21:R786-93. 2011.... - Population genetics of the frog-killing fungus Batrachochytrium dendrobatidisJess 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... - Designing experiments using spotted microarrays to detect gene regulation differences within and among speciesJeffrey 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... - Fungal multilocus sequence typing--it's not just for bacteriaJohn 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?.. - Geographic barriers isolate endemic populations of hyperthermophilic archaeaRachel 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... - Population structure and gene evolution in Saccharomyces cerevisiaeErlend Aa
Department of Pharmacy, University of Troms, Troms, 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... - The class mesomycetozoea: a heterogeneous group of microorganisms at the animal-fungal boundaryLeonel 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... - Estimation of nucleotide substitution rates in Eurotiomycete fungiTakao Kasuga
Mol Biol Evol 19:2318-24. 2002 
New Paracoccidioides brasiliensis isolate reveals unexpected genomic variability in this human pathogenLilia 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...- Concerted evolution in the repeats of an immunomodulating cell surface protein, SOWgp, of the human pathogenic fungi Coccidioides immitis and C. posadasiiHanna Johannesson
Department of Evolution, Genomics and Systematics, Evolutionary Biology Centre, Uppsala University, Sweden
Genetics 171:109-17. 2005.... - Cryptic speciation and recombination in the fungus Paracoccidioides brasiliensis as revealed by gene genealogiesDaniel R Matute
, , 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... - Disease surveillance in recombining pathogens: multilocus genotypes identify sources of human Coccidioides infectionsMatthew 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... - Rhynie chert: a window into a lost world of complex plant-fungus interactionsMary L Berbee
Department of Botany, The University of British Columbia, Vancouver BC, V6T 1Z4, Canada
New Phytol 174:475-9. 2007 - Microsatellite analysis of three phylogenetic species of Paracoccidioides brasiliensisDaniel R Matute
, , 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... - Reconstructing the early evolution of Fungi using a six-gene phylogenyTimothy 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... - New findings of Neurospora in Europe and comparisons of diversity in temperate climates on continental scalesDavid 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... - Determination of the substrate specificity of tripeptidyl-peptidase I using combinatorial peptide libraries and development of improved fluorogenic substratesYu 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.... - Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetesScott 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... - Conformationally constrained human calcitonin (hCt) analogues reveal a critical role of sequence 17-21 for the oligomerization state and bioactivity of hCtAthanasios Kazantzis
Physiological-Chemical Institute, Department of Physical Biochemistry, , 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... - Detection and selection of microsatellites in the genome of Paracoccidioides brasiliensis as molecular markers for clinical and epidemiological studiesErika Nascimento
, , 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... - 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....