Michael J Donoghue

Summary

Affiliation: Yale University
Country: USA

Publications

  1. pmc Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches
    Stephen A Smith
    National Evolutionary Synthesis Center, 2024 W Main St A200, Durham, NC 27705, USA
    BMC Evol Biol 9:37. 2009
  2. pmc Colloquium paper: a phylogenetic perspective on the distribution of plant diversity
    Michael J Donoghue
    Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, PO Box 208106, New Haven, CT 06520 8106, USA
    Proc Natl Acad Sci U S A 105:11549-55. 2008
  3. ncbi request reprint Combining historical biogeography with niche modeling in the Caprifolium clade of Lonicera (Caprifoliaceae, Dipsacales)
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Syst Biol 59:322-41. 2010
  4. doi request reprint Climate, niche evolution, and diversification of the "bird-cage" evening primroses (Oenothera, sections Anogra and Kleinia)
    Margaret E K Evans
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
    Am Nat 173:225-40. 2009
  5. doi request reprint Extreme environments select for reproductive assurance: evidence from evening primroses (Oenothera)
    Margaret E K Evans
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
    New Phytol 191:555-63. 2011
  6. doi request reprint Rates of molecular evolution are linked to life history in flowering plants
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, 21 Sachem Street, Post Office Box 208105, Yale University, New Haven, CT 06520 8105, USA
    Science 322:86-9. 2008
  7. ncbi request reprint Phylodiversity-dependent seedling mortality, size structure, and disease in a Bornean rain forest
    Campbell O Webb
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
    Ecology 87:S123-31. 2006
  8. pmc Explaining the distribution of breeding and dispersal syndromes in conifers
    Andrew B Leslie
    School of Forestry and Environmental Studies, Yale University, 195 Prospect Street, New Haven, CT 06511, USA, National Institute for Mathematical and Biological Synthesis, University of Tennessee, 1122 Volunteer Boulevard, Suite 106, Knoxville, TN 37996, USA, Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT 06520, USA
    Proc Biol Sci 280:20131812. 2013
  9. pmc Hemisphere-scale differences in conifer evolutionary dynamics
    Andrew B Leslie
    School of Forestry and Environmental Studies, Yale University, New Haven, CT 06511, USA
    Proc Natl Acad Sci U S A 109:16217-21. 2012
  10. doi request reprint Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms
    Jeremy M Beaulieu
    Department of Ecology and Evolutionary Biology, Yale University, P O Box 208106, New Haven, CT 10620 8106, USA and Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996 1610, USA
    Syst Biol 62:725-37. 2013

