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Evolution of fungi.

Pattern and Process of Fungal Evolution.

Figure 1. Bayesian phylogeny made from exon sequence from Neurospora crassa isolates showing two, genetically differentiated populations in what had been thought to be one population. Comparison of the genomes of the Louisiana and Caribbean (dotted line) populations revealed the "islands of differentiation" seen in Figure 2. (Ellison et al. 2011. PNAS 107:2831-2836).

Figure 2. Island of differentiation. (A. chromosome 3, B chromosome 7) uncovered by genome scans of Neurospora crassa individuals from the Louisiana (LA) and Caribbean (Carib) populations. Genes in these islands are candidates for those important to adaptation. The mean annual low temperature in Louisiana is 10 degrees C lower in than the Caribbean and,using growth as a measure of fitness, Louisiana individuals were more fit than Caribbean individuals at low temperature.  A Louisiana strain with a gene deletion for PAC 10 (prefoldin) or for MRH4 (RNA helicase) also showed lower fitness than wild type at low temperature, leaving intact our hypothesis that genes in the islands are important for adaptation to growth at low temperature. (Ellison et al. 2011. PNAS 107:2831-2836).

• 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.
   
• Turner, E., Jacobson, D. J. and J. W. Taylor. 2011. Genetic architecture of a reinforced, postmating, reproductive isolation barrier between Neurospora species indicates evolution via natural selection. PLoS Genetics 7(8): e1002204. doi: 10.1371/journal.pgen.1002204
   
• Ellison, C. E., Stajich, J. E., Jacobson D. J., Lapidus, A., Foster, B., Aerts. A., Riley, R., Lindquist, E. A., Grigoriev, I. V., and J. W. Taylor. 2011. Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma. Genetics 189:55-69. doi: 10.1534/genetics.111.130690
   
• Gilbert, L. B., Kasuga, T., Glass, N. L., Taylor, J. W. 2011. Array CGH Phylogeny: How accurate are Comparative Genomic Hybridization-based trees? BMC Genomics. 12: Article Number: 487 doi: 10.1186/1471-2164-12-487
   
• Gilbert, L. B., Chae, L., Kasuga, T., Taylor, J. W. 2011. Array Comparative Genomic Hybridizations: Assessing the ability to recapture evolutionary relationships using an in silico approach. BMC Genomics. 12: Article Number: 456 . doi: 10.1186/1471-2164-12-456
   
• Anna Muszewska, A., Taylor, J. W., Szczęsny, P. and M. Grynberg. 2011. Independent subtilases expansions in fungi associated with animals. Molecular Biology and Evolution 28: 3395-3404. doi:10.1093/molbev/msr176
   
• Roper, M., Ellison, C., Taylor, J., and N. L. Glass. 2011. Nuclear and genome dynamics in multinucleate ascomycete fungi. Current Biology 21(18): R786-R793.
   
• Prachand Shrestha, Timothy M. Szaro, Thomas D. Bruns and John W. Taylor. 2011. Systematic search for cultivatable fungi that best deconstruct cell walls of Miscanthus and sugarcane in the field. Applied Environmental Microbiology 77(15): 5490–5504. doi:10.1128/AEM.02996-10.
   
• Taylor, J. W., 2011. One Fungus = One Name: DNA and fungal nomenclature twenty years after PCR. IMA Fungus 2: 113-120.
   
• Hawksworth, D. L., Crous, P. W., Redhead, S. A., Reynolds, D. R., Samson, R. A., Seifert, K. A., Taylor, J. W., Wingfield, M. J., et al. 2011. The Amserdam declaration on fungal nomenclature. IMA Fungus. 2: 105-112.
   
• John W. Taylor. 2011. Keynote paper: The poetry of mycological accomplishment and challenge. Fungal Biology Reviews 25: 3-13.
   
• Ellison, C. E., C. Hall, D. Kowbel, J. Welch, R. B. Brem, N. L. Glass, and J. W. Taylor. 2011. Population genomics and local adaptation in wild isolates of a model microbial eukaryote. Proceedings of the National Academy of Science (USA) 107:2831-2836.
   
• John W. Taylor and Christopher E. Ellison. 2010. Mushrooms: Morphological complexity in the fungi. PNAS 107(26): 11655-11656.
   
• E. Turner, D.J. Jacobson and J.W Taylor. 2010. Reinforced postmating reproductive isolation barriers in Neurospora, an Ascomycete microfungus. Journal of Evolutionary Biology 23: 1642–1656.
   
• Hawksworth, D. L., J. A. Cooper, et al. 2010. Proposals 117-119: To make the pre-publication deposit of key nomenclatural information in a recognized repository a requirement for valid publication of organisms treated as fungi under the CODE. Mycotaxon 111: 514-519.
   
