Timothy Y James

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. doi request reprint Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia
    Timothy Y James
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Curr Biol 23:1548-53. 2013
  2. pmc Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses
    Jeri Lynn Parrent
    Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ulls Väg 26A, SE 750 07 Uppsala, Sweden
    BMC Evol Biol 9:148. 2009
  3. doi request reprint No jacket required--new fungal lineage defies dress code: recently described zoosporic fungi lack a cell wall during trophic phase
    Timothy Y James
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
    Bioessays 34:94-102. 2012
  4. pmc A single mating-type locus composed of homeodomain genes promotes nuclear migration and heterokaryosis in the white-rot fungus Phanerochaete chrysosporium
    Timothy Y James
    Department of Ecology and Evolutionary Biology, 830 N University, University of Michigan, Ann Arbor, MI 48109, USA
    Eukaryot Cell 10:249-61. 2011
  5. doi request reprint Trikaryon formation and nuclear selection in pairings between heterokaryons and homokaryons of the root rot pathogen Heterobasidion parviporum
    Timothy Y James
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, 752 36 Uppsala, Sweden
    Mycol Res 113:583-90. 2009
  6. pmc Rapid global expansion of the fungal disease chytridiomycosis into declining and healthy amphibian populations
    Timothy Y James
    Department of Biology, Duke University, Durham, NC, USA
    PLoS Pathog 5:e1000458. 2009
  7. pmc Evolution of the bipolar mating system of the mushroom Coprinellus disseminatus from its tetrapolar ancestors involves loss of mating-type-specific pheromone receptor function
    Timothy Y James
    Department of Biology, Duke University, Durham, North Carolina 27708, USA
    Genetics 172:1877-91. 2006
  8. ncbi request reprint A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota)
    Timothy Y James
    Department of Biology, Duke University, Durham, North Carolina 27708, USA
    Mycologia 98:860-71. 2006
  9. doi request reprint Evolutionary significance of imbalanced nuclear ratios within heterokaryons of the basidiomycete fungus Heterobasidion parviporum
    Timothy Y James
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, 752 36, Uppsala, Sweden
    Evolution 62:2279-96. 2008
  10. doi request reprint Extensive trans-specific polymorphism at the mating type locus of the root decay fungus Heterobasidion
    Linda T A van Diepen
    Department of Ecology and Evolutionary Biology, University of Michigan
    Mol Biol Evol 30:2286-301. 2013