Detail Information

Publications33

  1. pmc Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches
    Stephen A Smith
    National Evolutionary Synthesis Center, 2024 W Main St A200, Durham, NC 27705, USA
    BMC Evol Biol 9:37. 2009
    ..Although these methods are continually being developed, they have yet to be made fully accessible to comparative biologists making extremely large trees rare...
  2. pmc Colloquium paper: a phylogenetic perspective on the distribution of plant diversity
    Michael J Donoghue
    Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, PO Box 208106, New Haven, CT 06520 8106, USA
    Proc Natl Acad Sci U S A 105:11549-55. 2008
    ..These observations highlight the role of phylogenetic knowledge and historical biogeography in explanations of global biodiversity patterns. They also have implications for the future of biodiversity...
  3. ncbi request reprint Combining historical biogeography with niche modeling in the Caprifolium clade of Lonicera (Caprifoliaceae, Dipsacales)
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Syst Biol 59:322-41. 2010
    ..These results suggest a possible model for the origin of the Madrean-Tethyan disjunction pattern...
  4. doi request reprint Climate, niche evolution, and diversification of the "bird-cage" evening primroses (Oenothera, sections Anogra and Kleinia)
    Margaret E K Evans
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
    Am Nat 173:225-40. 2009
    ..Our data are also consistent with Axelrod's hypothesis that the spread of arid conditions in western North America stimulated diversification of arid-adapted lineages...
  5. doi request reprint Extreme environments select for reproductive assurance: evidence from evening primroses (Oenothera)
    Margaret E K Evans
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
    New Phytol 191:555-63. 2011
    ..We discuss possible explanations for this pattern and possible implications with respect to anthropogenic climate change...
  6. doi request reprint Rates of molecular evolution are linked to life history in flowering plants
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, 21 Sachem Street, Post Office Box 208105, Yale University, New Haven, CT 06520 8105, USA
    Science 322:86-9. 2008
    ....
  7. ncbi request reprint Phylodiversity-dependent seedling mortality, size structure, and disease in a Bornean rain forest
    Campbell O Webb
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
    Ecology 87:S123-31. 2006
    ....
  8. pmc Explaining the distribution of breeding and dispersal syndromes in conifers
    Andrew B Leslie
    School of Forestry and Environmental Studies, Yale University, 195 Prospect Street, New Haven, CT 06511, USA, National Institute for Mathematical and Biological Synthesis, University of Tennessee, 1122 Volunteer Boulevard, Suite 106, Knoxville, TN 37996, USA, Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT 06520, USA
    Proc Biol Sci 280:20131812. 2013
    ..In general, we argue that such persistence explanations should be considered alongside 'key innovation' hypotheses in explaining the phylogenetic distribution of traits. ..
  9. pmc Hemisphere-scale differences in conifer evolutionary dynamics
    Andrew B Leslie
    School of Forestry and Environmental Studies, Yale University, New Haven, CT 06511, USA
    Proc Natl Acad Sci U S A 109:16217-21. 2012
    ....
  10. doi request reprint Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms
    Jeremy M Beaulieu
    Department of Ecology and Evolutionary Biology, Yale University, P O Box 208106, New Haven, CT 10620 8106, USA and Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996 1610, USA
    Syst Biol 62:725-37. 2013
    ....
  11. ncbi request reprint Correlates of diversification in the plant clade Dipsacales: geographic movement and evolutionary innovations
    Brian R Moore
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
    Am Nat 170:S28-55. 2007
    ....
  12. ncbi request reprint Fruit evolution and diversification in campanulid angiosperms
    Jeremy M Beaulieu
    Department of Ecology and Evolutionary Biology, Yale University, P O Box 208106, New Haven, Connecticut, 10620
    Evolution 67:3132-44. 2013
    ....
  13. pmc A Southern Hemisphere origin for campanulid angiosperms, with traces of the break-up of Gondwana
    Jeremy M Beaulieu
    Department of Ecology and Evolutionary Biology, Yale University, P O Box 208106, New Haven, CT 06520 8106, USA
    BMC Evol Biol 13:80. 2013
    ....
  14. pmc Diversification of CYCLOIDEA-like genes in Dipsacaceae (Dipsacales): implications for the evolution of capitulum inflorescences
    Sara E Carlson
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520 8106, USA
    BMC Evol Biol 11:325. 2011
    ....
  15. pmc Bioactive endophytes warrant intensified exploration and conservation
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
    PLoS ONE 3:e3052. 2008
    ..Here we provide direct evidence from bioassays of endophytes isolated from tropical plants and bioinformatic analyses that novel biology will indeed yield novel chemistry of potential value...
  16. ncbi request reprint Viburnum phylogeny: evidence from the duplicated nuclear gene GBSSI
    Richard C Winkworth
    Department of Ecology and Evolutionary Biology, Yale University, P O Box 208105, New Haven, CT 06520 8105, USA
    Mol Phylogenet Evol 33:109-26. 2004
    ..The presence of additional copies appears to be correlated with polyploidy in these clades. Placement of the homoeologues in our gene trees suggests the possibility of a hybrid origin for these polyploids...
  17. doi request reprint Expanded phylogenetic and dating analyses of the apples and their relatives (Pyreae, Rosaceae)
    Eugenia Y Y Lo
    Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06520, USA
    Mol Phylogenet Evol 63:230-43. 2012
    ..At least five major, early Old World-New World disjunctions were detected and these vicariance events are generally most consistent with movement through the Beringia...
  18. pmc Patterns in the assembly of temperate forests around the Northern Hemisphere
    Michael J Donoghue
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Philos Trans R Soc Lond B Biol Sci 359:1633-44. 2004
