The main areas in which we publish are:


Fungal mating systems and population genetics

  • Nieuwenhuis, B. P. S., and T. Y. James. (2016). The frequency of sex in fungi. Phil. Trans. R. Soc. B. 371: 20150540. pdf
  • Jackson, D., A. T. Zemenick, B. Malloure, C. A. Quandt, and T. Y. James. (2016). Fine-scale spatial genetic structure of a fungal parasite of coffee scale insects. J. Invert. Pathol. 139: 34-41. 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
  • James, T. Y., S. Sun, W. Li, J. Heitman, H.-C. Kuo, Y.-H. Lee, F. O. Asiegbu, and Å. Olson. (2013). Polyporales genomes reveal the genetic architecture underlying tetrapolar and bipolar mating systems. Mycologia 105: 1374-1390. 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
  • Heitman, J. E., S. Sun, and T. Y. James. (2013). Evolution of fungal sexual reproduction. Mycologia 105: 1-27. 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
  • van Peer, A. F., S.-Y. Park, P.-G. Shin, K.-Y. Jang, Y.-B. Yoo, Y.-J. Park, B.-M. Lee, G.-H. Sung, T. Y. James, and W.-S. Kong. (2011). Comparative genomics of the mating-type loci of the mushroom Flammulina velutipes reveals widespread synteny and recent inversions. PLoS ONE 6: e22249. pdf
  • James, T. Y., M. Lee, and L. T. A. van Diepen. (2011). A single mating-type locus comprised of homeodomain genes promotes nuclear migration and heterokaryosis in the white-rot fungus Phanerochaete chrysosporium. Eukaryot. Cell 10: 249-261. pdf
  • Li, M. J. Liang, Y. Li, B. Feng, Z.-L. Yang, T. Y. James, and J. Xu. (2010). Genetic diversity of Dahongjun, the commercially important “Big Red Mushroom” from southern China. PLoS One 5: e10684. pdf
  • Strandberg, R., K. Nygren, A. Menkis, T. Y. James, L. Wik, J. E. Stajich, and H. Johannesson. 2010. Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora. Fungal Genet. Biol. 47: 869-878. pdf
  • James, T. Y., S. Johannson, and H. Johannesson. (2009). Trikaryon formation and nuclear selection in pairings between heterokaryons and homokaryons of the root rot pathogen Heterobasidion parviporum. Mycol. Res. 113: 583-590. 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., 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. 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
  • Kües, U., T. Y. James, R. Vilgalys, and M. Challen (2001). The chromosomal region containing pab-1, mip, and the A mating type locus of the secondarily homothallic basidiomycete Coprinus bilanatus. Curr. Genet. 39: 16-24. pdf
  • James, T. Y., J.-M. Moncalvo, S. Li, and R. Vilgalys (2001). Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune. Genetics. 157: 149-161. pdf
  • James, T. Y., D. Porter, J. L. Hamrick, and R. Vilgalys. (1999). Evidence for limited intercontinental gene flow in the cosmopolitan mushroom, Schizophyllum commune. Evolution 53: 1665-1677. pdf