• Daniel E. Neafsey, Bridget M. Barker, Thomas J. Sharpton, Jason E. Stajich, Daniel J. Park, Emily Whiston, Chiung-Yu Hung, Cody McMahan, Jared White, Sean Sykes, David Heiman, Sarah Young, Qiandong Zeng, Amr Abouelleil, Lynne Aftuck, Daniel Bessette, Adam Brown, Michael FitzGerald, Annie Lui, J. Pendexter Macdonald, Margaret Priest, Marc J. Orbach, John N. Galgiani, Theo N. Kirkland, Garry T. Cole, Bruce W. Birren, Matthew R. Henn, John W. Taylor and Steven D. Rounsley. 2009. Population genomic sequencing of Coccidioides fungi reveals recent hybridization and transposon control. Geneome Research 19: 1722-1731.
   
• Berbee ML & Taylor JW. 2010. Dating the molecular clock in fungi -- how close are we? Fungal Biology Reviews 24: 1–16.
   
• Stajich, JE, Berbee, ML, Blackwell, M, Hibbett, DS, James, TY, Spatafora, JW, Taylor, JW. 2009. The Fungi. Current Biology 19(18): R840-845.
   
• James TY, Litvintseva AP, Vilgalys R, Morgan JAT, Taylor JW, Fisher MC, Berger L, Weldon C, du Preez L, Longcore JE. 2009. Rapid global expansion of the fungal disease Chytridiomycosis into declining and healthy amphibian populations. PLoS Pathogens 5: e1000458.
   
• Thomas J. Sharpton, Jason E. Stajich, Steven D. Rounsley, Malcolm J. Gardner, Jennifer R. Wortman, Vinita S. Jordar, Rama Maiti, Chinnappa D. Kodira, Daniel E. Neafsey, Qiandong Zeng, Chiung-Yu Hung, Cody McMahan, Anna Muszewska, Marcin Grynberg, M. Alejandra Mandel, Ellen M. Kellner, Bridget M. Barker, John N. Galgiani, Marc J. Orbach, Theo N. Kirkland, Garry T. Cole, Matthew R. Henn, Bruce W. Birren, and John W. Taylor. 2009. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Research 19(10): 1722-1731. doi: 10.1101/gr.087551.108.
   
• Christopher F. Villalta, David J. Jacobson and John W. Taylor. 2009. Three new phylogenetic and biological Neurospora species: N. hispaniola, N. metzenbergii and N. perkinsii. Mycologia 101(6): 777-789.
   
• Vilela, R., Rosa, PS, Belone, AFF, Taylor JW, Diorio SM, Mendoza, L. 2009. Molecular phylogeny of animal pathogen Lacazia loboi inferred from rDNA and DNA coding sequences. Mycological Research 113: 851-857.
   
• Thomas J. Sharpton, Daniel E. Neafsey, James E. Galagan and John W. Taylor. 2008. Mechanisms of intron gain and loss in Cryptococcus. Genome Biology 2008, 9:R24 (doi:10.1186/gb-2008-9-1-r24).
   
• Bidartondo, M. et al.  2008. Preserving Accuracy in GenBank. Science (letters) 319:1616.
   
• Carrero, L.L., Nino-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 San-Blas, G. 2008. New Paracoccidioides brasiliensis isolate reveals unexpected genomic variability in this human pathogen. Fungal Genetics and Biology 45(5): 605-612.
   
• Heitman, J., Kronstad, J.W., Taylor, J.W., and Casselton, L.A. 2007. Sex in fungi: molecular determination and evolutionary implications. In Sex in fungi: molecular determination and evolutionary implications. ASM Press, Washington USA. p. xxv + 542 pp. Table of contents.
   
• 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.
   
• Mary L. Berbee, John W. Taylor. 2007. Rhynie chert: a window into a lost world of complex plant-fungus interactions. New Phytologist 174(3): 475–479. doi:10.1111/j.1469-8137.2007.02080.x
   
• 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.
   
• John W. Taylor & Mary L. Berbee. 2006. Dating divergences in the Fungal Tree of Life: review and new analyses. Mycologia 2006 98: 838-849.
   
• Meredith Blackwell, David S. Hibbett, John W. Taylor & Joseph W. Spatafora. 2006. Research Coordination Networks: a phylogeny for kingdom Fungi (Deep Hypha). Mycologia 2006 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.
   
• 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
   
• 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.
   
• 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.
   
• Matute, D.R., Sepulveda, V.E., Quesada, L.M., Goldman, G.H., Taylor, J.W., Restrepo, A., McEwen, J.G. 2006. Microsatellite analysis of three phylogenetic species of Paracoccidioides brasiliensis. J. Clinical Microbiology 44: 2153-2157.
   
• 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.
   
• Taylor, J.W. 2006. Evolution of human-pathogenic fungi: Phylogenies and species. Pp. 113-132 and Color Plate 5. In: Molecular Principles of Fungal Pathogenesis, J. Heitman et al. (eds). ASM Press, Washington, D.C.
   
• 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.
   
• Matute, D.R., McEwen, J.G., Montes, B.A., San-Blas, G., Bagagli, E., Rauscher, J.T., Restrepo, A., Morais, F., Nino-Vega, G., Taylor, J.W. 2006. Cryptic speciation and recombination in the fungus Paracoccidioides brasiliensis as revealed by gene genealogies. Molecular Biology and Evolution 23: 65-73.