    ..Fortunately, many more plant groups show relevant disjunction patterns and could soon be added to such analyses...
  19. pmc Barcoding success as a function of phylogenetic relatedness in Viburnum, a clade of woody angiosperms
    Wendy L Clement
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    BMC Evol Biol 12:73. 2012
    ..For 112 Viburnum species, we evaluated rbcL + matK, as well as the chloroplast regions rpl32-trnL, trnH-psbA, trnK, and the nuclear ribosomal internal transcribed spacer region (nrITS)...
  20. ncbi request reprint Increasing data transparency and estimating phylogenetic uncertainty in supertrees: Approaches using nonparametric bootstrapping
    Brian R Moore
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
    Syst Biol 55:662-76. 2006
    ..These methods have been implemented in the freely available program, tREeBOOT...
  21. doi request reprint Mitochondrial sequence data and Dipsacales phylogeny: mixed models, partitioned Bayesian analyses, and model selection
    Richard C Winkworth
    Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT 06520, USA
    Mol Phylogenet Evol 46:830-43. 2008
    ..We suggest incongruent signal has contributed to our inability to confidently resolve these problem areas...
  22. pmc Allopolyploid speciation in Persicaria (Polygonaceae): insights from a low-copy nuclear region
    Sang Tae Kim
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 8106, USA
    Proc Natl Acad Sci U S A 105:12370-5. 2008
    ..Hybridization events fostered by human introductions may be fueling the production of new species that have the potential to become aggressive weeds...
  23. doi request reprint Pereskia and the origin of the cactus life-form
    Erika J Edwards
    Department of Ecology and Evolutionary Biology and the Peabody Museum of Natural History, Yale University, P O Box 208105, New Haven, Connecticut 06511, USA
    Am Nat 167:777-93. 2006
    ..We interpret these ecological traits as potentially important drivers of evolutionary innovation in the cacti...
  24. ncbi request reprint Incongruence between cpDNA and nrITS trees indicates extensive hybridization within Eupersicaria (Polygonaceae)
    Sang Tae Kim
    Department of Ecology and Evolutionary Biology, Yale University, P O Box 208106, New Haven, Connecticut 06520 8106 USA
    Am J Bot 95:1122-35. 2008
    ..Repeated allotetraploidy (as distinct from radiation at the tetraploid level) now appears to be the key mechanism governing the diversification of this taxonomically challenging group...
  25. pmc Phylogenetic analysis of the "ECE" (CYC/TB1) clade reveals duplications predating the core eudicots
    Dianella G Howarth
    Department of Ecology and Evolutionary Biology, Yale University, P O Box 208106, New Haven, CT 06520 8106, USA
    Proc Natl Acad Sci U S A 103:9101-6. 2006
    ..DipsCYC3B is expressed in flower and petal primordia, possibly most strongly in the ventral petal...
  26. pmc The root of the angiosperms revisited
    Michael J Zanis
    School of Biological Sciences, Washington State University, Pullman, WA 99164 4236, USA
    Proc Natl Acad Sci U S A 99:6848-53. 2002
    ..Although we cannot conclusively choose between Amborella vs. Amborella + Nymphaeales as sister to all other angiosperms, most analyses favor the former rooting...
  27. ncbi request reprint Recreating a functional ancestral archosaur visual pigment
    Belinda S W Chang
    Laboratory of Molecular Biology and Biochemistry, The Rockefeller University, New York, NY 10021, USA
    Mol Biol Evol 19:1483-9. 2002
    ..Our results show that ancestral genes from ancient organisms can be reconstructed de novo and tested for function using a combination of phylogenetic and biochemical methods...
  28. ncbi request reprint The relevance of phylogeny to studies of global change
    Erika J Edwards
    Geography Department and the Institute for Computational Earth System Science, University of California, Santa Barbara, CA 93106, USA
    Trends Ecol Evol 22:243-9. 2007
    ..We outline how phylogenetics can guide better taxon sampling of key physiological traits, and discuss how the emerging field of phyloinformatics presents a promising new framework for scaling from organism physiology to global processes...
  29. ncbi request reprint Adaptive evolution in the photosensory domain of phytochrome A in early angiosperms
    Sarah Mathews
    Division of Biological Sciences, University of Missouri, USA
    Mol Biol Evol 20:1087-97. 2003
    ..The episode of selection occurred very early in the history of flowering plants, suggesting that innovation in phyA may have given the first angiosperms some adaptive advantage...
  30. ncbi request reprint Explosive radiation of Malpighiales supports a mid-cretaceous origin of modern tropical rain forests
    Charles C Davis
    Department of Ecology and Evolutionary Biology, University of Michigan Herbarium, Ann Arbor, Michigan 48108 2287, USA
    Am Nat 165:E36-65. 2005
    ..This case illustrates that dated phylogenies can provide an important new source of evidence bearing on the timing of major environmental changes, which may be especially useful when fossil evidence is limited or controversial...
  31. ncbi request reprint The small-world dynamics of tree networks and data mining in phyloinformatics
    William H Piel
    Institute of Evolutionary and Ecological Sciences, Kaiserstraat 63, Leiden University 2311 GP Leiden, The Netherlands
    Bioinformatics 19:1162-8. 2003
    ..Here we apply similar analyses to networks of phylogenetic trees in order to understand how synthetic information can emerge from a database of phylogenies...
  32. ncbi request reprint A likelihood framework for inferring the evolution of geographic range on phylogenetic trees
    Richard H Ree
    Department of Botany, Field Museum of Natural History, Chicago, Illinois 60605, USA
    Evolution 59:2299-311. 2005
    ....
  33. pmc Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae
    Charles C Davis
    Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 99:6833-7. 2002
    ..This Laurasian migration route may explain many other extant lineages that exhibit western Gondwanan distributions...