The main areas in which we publish are:


Select publications, for a full list see Tim James Google Scholar profile

Fungal mating systems and population genetics

  • James, T. Y., L. A. Michelotti, A. D. Glasco, R. A. Clemons, R. A. Powers, E. S. James, D. R. Simmons, F. Bai, and S. Ge. (2019). Adaptation by loss of heterozygosity in Saccharomyces cerevisiae clones under divergent selection. Genetics 213: 665-683. pdf
  • Nieuwenhuis, B. P. S., and T. Y. James. (2016). The frequency of sex in fungi. Phil. Trans. R. Soc. B. 371: 20150540. pdf
  • James, T. Y. (2015). Why mushrooms have evolved to be so promiscuous: Insights from evolutionary and ecological patterns. Fungal Biol. Rev. 29: 167-178. pdf
  • Baranova, M. A., M. D. Logacheva, A. A. Penin, V. B. Seplyarskiy, Y. Safanova, S. A. Naumenko, A. V. Klepikova, E. S. Gerasimov, G. A. Bazykin, T. Y. James, and A. S. Kondrashov. (2015). Extraordinary genetic diversity in a wood decay mushroom. Mol. Biol. Evol. 32: 2775-2783. pdf
  • van Diepen, L. T. A., Å, Olson, K. Ihrmark, J. Stenlid, and T. Y. James. (2013). Extensive trans-specific polymorphism at the mating type locus of the root decay fungus Heterobasidion. Mol. Biol. Evol. 30: 2286-2301. pdf
  • Malloure, B. M., and T. Y. James. (2013). Inbreeding depression in urban environments of the bird’s nest fungus Cyathus stercoreus (Basidiomycota). Heredity 110: 355-362. pdf
  • James, T. Y. (2012). Ancient yet fast: rapid evolution of mating genes and mating systems in Fungi. In R. S. Singh, J. Xu, and R. J. Kulathinal [eds]. pp. 187-200. Evolution in the Fast Lane: Rapidly Evolving Genes and Genetic Systems. Oxford University Press, Oxford, U.K. pdf
  • James, T. Y., J. Stenlid, Å. Olson, and H. Johannesson. (2008). Evolutionary significance of imbalanced nuclear ratios within heterokaryons of the basidiomycete fungus Heterobasidion parviporum. Evolution 62: 2279-2296. pdf
  • James, T. Y. (2007). Analysis of mating-type locus organization and synteny in mushroom fungi- beyond model species. pp. 317-331. In J. Heitman, J. Kronstad, J. W. Taylor, and L. A. Casselton [eds.]. Sex in fungi: molecular determination and evolutionary implications. ASM Press, Washington, D. C. pdf
  • James, T. Y., P. Srivilai, U. Kües, and R. Vilgalys. (2006). Evolution of the bipolar mating system of the mushroom Coprinellus disseminatus from its tetrapolar ancestors involves loss of mating-type-specific pheromone receptor function. Genetics 172: 1877-1891. pdf
  • James, T. Y., S.-R. Liou, and R. Vilgalys. (2004). The genetic structure and diversity of the A and B mating-type genes from the tropical oyster mushroom, Pleurotus djamor. Fungal Genet. Biol. 41: 813-825. pdf
  • James, T. Y., and R. Vilgalys (2001). Abundance and diversity of Schizophyllum commune spore clouds in the Caribbean detected by selective sampling. Mol. Ecol.10: 471-480. pdf



