Jeff J Doyle

Summary

Affiliation: Cornell University
Country: USA

Publications

  1. ncbi request reprint Genomes, multiple origins, and lineage recombination in the Glycine tomentella (Leguminosae) polyploid complex: histone H3-D gene sequences
    Jeff J Doyle
    L H Bailey Hortorium, Cornell University, Ithaca, New York 14853, USA
    Evolution 56:1388-402. 2002
  2. pmc The rest of the iceberg. Legume diversity and evolution in a phylogenetic context
    Jeff J Doyle
    LH Bailey Hortorium, Department of Plant Biology, 462 Mann Library, Cornell University, Ithaca, New York 14853, USA
    Plant Physiol 131:900-10. 2003
  3. pmc Widespread genome duplications throughout the history of flowering plants
    Liying Cui
    Department of Biology, The Pennsylvania State University, University Park 16802, USA
    Genome Res 16:738-49. 2006
  4. doi request reprint Phylogenetic perspectives on the origins of nodulation
    Jeff J Doyle
    Department of Plant Biology, Cornell University, Ithaca, NY, USA
    Mol Plant Microbe Interact 24:1289-95. 2011
  5. ncbi request reprint Phylogenetic utility of histone H3 intron sequences in the perennial relatives of soybean (Glycine: Leguminosae)
    J J Doyle
    L H Bailey Hortorium, Cornell University, Ithaca, New York 14853, USA
    Mol Phylogenet Evol 6:438-47. 1996
  6. doi request reprint Dating the origins of polyploidy events
    Jeff J Doyle
    Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
    New Phytol 186:73-85. 2010
  7. ncbi request reprint Trees within trees: genes and species, molecules and morphology
    J J Doyle
    L H Bailey Hortorium, 462 Mann Library Building, Cornell University, Ithaca, New York 14853, USA
    Syst Biol 46:537-53. 1997
  8. doi request reprint Evolutionary genetics of genome merger and doubling in plants
    Jeff J Doyle
    Department of Plant Biology, Cornell University, Ithaca, New York 14850, USA
    Annu Rev Genet 42:443-61. 2008
  9. ncbi request reprint Evolution of genes and taxa: a primer
    J J Doyle
    L H Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA
    Plant Mol Biol 42:1-23. 2000
  10. ncbi request reprint Incongruence in the diploid B-genome species complex of Glycine (Leguminosae) revisited: histone H3-D alleles versus chloroplast haplotypes
    J J Doyle
    L H Bailey Hortorium, Cornell University, Ithaca, New York 14853, USA
    Mol Biol Evol 16:354-62. 1999