Detail Information

Publications21

  1. doi request reprint Shared signatures of parasitism and phylogenomics unite Cryptomycota and microsporidia
    Timothy Y James
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Curr Biol 23:1548-53. 2013
    ..The Rozella proteome has not undergone major contraction like microsporidia; instead, several classes have undergone expansion, such as host-effector, signal-transduction, and folding proteins...
  2. pmc Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses
    Jeri Lynn Parrent
    Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Ulls Väg 26A, SE 750 07 Uppsala, Sweden
    BMC Evol Biol 9:148. 2009
    ..Using bioinformatic and PCR-based analyses, we tested for GH32 gene presence in all available fungal genomes and an additional 149 species representing a broad phylogenetic and ecological range of biotrophic fungi...
  3. doi request reprint No jacket required--new fungal lineage defies dress code: recently described zoosporic fungi lack a cell wall during trophic phase
    Timothy Y James
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
    Bioessays 34:94-102. 2012
    ..Rather than evolutionary intermediates, the cryptomycota may be strange, divergent fungi that evolved from an ancestor with a nearly complete suite of classical fungal-specific characters...
  4. pmc A single mating-type locus composed of homeodomain genes promotes nuclear migration and heterokaryosis in the white-rot fungus Phanerochaete chrysosporium
    Timothy Y James
    Department of Ecology and Evolutionary Biology, 830 N University, University of Michigan, Ann Arbor, MI 48109, USA
    Eukaryot Cell 10:249-61. 2011
    ..The partial uncoupling of nuclear migration and mating incompatibility in this species may be predicted to lead to parasexual recombination and may have contributed to the homothallic behavior observed in previous studies...
  5. doi request reprint Trikaryon formation and nuclear selection in pairings between heterokaryons and homokaryons of the root rot pathogen Heterobasidion parviporum
    Timothy Y James
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, 752 36 Uppsala, Sweden
    Mycol Res 113:583-90. 2009
    ..The high rate of trikaryon formation in this study suggests that fungi with multinucleate cells may have the potential for greater genetic diversity and recombination relative to dikaryotic fungi...
  6. pmc Rapid global expansion of the fungal disease chytridiomycosis into declining and healthy amphibian populations
    Timothy Y James
    Department of Biology, Duke University, Durham, NC, USA
    PLoS Pathog 5:e1000458. 2009
    ..The widespread occurrence of the same lineage in both healthy and declining populations suggests that the outcome of the disease is contingent on environmental factors and host resistance...
  7. pmc Evolution of the bipolar mating system of the mushroom Coprinellus disseminatus from its tetrapolar ancestors involves loss of mating-type-specific pheromone receptor function
    Timothy Y James
    Department of Biology, Duke University, Durham, North Carolina 27708, USA
    Genetics 172:1877-91. 2006
    ..Although mating type in C. disseminatus is controlled by only the transcription factor genes, cellular functions appear to be conserved for both groups of genes...
  8. ncbi request reprint A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota)
    Timothy Y James
    Department of Biology, Duke University, Durham, North Carolina 27708, USA
    Mycologia 98:860-71. 2006
    ..The Blastocladiales appears to be the sister taxon of most nonflagellated fungi. Based on molecular phylogenetic and ultrastructural characters this order is elevated to a phylum, the Blastocladiomycota...
  9. doi request reprint Evolutionary significance of imbalanced nuclear ratios within heterokaryons of the basidiomycete fungus Heterobasidion parviporum
    Timothy Y James
    Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, 752 36, Uppsala, Sweden
    Evolution 62:2279-96. 2008
    ....
  10. doi request reprint Extensive trans-specific polymorphism at the mating type locus of the root decay fungus Heterobasidion
    Linda T A van Diepen
    Department of Ecology and Evolutionary Biology, University of Michigan
    Mol Biol Evol 30:2286-301. 2013
    ..In doing so, increased divergence should decrease recombination among alleles and as a by-product create incompatibilities in the functional domains not involved in allele recognition but in regulating sexual development. ..
  11. ncbi request reprint Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone
    Erica A Morehouse
    Department of Biology, Biological Sciences Building, Room 139, Duke University, Durham, NC 27708, USA
    Mol Ecol 12:395-403. 2003
    ..dendrobatidis is diploid and primarily reproduces clonally. In contrast to the lack of nucleotide polymorphism, electrophoretic karyotyping of multiple strains demonstrated a number of chromosome length polymorphisms...
  12. doi request reprint Polyporales genomes reveal the genetic architecture underlying tetrapolar and bipolar mating systems
    Timothy Y James
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109
    Mycologia 105:1374-90. 2013
    ..The data are consistent with multiple origins of bipolarity within the Agaricomycetes and Polyporales, although the alternative hypothesis that tetrapolarity and bipolarity are reversible states needs better testing. ..
  13. ncbi request reprint Reconstructing the early evolution of Fungi using a six-gene phylogeny
    Timothy Y James
    Department of Biology, Duke University, Durham, North Carolina 27708 0338, USA
    Nature 443:818-22. 2006
    ..The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree...
  14. ncbi request reprint Phylogeny of the Zygomycota based on nuclear ribosomal sequence data
    Merlin M White
    Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence 66045 7534, USA
    Mycologia 98:872-84. 2006
    ..Clades are discussed with special reference to traditional classifications, mapping morphological characters and ecology, where possible, as a snapshot of our current phylogenetic perspective of the Zygomycota...
  15. doi request reprint Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA
    Teresita M Porter
    Duke University, Biology Department, Campus Box 90338, Durham, NC 27708, USA
    Fungal Biol 115:381-92. 2011
    ..We provide this rDNA phylogeny as a preliminary framework to guide further taxon and gene sampling and to facilitate future ecological, morphological, and systematic studies...
  16. doi request reprint Conflict between reproductive gene trees and species phylogeny among heterothallic and pseudohomothallic members of the filamentous ascomycete genus Neurospora
    Rebecka Strandberg
    Department of Evolutionary Biology, Uppsala University, Norbyvagen 18D, SE 752 36 Uppsala, Sweden
    Fungal Genet Biol 47:869-78. 2010
    ..Taken together, the results presented here highlight complex evolutionary trajectories of reproductive genes in the fungal kingdom, which may be of importance for reproductive behavior in natural populations...
  17. doi request reprint Evolution of fungal sexual reproduction
    Joseph Heitman
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
    Mycologia 105:1-27. 2013
    ....
  18. ncbi request reprint Evolution of the gene encoding mitochondrial intermediate peptidase and its cosegregation with the A mating-type locus of mushroom fungi
    Timothy Y James
    Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
    Fungal Genet Biol 41:381-90. 2004
    ..Phylogenetic analysis of MIP sequences from diverse mushroom species agrees with the current organismal phylogeny, suggesting the sequences are generally orthologous...
  19. ncbi request reprint One hundred and seventeen clades of euagarics
    Jean Marc Moncalvo
    Department of Biology, Duke University, Durham, NC 27708, USA
    Mol Phylogenet Evol 23:357-400. 2002
    ..Several clades are best supported by ecological, biochemical, or trophic habits rather than by morphological similarities...
  20. ncbi request reprint The genetic structure and diversity of the A and B mating-type genes from the tropical oyster mushroom, Pleurotus djamor
    Timothy Y James
    Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
    Fungal Genet Biol 41:813-25. 2004
    ..It is hypothesized that the A mating-type locus of P. djamor is comprised of only one homeodomain pair, which may explain the lower number of A mating-type alleles relative to other mushroom species...
  21. ncbi request reprint The pab1 gene of Coprinus cinereus encodes a bifunctional protein for para-aminobenzoic acid (PABA) synthesis: implications for the evolution of fused PABA synthases
    Timothy Y James
    Duke University, Department of Biology, Durham, NC, USA 27708, USA
    J Basic Microbiol 42:91-103. 2002
    ....