Chytridiomycosis of amphibians

  • Russell, I. D., J. G. Larson, R. von May, I. A. Holmes, T. Y. James, and A. R. Davis-Rabosky (2019). Widespread chytrid infection across frogs in the Peruvian Amazon suggests critical role for low elevation in pathogen spread and persistence. PloS ONE 14: e0222718. pdf
  • Ribeiro, L., T. Carvalho, T. S. Jenkinson, D. da Silva Leite, C. G. Becker, T. Y. James, and L. F. Toledo. (2019). Bullfrog farms release virulent zoospores of the frog-killing fungus into the natural environment Sci. Rep. 9: 13422. pdf
  • Belasen, A. M., M. C. Bletz, D. da Silva Leite, L. F. Toledo, and T. Y. James. (2019). Long-term habitat fragmentation is associated with reduced immunogenetic diversity and increased infections in amphibian hosts. Front. Ecol. Evol. 6: 236. pdf
  • Greenspan, S. E., C. Lambertini, T. Carvalho, T. Y. James, L. F. Toledo, C. F. B. Haddad, and C. G. Becker (2018). Hybrids of amphibian chytrid show high virulence in native hosts. Sci. Rep. 8: 9600. pdf
  • Jenkinson, T. S., D. Rodriguez, R. A. Clemons, L. A. Michelotti, K. R. Zamudio, L. F. Toledo, J. E. Longcore, and T. Y. James. (2018). Globally invasive genotypes of the amphibian chytrid outcompete an enzootic lineage in coinfections. Proc. Roy. Soc. B. 285: 20181894. pdf
  • Betancourt-Román, C. M., C. C. O’Neil, and T. Y. James. (2016). Rethinking the role of non-vertebrate hosts in the life cycle of the amphibian chytridiomycosis pathogen. Parasitology 143: 1723-1729. pdf
  • Jenkinson, T. S., C. M. Betancourt Román, C. Lambertini, A. V. Aguilar, C. H. L. Nunes de Almeida, J. Ruggeri, A. M. Belasen, D. da Silva Leite, K. R. Zamudio, J. E. Longcore, L. F. Toledo, and T. Y. James. (2016). Amphibian-killing chytrid in Brazil comprises both stable endemic and recently expanded populations. Mol. Ecol. 25: 2978-2996. pdf
  • James, T. Y., L. F. Toledo, D. Rödder, D. da Silva Leite, A. M. Belasen, C. M. Betancourt Román, T. S. Jenkinson, C. Soto-Azat, C. Lambertini, A. V. Longo, J. Ruggeri, J. P. Collins, P. Burrowes, K. R. Lips, K. R. Zamudio, and J. E. Longcore. (2015). Disentangling the host, pathogen, and environmental determinants of a recently emerged wildlife diseases: Lessons from the first 15 years of amphibian chytridiomycosis research. Ecol. Evol. 5: 4079-4097. pdf
  • Schloegel, L. M., L. F. Toledo, J. E. Longcore, S. E. Greenspan, C. A. Viera, M. Lee, S. Zhao, C. Wangen, C. M. Ferreira, M. Hipolito, A. J. Davies, P. Daszak, C. A. Cuomo, T. Y. James. (2012). Novel, panzootic, and hybrid genotypes of amphibian chytridiomycosis associated with the bullfrog trade. Mol. Ecol. 21: 5162-5177. pdf
  • James T. Y., A. P. Litvintseva, , R. Vilgalys, J. A. T. Morgan, J. W. Taylor, M. C. Fisher, L. Berger, C. Weldon, L. du Preez, and J. E. Longcore. (2009) Rapid global expansion of the fungal disease chytridiomycosis into declining and healthy amphibian populations. PLoS Pathog. 5: e1000458. pdf
  • Harris, R. N., T. Y. James, A. Lauer, M. A. Simon, and A. Patel. (2006). Amphibian pathogen Batrachochytrium dendrobatidis is inhibited by the cutaneous bacteria of amphibian species. EcoHealth 3: 53-56. pdf
  • James, T. Y., and R. Vilgalys. (2006). Amphibian chytridiomycosis as an emerging infectious disease of wildlife: what can we learn from the earliest diverging fungi? pp. 271-278. In J. Heitman, S. G. Filler, J. E. Edwards, Jr., and A. P. Mitchell [eds.]. Molecular Principals of Fungal Pathogenesis. ASM Press, Washington, D. C. pdf