Detail Information

Publications33

  1. ncbi request reprint Genomes, multiple origins, and lineage recombination in the Glycine tomentella (Leguminosae) polyploid complex: histone H3-D gene sequences
    Jeff J Doyle
    L H Bailey Hortorium, Cornell University, Ithaca, New York 14853, USA
    Evolution 56:1388-402. 2002
    ..These features parallel the other component of the Glycine subgenus Glycine polyploid complex, G. tabacina, one of whose races shares a diploid genome with a G. tomentella polyploid race...
  2. pmc The rest of the iceberg. Legume diversity and evolution in a phylogenetic context
    Jeff J Doyle
    LH Bailey Hortorium, Department of Plant Biology, 462 Mann Library, Cornell University, Ithaca, New York 14853, USA
    Plant Physiol 131:900-10. 2003
  3. pmc Widespread genome duplications throughout the history of flowering plants
    Liying Cui
    Department of Biology, The Pennsylvania State University, University Park 16802, USA
    Genome Res 16:738-49. 2006
    ..We hypothesize that evidence of an ancient duplication observed in the Nuphar data may represent a genome duplication in the common ancestor of all or most extant angiosperms, except Amborella...
  4. doi request reprint Phylogenetic perspectives on the origins of nodulation
    Jeff J Doyle
    Department of Plant Biology, Cornell University, Ithaca, NY, USA
    Mol Plant Microbe Interact 24:1289-95. 2011
    ..Although polyploidy may have played a role in the origin of papilionoid legume nodules, it did not do so in other legumes, nor did the prerosid whole-genome triplication lead directly to the predisposition of nodulation...
  5. ncbi request reprint Phylogenetic utility of histone H3 intron sequences in the perennial relatives of soybean (Glycine: Leguminosae)
    J J Doyle
    L H Bailey Hortorium, Cornell University, Ithaca, New York 14853, USA
    Mol Phylogenet Evol 6:438-47. 1996
    ..The H3-D locus appears to be a useful source of phylogenetic characters for interspecific studies in Glycine, providing resolution among taxa whose relationships were unresolved in previous studies...
  6. doi request reprint Dating the origins of polyploidy events
    Jeff J Doyle
    Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
    New Phytol 186:73-85. 2010
    ..Estimating the date of origin of a polyploid is difficult, and in some circumstances impossible. Skepticism about dates of polyploid origins is clearly warranted...
  7. ncbi request reprint Trees within trees: genes and species, molecules and morphology
    J J Doyle
    L H Bailey Hortorium, 462 Mann Library Building, Cornell University, Ithaca, New York 14853, USA
    Syst Biol 46:537-53. 1997
    ..Nevertheless, expression patterns and orthology relationships of genes involved in the expression of phenotypes can in theory provide criteria for homology assessment of morphological characters...
  8. doi request reprint Evolutionary genetics of genome merger and doubling in plants
    Jeff J Doyle
    Department of Plant Biology, Cornell University, Ithaca, New York 14850, USA
    Annu Rev Genet 42:443-61. 2008
    ..Further studies are required for general patterns to be elucidated, involving different plant families, kinds of polyploidy, and polyploids of different ages...
  9. ncbi request reprint Evolution of genes and taxa: a primer
    J J Doyle
    L H Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA
    Plant Mol Biol 42:1-23. 2000
    ....
  10. ncbi request reprint Incongruence in the diploid B-genome species complex of Glycine (Leguminosae) revisited: histone H3-D alleles versus chloroplast haplotypes
    J J Doyle
    L H Bailey Hortorium, Cornell University, Ithaca, New York 14853, USA
    Mol Biol Evol 16:354-62. 1999
    ..Divergences among chloroplast DNA haplotypes involved in such transgressive patterns appear to be more recent than speciation events, suggesting hybridization rather than lineage sorting...
  11. doi request reprint A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species
    Daniel C Ilut
    Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA
    Am J Bot 99:383-96. 2012
    ....
  12. ncbi request reprint Testing the polyploid past of soybean using a low-copy nuclear gene--is Glycine (Fabaceae: Papilionoideae) an auto- or allopolyploid?
    Shannon C K Straub
    L H Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, NY, USA
    Mol Phylogenet Evol 39:580-4. 2006
  13. doi request reprint The reticulate history of Medicago (Fabaceae)
    Iván J Maureira-Butler
    Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
    Syst Biol 57:466-82. 2008
    ..A sensitivity analysis showed that our conclusions remain unchanged using a larger effective population size and/or longer generation time...
  14. doi request reprint Anatomical, biochemical, and photosynthetic responses to recent allopolyploidy in Glycine dolichocarpa (Fabaceae)
    Jeremy E Coate
    Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA
    Am J Bot 99:55-67. 2012
    ....
  15. pmc Quantifying whole transcriptome size, a prerequisite for understanding transcriptome evolution across species: an example from a plant allopolyploid
    Jeremy E Coate
    Department of Plant Biology, Cornell University, Ithaca, New York, USA
    Genome Biol Evol 2:534-46. 2010
    ....
  16. ncbi request reprint Evolutionary dynamics and preferential expression of homeologous 18S-5.8S-26S nuclear ribosomal genes in natural and artificial glycine allopolyploids
    Simon Joly
    L H Bailey Hortorium, Cornell University, Ithaca, New York, USA
    Mol Biol Evol 21:1409-21. 2004
    ..The establishment of preferential expression in Glycine allopolyploids appears to be either stochastic within lineages or genotype specific...
  17. pmc Multiple origins and nrDNA internal transcribed spacer homeologue evolution in the Glycine tomentella (Leguminosae) allopolyploid complex
    Jason T Rauscher
    L H Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA
    Genetics 166:987-98. 2004
    ..This evidence for diverse patterns of nrDNA molecular evolution and multiple origins of polyploid races will provide a useful system for future studies of natural variation in patterns of nrDNA expression...
  18. ncbi request reprint Internal transcribed spacer repeat-specific primers and the analysis of hybridization in the Glycine tomentella (Leguminosae) polyploid complex
    Jason T Rauscher
    L H Bailey Hortorium, 228 Plant Science, Cornell University, Ithaca, NY 14853, USA
