Select Publications

The main areas in which we publish are:

• Fungal mating systems and population genetics
• Chytridiomycosis of amphibians
• Fungal phylogeny
• Chytrid systematics and diversity
• Fungal genomics and molecular evolution
• Fungal ecology

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

Fungal mating systems and population genetics

• James, T. Y. (2023). Sex without sexes: can the cost of finding a mate explain diversity in fungal mating systems? Integr. Comp. Biol. 63: 922-935. pdf
• McTaggart, A. R., J. C. Slot, K. McKernan, S. McLaughlin, C. Barlow, C. Appleyard, T. L. Bartlett, L. N. Warne, L. S. Shuey, A. Drenth, and T. Y. James (2023). Domestication through clandestine cultivation constrained genetic diversity in magic mushrooms relative to naturalized populations. Curr. Biol. 33: 5147-5159. pdf
• 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
• 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

Chytridiomycosis of amphibians

• Clemons, R. A., M. Yacoub, E. Faust, L. F. Toledo, T. S. Jenkinson, T. Carvalho, D. R. Simmons, E. Kalinka, L. Fritz-Laylin, T. Y James, and J. E. Stajich. (2024). Endogenized hypervirulence-associated DNA virus BdDV-1 is primarily restricted to enzootic lineages of the amphibian pathogen Batrachochytrium dendrobatidis. Curr. Biol. 34: 1469-1478. pdf
• Carvalho, T., A. M. Belasen, L. F. Toledo, and T. Y. James. (2024). Coevolution of a generalist pathogen with many hosts: the case of the amphibian chytrid Batrachochytrium dendrobatidis. Curr. Opin. Microbiol. 78: 102435. pdf
• Belasen, A. M., K. R. Amses, C. G. Becker, R. A. Clemons, L. F. Toledo, and T. Y. James. (2022). Habitat fragmentation in the Brazilian Atlantic Forest is associated with erosion of frog immunogenetic diversity and increased fungal infections. Immunogenetics. 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
• 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

Fungal phylogeny

• Dirks, A. C., O. G. Mohamed, P. Schultz, A. N. Miller, A. Tripathi, and T. Y. James. (2023). Not all bad: Gyromitrin has a limited distribution in the false morels as determined by a new ultra high-performance liquid chromatography method. Mycologia 115: 1-15. pdf
• 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
• 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
• 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
• 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
• 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

Fungal genomics and molecular evolution

• Amses, K. R., D. R. Simmons, J. E. Longcore, S. J. Mondo, K. Seto, G. H. Jerônimo, A. E. Bonds, C. A. Quandt, W. J. Davis, Y. Chang, B. A. Federici, A. Kuo, K. LaButti, J. Pangilinan, W. Andreopoulos, A. Tritt, R. Riley, H. Hundley, J. Johnson, A. Lipzen, K. Barry, B. F. Lang, C. A. Cuomo, N. E. Buchler, I. V. Grigoriev, J. W. Spatafora, J. E. Stajich, T Y. James. (2022). Diploid-dominant life cycles characterize the early evolution of Fungi. Proc. Natl. Acad. Sci. USA. 36: e2116841119. pdf
• Michelotti, L. A., S. Sun, J. Heitman, and T. Y. James. (2022). Clonal evolution in serially passaged Cryptococcus neoformans x deneoformans hybrids reveals a heterogenous landscape of genomic change. Genetics 220: iyab142. pdf.
• 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

Fungal ecology

• Quandt, C. A., J. A. Marino, Jr., D. R. Simmons, W. J. Davis, B. T. Hassett, K. T. Picard, and T. Y. James. (2023). Evaluating the diversity of the enigmatic fungal phylum Cryptomycota across habitats using 18S rRNA metabarcoding. Fungal Ecol. 64: 101248. pdf
• Marino, J., V. Denef, G. Dick, M. Duhaime, and T. Y. James. (2022). Fungal community dynamics associated with harmful cyanobacterial blooms in two Great Lakes. J. Great Lakes Res. 48: 1021-1031. pdf
• Andrew, C., J. M. Diez, T. Y. James, and H. Kauserud. (2019). Fungarium specimens – a largely untapped source in global change biology and beyond. Phil. Trans. R. Soc. B. 374: 20170392. 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
• 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