2000-2008
Sharpton, T. J., Neafsey, D. E., Galagan, J. E., Taylor, J. W. 2008. Mechanisms of intron gain and loss in
Cryptococcus. Genome Biology 9:R24
Carrero, L. L., Niño-Vega, G., Teixeira, M.M., Carvalho, M.J.A., Soares, C.M.A., Pereira, M., Jesuino, R.S.A., McEwen, J.G., Mendoza, L., , Taylor, J.W., Felipe, M.S., and G. San-Blas. 2008. New
Paracoccidioides brasiliensis isolate reveals unexpected genomic variability in this human pathogen. Fungal Genetics and Biology 45:605-612.
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.
Berbee, M. L., and J. W. Taylor. 2007. Rhynie chert: a window into a lost world of complex plant-fungus interactions. New Phytologist 174:475-479.
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.
Taylor, J.W. and M. L. Berbee. (2006). Dating divergences in the Fungal Tree of Life: Review and new analyses. Mycologia 98:838-849.
Blackwell, M., Hibbett, D. S., Taylor, J. W., Spatafora, J.W. (2006). Research coordination networks: A phylogeny for kingdom fungi (Deep Hyphae). Mycologia 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.
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.
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.
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
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.
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.
Daniel R. Matute, D.R, McEwen, J.G., Puccia, R., Montes, B.A., San-Blas, G., Bagagli, E., Rauscher, J.T., Restrepo, A., Morais, F., Niño-Vega, G., and J. W. Taylor. 2006.
Cryptic speciation and recombination in the fungus
Paracoccidioides brasiliensis as revealed by gene genealogies. Molecular Biology and Evolution 23:65-73
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. The novel and endemic pathogen hypotheses: Competing explanations for the origin of emerging infectious diseases of wildlife. Conservation Biology 19:1441-1447.
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.
Whitaker, R.J., Grogan, D.W., and J.W. Taylor. 2005. Recombination Shapes the Natural Population Structure of the Hyperthermophilic Archaeon
Sulfolobus “islandicus”. Molecular Biology and Evolution 22: 2354-2361.
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.
Pringle, A., Baker, D.M., Platt, J.L., Wares, J.P., Latgé, J.P., and J.W.Taylor. 2005. Cryptic speciation in the cosmopolitan and clonal human pathogenic fungus Aspergillus fumigatus. Evolution 59: 1886-1899.
Pawlowska, T. and J. W. Taylor. 2005. Arbuscular mycorrhizal fungi: Hyphal fusion and multigenomic structure (reply). Nature 433:E4.
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
Townsend, J.P. and J. W. Taylor. 2005. Designing experiments using spotted microarrays to detect gene regulation differences within and among species. Methods in Enzymology 395:597-617.
Dettman, J.R. and J. W. Taylor. 2004. Mutation and evolution of microsatellite loci in Neurospora. Genetics 168:1231-1248.
Taylor, J.W., Spatafora, J., O’Donnell, K., Lutzoni,. F., James. T., Hibbett, D.S., Geiser. D., Bruns, T.D., and M. Blackwell. 2004. Pp. 171-194. The relationships of fungi. In: Cracraft, J. and Donoghue, M (eds.) The Tree of Life. Oxford.
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 immitis, Coccidioides posadasii and their closest relatives. Molecular Biology and Evolution 21:1134-1145.
Pawlowska, T. and J. W. Taylor. 2004. Disconcerted evolution in arbuscular mycorrhizal fungi. Nature 427:733-737.
Jacobson, D.J., Powell, A.J., Dettman, J.R., Saenz, G.S., Barton, M.M., Hiltz, M.D., Dvorachek, W.H., Jr., J.W. Taylor and D.O. Natvig. 2004. Neurospora in western North America: a model system in the backyard. Mycologia 96:66-74.
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.
Andersen, B., Nielsen, K.F., Thrane, U. Szaro, T. Taylor, J.W. and B.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.
Kroken, S., Glass, N.L., Taylor, J.W., Yoder, O.C., and B.G. Turgeon. 2003. Phylogenomic analysis of type I polyketide synthase genes in pathogenic and saprobic ascomycetes. Proc. Natl Acad. Sci. (USA) 100:15670-15675.
Kasuga, T., T. J. White, Gina Koenig, J. McEwen, A. Restrepo, E. Castaneda, C. de S. Lacaz, E, M. Heins-Vaccari, R. S. de Freitas, R. M. Zancope-Oliveira, Z. Qin, R. Negroni, D. A. Carter, Y. Mikami, M. Tamura, M. L. Taylor, G. F. Miller, N. Poonwan and J. W. Taylor. 2003. Phylogeography of the fungal pathogen Histoplasma capsulatum. Molecular Ecology 12:3383-3401
Dettman, J.R., Jacobson, D. J. and J.W. Taylor. 2003. A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote, Neurospora. Evolution 57:2703-2720.