Chytridiomycosis of amphibians

  • 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
  • Lambertini, C., C. G. Becker, T. S. Jenkinson, D. Rodriguez, D. da Silva Leite, T. Y. James, K. R. Zamudio, and L. F. Toledo. (2016). Local phenotypic variation in amphibian-killing fungus predicts infection dynamics. Fungal Ecol. 20: 15-21. 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
  • Shaw, S. D., L. Berger, S. Bell, S. Dodd, T. Y. James, L. F. Skerratt, P. J. Bishop, and R. Speare. (2014). Baseline cutaneous bacteria of free-living New Zealand native frogs (Leiopelma archeyi and Leiopelma hochstetteri) and implications for their role in defense against the amphibian chytrid (Batrachochytrium dendrobatidis). J. Wildlife Dis. 50: 723-732. pdf
  • Rosenblum, E. B., T. Y. James, K. R. Zamudio, T. J. Poorten, D. Ilut, D. Rodriguez, J. M. Eastman, K. Richards-Hrdlicka, S. Joneson, T. S. Jenkinson, J. E. Longcore, G. Parra Olea, L. F. Toledo, M. L. Arellano, E. M. Medina, S. Restrepo, S. V. Flechas, L. Berger, C. J. Briggs, J. E. Stajich. (2013). Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data. Proc. Natl. Acad. Sci. U. S. A. 110: 9385-9390. 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
  • Garland, S., T. Y. James, D. Blair, L. Berger, and L. F. Skerratt. (2011). Polymorphic repetitive loci of the amphibian pathogen Batrachochytrium dendrobatidis. Dis. Aquat. Organ. 97: 1-9. pdf
  • Rosenblum, E. B., M. C. Fisher, T. Y. James, J. E. Stajich, J. E. Longcore, L. R. Gentry, and T. J. Poorten. (2010). A molecular perspective on the biology of the emerging pathogen Batrachochytrium dendrobatidis. Dis. Aquat. Org. 92: 131-147. pdf
  • Schloegel, L. M., C. M. Ferreira, T. Y. James, M. Hipolito, J. E. Longcore, A. D. Hyatt, M. Yabsley, A. M. C. Martins-Martins, R. Mazzoni, A. J. Davies, and P. Daszak. (2010). The North American Bullfrog (Rana catesbeiana) as a reservoir for the spread of Batrachochytrium dendrobatidis in Brazil. Animal Conserv. 13: 53-61. 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
  • Walker, S. F., J. Bosch, T. Y. James, A. P. Litvintseva, J. A. O. Valls, S. Piña, G. García, G. A. Rosa, A. A. Cunningham, S. Hole, R. Griffiths, and M. C. Fisher. (2008). Introduced pathogens threaten species recovery programs. Current Biology 18: R853-R854. 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
  • 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. pdf



Fungal phylogeny

  • 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
  • Haag, K. L., T. Y. James, J.-F. Pombert, R. Larsson, T. M. M. Schaer, D. Refardt, and D. Ebert. (2014). Evolution of a morphological novelty occurred before genome compaction in a lineage of extreme parasites. Proc. Natl. Acad. Sci. U. S. A. 111: 15480-15485. 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
  • Stajich, J. E., M. L. Berbee, M. Blackwell, D. S. Hibbett, T. Y. James, J. W. Spatafora, and J. W. Taylor. 2009. The Fungi. Curr. Biol. 19: R840-R845. pdf
  • Hibbett, D. S., et al. (2007). A higher-level phylogenetic classification of the Fungi. Mycol. Res. 111: 509-547. 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
  • Lutzoni, F., et al. (2004). Assembling the fungal tree of life: Progress, classification, and evolution of subcellular traits Am. J. Bot. 91: 1446-1480. pdf
  • Moncalvo, J.-M., R. Vilgalys, S. A. Redhead, J. E. Johnson, T. Y. James, M. C. Aime, V. Hofstetter, S. Verduin, E. Larsen, T. J. Baroni, R. G. Thorn, S. Jacobsson, H. Clémençon, and O. K. Miller, Jr. (2002) One hundred and seventeen clades of euagarics. Mol. Phylogenet. Evol. 23: 357-400. pdf


Chytrid systematics

  • Jerônimo, G. H., A. L. de Jesus, A. V. Marano, T. Y. James, J. I. de Souza, S. C. O. Rocha, and C. L. A. Pires-Zottarelli. (2015). Diversidade de Blastocladiomycota e Chytridiomycota do Parque Estadual da Ilha do Cardoso, Cananéia, SP, Brasil. Hoehnea 42: 135-163. pdf
  • Longcore, J. E. P. M. Letcher, and T. Y. James. (2011). Homolaphlyctis polyrhiza gen. et sp. nov., a species in the Rhizophydiales (Chytridiomycetes) with multiple rhizoidal axes. MycoTaxon 118: 433-440. pdf
  • Porter, T. M., W. Martin, T. Y. James, J. E. Longcore, F. Gleason, P. H. Adler, P. M. Letcher, and R. Vilgalys (2011). Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal data. Fungal Biol. 115: 381-392. 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
  • 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. pdf
  • James, T. Y., D. Porter, C. A. Leander, R. Vilgalys, and J. E. Longcore. (2000) Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics. Can. J. Bot. 78: 336-350. pdf

Fungal genomics and molecular evolution
  • 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
  • Ferandez-Fueyo, E., et al. (2012). Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis. Proc. Natl. Acad. Sci. U. S. A. 109: 5458-5463. pdf
  • Å. Olson, et al. (2012). Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. New Phytol. 194: 1001-1013. pdf
  • Padamsee, M., et al. (2012). The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction. Fungal Genet. Biol. 49: 217-226. 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
  • Martinez, D., et al. (2009). Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc. Natl. Acad. Sci. USA. 106: 1954-1959. 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

  • 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