Fungal phylogeny

  • James, T. Y., J. E. Stajich, C. T. Hittinger, and A. Rokas. (2020). Towards a fully resolved fungal tree of life. Annu. Rev. Microbiol. 74: 291-313. pdf
  • Davis, W. J., K. R. Amses, G. L. Benny, D. Carter-House, Y. Chang, I. V. Grigoriev, M. E. Smith, J. W. Spatafora, J. E. Stajich, and T. Y. James (2019). Genome-scale phylogenetics analyses reveals a monophyletic Zoopagales (Zoopagomycota, Fungi) with predacious taxa evolving from mycoparasite ancestors. Mol. Phylogenet. Evol. 133: 152-163. pdf
  • Quandt, C. A., D. Beaudet, D. Corsaro, J. Walochnik, R. Michel, N. Corradi, and T. Y. James. (2017). The genome of an intranuclear parasite, Paramicrosporidium saccamoebae, unveils alternative adaptations to obligate intracellular parasitism. eLife 6: e29594. pdf
  • Berbee, M. L., T. Y. James, and C. Strullu-Derrien. (2017). Early diverging Fungi: Diversity and impact at the dawn of terrestrial life. Annu. Rev. Microbiol. 71: 41-60. pdf
  • Spatafora, J. W., Y. Chang, G. L. Benny, K. Lazarus, M. E. Smith, M. L. Berbee, G. Bonito, N. Corradi, I. Grigoriev, A. Gryganskyi, T. Y. James, K. O’Donnell, T. N. Taylor, J. Uehling, R. Vilgalys, M. M. White, and J. E. Stajich. (2016). A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data. Mycologia 108: 1028-1046. pdf
  • James, T. Y., A. Pelin, L. Bonen, S. Arhendt, D. Sain, N. Corradi, and J. E. Stajich. (2013). Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia. Curr. Biol. 23: 1548-1553. pdf
  • James, T. Y., M. L. Berbee. (2012). No jacket required- new fungal lineage defies dress code. BioEssays 34: 94-102. pdf
  • Rosling, A., F. Cox, K. Cruz-Martinez, K. Ihrmark, G.-A. Grelet, B. L. Lindahl, A. Menkis, and T. Y. James (2011). Archaeorhizomycetes: unearthing an ancient class of ubiquitous soil fungi. Science 333: 876-879. pdf
  • White, M. M., T. Y. James, K. O’Donnell, M. J. Cafaro, Y. Tanabe, and J. Sugiyama. (2006). Phylogeny of the Zygomycota based on nuclear ribosomal sequence data. Mycologia 98: 872-884. pdf
  • James, T. Y., F. Kauff, C. Schoch, P. B. Matheny, V. Hofstetter, C. Cox, G. Celio, and the AFTOL working group (2006). Reconstructing the early evolution of the fungi using a six gene phylogeny. Nature 443: 818-822. pdf


Chytrid systematics

  • Longcore, J. E., S. Qin, D. R. Simmons, and T. Y. James (2020). Quaeritorhiza haematococci gen. et sp. nov., a parasitic chytrid of the commercially grown alga, Haematococcus pluvialis. Mycologia 112: 606-615. pdf
  • Davis, W. J., G. H. Jerônimo, D. R. Simmons, C. A. Quandt, and T. Y. James. (2019). Revisiting the aquatic phycomycete biota of the Douglas Lake region since the time of Dogma and Sparrow. Philipp. J. Syst. Biol. 13: 1-14. pdf
  • Jerônimo, G. H., A. L. Jesus, D. R. Simmons, T. Y. James, and C. L. A. Pires-Zottarelli. (2019). Novel taxa in Cladochytriales (Chytridiomycota): Karlingiella (gen. nov.) and Nowakowskiella crenulata (sp. nov.). Mycologia 111: 506-516. pdf
  • Powell, M. J., P. M. Letcher, and T. Y. James. (2017). Ultrastructural characterization of the host-parasite interface between Allomyces anomalus (Blastocladiomycota) and Rozella allomycis (Cryptomycota). Fungal Biol. 121: 561-572. pdf
  • Simmons, D. R., T. Y. James, A. F. Meyer, and J. E. Longcore. (2009). Lobulomycetales, a new order in the Chytridiomycota. Mycol. Res. 113: 450-160. pdf
  • Hoffman, Y., C. Aflalo, A. Zarka, J. Gutman, T. Y. James, and S. Boussiba. (2008). Isolation and characterization of a novel chytrid species (Phylum Blastocladiomycota), parasitic on the green alga Haematococcus. Mycol. Res. 112: 70-81. pdf

Fungal genomics and molecular evolution
  • Myers, J. M., A. E. Bonds, R. A. Clemons, N. Thapa, D. R. Simmons, D. Carter-House, J. Ortanez, P. Liu, A. Miralles-Durán, J. E. Longcore, G. M. Bonito, J. E. Stajich, J. W. Spatafora, Y. Chang, L. M. Corrochano, A. Gryganskyi, I. V. Grigoriev, and T. Y. James. (2020). Survey of early-diverging lineages of fungi reveals abundant and diverse mycoviruses. mBio 11: e02027-20. pdf
  • Amses, K. R., W. J. Davis, and T. Y. James. (2020). scgid: a consensus approach to contig filtering and genome prediction from single cell sequencing libraries of uncultured eukaryotes. Bioinformatics 36: 1994-2000. pdf
  • Boyce, G. R., E. Gluck-Thaler, J. C. Slot, J. E. Stajich, W. J. Davis, T. Y. James, J. R. Cooley, D. G. Panaccione, J. Eilenberg, H. H. De Fine Licht, A. M. Macias, M. C. Berger, K. L. Wickert, C. M. Stauder, E. J. Spahr, M. D. Maust, A. M. Metheny, C. Simon, G. Kritsky, K. T. Hodge, R. A. Humber, T. Gullion, D. P. G. Short, T. Kijimoto, D. Mozgai, N. Arguedas, M. T. Kasson. (2019). Psychoactive plant- and mushroom-associated alkaloids from two behavior modifying cicada pathogens. Fungal Ecol. 41: 147-164. pdf
  • Bewick, A. J., B. T. Hofmeister, R. A. Powers, S. J. Mondo, I. V. Grigoriev, T. Y. James, J. E. Stajich, and R. J. Schmitz. (2019). Diversity of cytosine methylation across the fungal tree of life. Nat. Ecol. Evol. 3: 479-490. pdf
  • Ahrendt, S. R., C. A. Quandt, D. Ciobanu, A. Clum, A. Salamov, B. Andreopoulos, J.-F. Cheng, T. Woyke, A. Pelin, B. Henrissat, G. L. Benny, M. E. Smith, T. Y. James, and I. V. Grigoriev. (2018). Leveraging single-cell genomics to expand the Fungal Tree of Life. Nat. Microbiol. 3: 1417-1428. pdf
  • Phadke, S. S., C. J. Maclean, S. Y. Zhao, E. A. Mueller, L. A. Michelotti, K. L. Norman, A. Kumar, and T. Y. James. (2018). Genome-wide screen for yeast genes contributing to opportunistic pathogenicity in an invertebrate model host. G3 Genes Genom. Genet. 8: 63-78. pdf
  • Mondo, S. J., R. O. Dannebaum, R. C. Kuo, K. B. Louie, A. J. Bewick, K. LaButti, S. Haridas, A. Kuo, A. Salamov, S. R. Ahrendt, R. Lau, B. P. Bowen, A. Lipzen, W. Sullivan, W. B. Andreopoulos, A. Clum, E. Lindquist, C. Daum, T. R. Northen, G. K. Ramamoorthy, R. J. Schmitz, A. Gryganskyi, D. Culley, J. Magnuson, T. Y. James, M. A. O’Malley, J. E. Stajich, J. W. Spatafora, A. Visel, and I. V. Grigoriev. (2017). Widespread adenine N6-methylation of active genes in fungi. Nat. Genet. 49: 964-968. pdf
  • Seplyarskiy, V. B., M. A. Baranova, E. V. Leushkin, M. D. Logacheva, A. A. Penin, A. S. Kondrashov, and T. Y. James. (2014). Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Mol. Biol. Evol. 31: 3016-3025. pdf
  • Stajich, J. E., (2010). Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc. Natl. Acad. Sci. U. S. A. 107:11889-11894. pdf
  • Parrent, J. L., T. Y. James, R. Vasaitis and A. F. S. Taylor. (2009). Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses. BMC Evol. Biol. 9: 148. pdf
  • Hoegger, P. J., S. Kilaru, T. Y. James, J. R. Thacker, and U. Kües. (2006). Phylogenetic comparison and classification of laccase and related multicopper oxidase protein sequences. FEBS Journal 273: 2308-2326. pdf


Fungal ecology

  • Zak, D. R., P. T. Pellitier, W. A. Argiroff, B. T. Castillo, T. Y. James, L. E. Nave, C. Averill, K. Beidler, J. Bhatnagar, J. Blesh, A. T. Classen, M. Craig, C. W. Fernandez, P. Gundersen, R. Johansen, R. T. Koide, E. A. Lilleskov, B. D. Lindahl, K. Nadelhoffer, R. P. Phillips, A. Tunlid. (2019). Exploring the function of ectomycorrhizal fungi in soil organic matter dynamics. New Phytol. 223: 33-39. pdf
  • Castillo, B. T., L. E. Nave, J. M. Le Moine, T. Y. James, and K. J. Nadelhoffer. (2018). Impacts of experimentally accelerated forest succession on below-ground plant and fungal communities. Soil Biol. Biochem. 125: 44-53. pdf
  • Tedersoo, L., M. Bahram, R. Puusepp, R. H. Nilsson, and T. Y. James. (2017). Novel soil-inhabiting clades fill gaps in the fungal tree of life. Microbiome. 5: 42. pdf
  • James, T. Y., J. A. Marino, I. Perfecto, and J. Vandermeer. (2016). Identification of coffee rust mycoparasites using single molecule DNA sequencing of infected pustules. Appl. Environ. Microbiol. 82: 631-639. pdf
  • Grossart, H.-P., C. Wurzbacher, T. Y. James, and M. Kagami. (2016). Discovery of dark matter fungi in aquatic ecosystems demands a reappraisal of the phylogeny and ecology of zoosporic fungi. Fungal Ecol. 19: 28-38. pdf
  • Duffy, M. A., T. Y. James, and A. Longworth. (2015). Ecology, virulence, and phylogeny of Blastulidium paedophthorum, a widespread brood parasite of Daphnia. Appl. Environ. Microbiol. 81: 5486-5496. pdf
  • Lazarus, K. L., and T. Y. James. (2015). Surveying the biodiversity of the early-diverging fungal phylum Cryptomycota using a targeted PCR approach. Fungal Ecol. 14: 62-70. pdf
  • Diez, J. M., I. Ibáñez, J. Silander, R. Primack, H. Higuchi, H. Kobori, A. Sen, and T. Y. James. (2014). Beyond seasonal climate: statistical estimation of phenological responses to weather. Ecol. Appl. 24: 1793-1802. pdf
  • Diez, J. M., T. Y. James, McMunn, M., Ibáñez, I. (2013). Predicting species-specific responses of fungi to climatic variation using historical records. Global Change Biol. 19: 3145-3154. pdf
  • Henkel, T. W., T. Y. James, S. L. Miller, M. C. Aime, and O. K. Miller, Jr. (2006). The mycorrhizal status of Pseudotulostoma volvata (Elaphomycetaceae, Eurotiales, Ascomycota). Mycorrhiza 16: 241-244. pdf