Timothy James

Research

Much of the obvious adaptive evolution in Fungi is observed in their diversification of mating systems and dispersal mechanisms. I study the evolution of sex and reproductive traits of Fungi and attempt to link these traits with phylogeny and population genetics. I am particularly interested in the intriguing phenomenon of heterokaryosis in Fungi. The heterokaryon is an alternative to diploidy in which multiple genetically different nuclei inhabit the same cell after mating occurs. I am studying genomic conflict in this system by measuring the degree to which the nuclei of a heterokaryon compete or cooperate with each other. Understanding this behavior includes investigating the role of pheromone signaling in the communication between nuclei.

In addition, our lab is interested in the evolution of the ancient aquatic fungi known as the chytrids. Our methodology includes molecular biology, phylogenetics, and fungal cultivation. Currently I am focusing on the following three projects:

1. Evolution of mating systems and nuclear behavior in mushroom fungi (Agaricomycetes)
2. Molecular systematics of ancient fungal lineages
3. Evolutionary genomics and population genetics of the chytrid fungal disease of amphibians

Select publications

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.

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.

James, T.Y., P. M. Letcher, J. E. Longcore, S. E. Mozley-Standridge, D. Porter, M. J. Powell, G. W. Griffith, R. Vilgalys. 2006. A molecular phylogeny of the flagellated Fungi (Chytridiomycota) and a proposal for a new phylum (Blastocladiomycota). Mycologia 98:860-871.

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.

James, T.Y., F. Kauff, C. Schoch, P. B. Matheny, V. Hofstetter, C. Cox, G. Celio, C. Gueidan, E. Fraker, J. Miadlikowska, H. T. Lumbsch, A. Rauhut, V. Reeb, A. E. Arnold, A. Amtoft, J. E. Stajich, K. Hosaka, G.-H. Sung, D. Johnson, B. O’Rourke, M. Crockett, M. Binder, J. M. Curtis, J. C. Slot, Z. Wang, A. W. Wilson, A. Schüßler, J. E. Longcore, K. O’Donnell, S. Mozley-Standridge, D. Porter, P. M. Letcher, M. J. Powell, J. W. Taylor, M. M. White, G. W. Griffith, D. R. Davies, R. A. Humber, J. B. Morton, J. Sugiyama, A. Y. Rossman, J. D. Rogers, D. H. Pfister, D. Hewitt, K. Hansen, S. Hambleton, R. A. Shoemaker, J. Kohlmeyer, B. Volkmann-Kohlmeyer, R. A. Spotts, M. Serdani, P. W. Crous, K. W. Hughes, K. Matsuura, E. Langer, G. Langer, W. A. Untereiner, R. Lücking, B. Büdel, D. M. Geiser, A. Aptroot, P. Diederich, I. Schmitt, M. Schultz, R. Yahr, D. Hibbett, F Lutzoni, D. McLaughlin, J. Spatafora, and R. Vilgalys. 2006. Reconstructing the early evolution of the fungi using a six gene phylogeny. Nature 443:818-822.

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.

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 Journal273:2308-2326.

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.

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.

James, T.Y., U. Kües, S. A. Rehner, and R. Vilgalys. 2004. Evolution of the gene encoding mitochondrial intermediate peptidase and its cosegregation with the A mating-type locus of mushroom fungi. Fungal Genet. Biol. 41:381-390.

Morehouse, E. A., T. Y. James, A. R. D. Ganley, R. Vilgalys, L. Berger, P. J. Murphy, and J. E. Longcore. 2003. Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone. Mol. Ecol. 12:395-403.