Dettman, J.R., Jacobson, D. J., Turner, E., Pringle, A. J., and J. W. Taylor. 2003. Recognizing species under biological and phylogenetic species concepts: Reproductive Isolation versus Phylogenetic Divergence. Evolution 57:2721-2741.
Whitaker, R. J., Grogan, D.W. and J. W. Taylor. 2003. Geographic barriers isolate endemic populations of hyporthermophilic Archaea. Science 301:976-978. [Perspective p. 925, NYT article, August 26, 2003, p. D3]
Taylor, J.W. and M. C. Fisher. 2003. Fungal multilocus sequence typing – it’s not just for bacteria. Current Opinion in Microbiology 6:351-356.
Pringle, A., Chen, D., Taylor, J.W. 2003. Sexual fecundity is correlated to size in the lichenized fungus Xanthoparmelia cumberlandia. The Bryologist 106:221-225.
Kasuga, T., White, T. J., Taylor, J.W. 2002. Estimation of nucleotide substitution rates in Eurotiomycete fungi. Molecular Biology and Evolution 19:2318-2324.
Högberg, N., Kroken, S., Thor, G., Taylor J. W. 2002. Reproductive mode and genetic variation suggest a North American origin of European Letharia vulpina, Molec. Ecol. 11:1191-1196.
LoBuglio, K. L, Taylor J. W. 2002. Recombination and genetic differentiation in the mycorrhizal fungus Cenococcum geophilum Fr. Mycologia 94:772-780.
Cruse, M., Telerant, R., Gallagher, T., Lee, T., Taylor, J. W. 2002. Cryptic species in Stachybotrys chartarum. Mycologia 94:814-822. Erratum: Mycologia 95:559 (2003).
Pringle, A. and J. W. Taylor. 2002. Fitness in filamentous fungi. Trends in Microbiology 10:474-481.
Mendoza, L., Taylor, J. W., and L. Ajello. 2002. The class Mesomycetozoea: a heterogeneous group of microorganisms at the animal-fungal boundary. Ann. Rev. Microbiol. 56:314-344.
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.
Kroken, S., Taylor, J.W. 2001. Outcrossing and recombination in the lichenized fungus Letharia. Fungal Geneics and Biology 34:83-92
Dettman, J.R., Harbinski, F.M. and J. W. Taylor. 2001. Ascospore morphology is a poor predictor of the phylogenetic relationships of Neurospora and Gelasinospora. Fungal Genet. Biol. 34: 49-61.
Carter, D.A., Taylor, J. W., Dechairo, B. Burt, A., Koenig, G. L. and 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 Genet. Biol. 34:37-48.
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.
Geiser, D. M, Dorner, J. W., Horn, B. W., Taylor, J.W. 2001. The phylogenetics of mycotoxin and sclerotium production in Aspergillus flavus and Aspergillus oryzae Fungal Genetics and Biology. 31: 169-179.
Mendoza, L., Ajello, L., and J. W. Taylor. 2001. The taxonomic status of Lacazia loboi and Rhinosporidium seeberi has been finally resolved with the use of molecular tools. Rev. Iberoam. Micol. 18:95-98.
Herr, R.A., Tarcha, E.J., Taborda, P.R., Taylor, J.W., Ajello, L. and L. Mendoza. 2001. Phylogenetic analysis of Lacazia loboi places this previously uncharacterized pathogen within the dimorphic Onygenales. J. Clinical Microbiology 39:309-314.
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
Kroken, S., Taylor, J.W. 2000. A gene genealogical approach to determine phylogenetic species boundaries in the lichenized fungus Letharia. Mycologia 93: 38-53.
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., Taylor, J.W. 2000. Phylogenetic species, reproductive mode and specificity of the green alga Trebouxia forming lichens with the fungal genus Letharia. The Bryologist 103:645-660.
Taylor, J. W. Jacobson, D. J., Kroken, S., Kasuga, T., Geiser, D. M, Hibbett, D. S. Fisher, M. C. 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology 31:21-32.
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.
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.
Berbee, M.L., Taylor, J.W. 2001 (published in 2000, labeled 2001 by Springer). Fungal Molecular Evolution: Gene Trees and Geologic Time. Pp. (229-246) In: The Mycota Vol. VIIB, Systematics and Evolution. D. J. McLaughlin, E. McLaughlin and P. A. Lemke, eds. Springer, Berlin.