    Mol Ecol 11:2691-702. 2002
    ..Other strategies, such as the use of exclusion primers, may detect rare parental repeat types in hybrids when previous hypotheses regarding the second parental species are lacking...
  19. doi request reprint Conservation genetics of Amorpha georgiana (Fabaceae), an endangered legume of the Southeastern United States
    Shannon C K Straub
    L H Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
    Mol Ecol 18:4349-65. 2009
    ....
  20. pmc Comparative evolution of photosynthetic genes in response to polyploid and nonpolyploid duplication
    Jeremy E Coate
    Department of Plant Biology, Cornell University, Ithaca, New York 14853 4301, USA
    Plant Physiol 155:2081-95. 2011
    ....
  21. doi request reprint Complex patterns of autopolyploid evolution in alfalfa and allies (Medicago sativa; Leguminosae)
    Tee Havananda
    Cornell University, Ithaca, New York 14853, USA
    Am J Bot 98:1633-46. 2011
    ....
  22. doi request reprint Isolation and characterization of thirteen polymorphic microsatellite loci in the A-genome perennial group of the legume genus Glycine
    Michael J Bronski
    L H Bailey Hortorium, Department of Plant Biology, Mann Library, Cornell University, Ithaca, NY 14853, USA Evolutionary Genetics Core Facility, Department of Ecology and Evolutionary Biology, Corson Hall, Cornell University, Ithaca, NY 14853, USA Center for Plant Biodiversity Research, CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
    Mol Ecol Resour 9:1547-50. 2009
    ..These markers will be useful in studying genetic variation, population structure, gene flow, and polyploidy within the A-genome group...
  23. ncbi request reprint Placing paleopolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families
    B E Pfeil
    Department of Plant Biology, 228 Plant Sciences Building, Cornell University, Ithaca, Ithaca, NY 14853, USA
    Syst Biol 54:441-54. 2005
    ..Our results suggest that G. max and M. truncatula, along with approximately 7000 other legume species from the same clade, share an ancient round of gene duplications, either due to polyploidy or to some other process...
  24. doi request reprint The wild side of a major crop: soybean's perennial cousins from Down Under
    Sue Sherman-Broyles
    Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA
    Am J Bot 101:1651-65. 2014
    ..Here we review what has been learned over the past 30 years and outline ongoing work on photosynthesis, nitrogen fixation, and floral biology, much of it drawing on new technologies and resources. ..
  25. ncbi request reprint Phylogenetic utility of the nuclear gene malate synthase in the palm family (Arecaceae)
    C E Lewis
    L. H. Bailey Hortorium, Cornell University, Ithaca, New York 14853, USA
    Mol Phylogenet Evol 19:409-20. 2001
    ..We found no evidence of multiple copies of the malate synthase gene in palm genomes...
  26. pmc HecA, a member of a class of adhesins produced by diverse pathogenic bacteria, contributes to the attachment, aggregation, epidermal cell killing, and virulence phenotypes of Erwinia chrysanthemi EC16 on Nicotiana clevelandii seedlings
    Clemencia M Rojas
    Department of Plant Pathology and L H Bailey Hortorium, Cornell University, Ithaca, NY 14853
    Proc Natl Acad Sci U S A 99:13142-7. 2002
    ..Our data suggest that filamentous hemagglutinin-like adhesins are broadly important virulence factors in both plant and animal pathogens...
  27. ncbi request reprint Enhanced rhizobial symbiotic capacity in an allopolyploid species of Glycine (Leguminosae)
    Adrian F Powell
    Cornell University, Section of Plant Biology, 412 Mann Library, Cornell University, Ithaca, New York 14853 USA
    Am J Bot 103:1771-1782. 2016
    ..Little is known, however, about the effects of allopolyploidy, which combines hybridity and genome doubling, on symbiotic interactions with rhizobial bacteria...
  28. doi request reprint Molecular phylogenetics of Amorpha (Fabaceae): an evaluation of monophyly, species relationships, and polyploid origins
    Shannon C K Straub
    L H Bailey Hortorium and Department of Plant Biology, Cornell University, 412 Mann Library, Ithaca, NY 14853, USA Electronic address
    Mol Phylogenet Evol 76:49-66. 2014
    ..fruticosa species complex. Putative progenitors for two other suspected allotetraploid species, A. confusa and A. crenulata, were identified as A. fruticosa and A. herbacea. ..
  29. doi request reprint Characterization of 12 polymorphic microsatellite markers for Georgia false indigo (Amorpha georgiana Wilbur var. georgiana), an endangered species, and their utility in other dwarf Amorpha L. species
    Shannon C K Straub
    L H Bailey Hortorium, Department of Plant Biology, Cornell University, 412 Mann Library, Ithaca, NY 14853, USA, Evolutionary Genetics Core Facility, Department of Ecology and Evolutionary Biology, Cornell University, E344 Corson Hall, Ithaca, NY 14853, USA
    Mol Ecol Resour 9:225-8. 2009
    ..confusa and Amorpha herbacea. The results also suggested that A. georgiana var. confusa is tetraploid rather than diploid...
  30. pmc Divergent evolutionary fates of major photosynthetic gene networks following gene and whole genome duplications
    Jeremy E Coate
    Department of Plant Biology, Cornell University, Ithaca, NY, USA
    Plant Signal Behav 6:594-7. 2011
    ....
  31. ncbi request reprint Paleopolyploidy and gene duplication in soybean and other legumes
    Randy C Shoemaker
    USDA ARS and Iowa State University, G401 Agronomy Hall, Ames, Iowa 50011, USA
    Curr Opin Plant Biol 9:104-9. 2006
    ..Recent progress has been made in understanding patterns of gene and genome duplication in the legume family, specifically in soybean...
  32. ncbi request reprint Mining EST databases to resolve evolutionary events in major crop species
    Jessica A Schlueter
    Interdepartmental Genetics, Department of Genetics Developmental and Cellular Biology, Iowa State University, Ames, IA 50011, USA
    Genome 47:868-76. 2004
    ..This analysis showed that some duplicates seemed to retain expression patterns between pairs, whereas others showed uncorrelated expression...
  33. pmc Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)
    Jim Leebens-Mack
    Department of Biology, Institute of Molecular Evolutionary Genetics, and Huck Institutes of Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
    OMICS 10:231-7. 2006
    ..Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors...