Stephen A Smith

Summary

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 An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants
    Stephen A Smith
    National Evolutionary Synthesis Center, Durham, NC 27705, USA
    Proc Natl Acad Sci U S A 107:5897-902. 2010
  3. pmc Life history influences rates of climatic niche evolution in flowering plants
    Stephen A Smith
    National Evolutionary Synthesis Center, 2024 W Main Street A200, Durham, NC 27705, USA
    Proc Biol Sci 276:4345-52. 2009
  4. 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
  5. doi request reprint The origins of C4 grasslands: integrating evolutionary and ecosystem science
    Erika J Edwards
    Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
    Science 328:587-91. 2010
  6. 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
  7. 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
  8. doi request reprint Understanding angiosperm diversification using small and large phylogenetic trees
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA
    Am J Bot 98:404-14. 2011
  9. doi request reprint Resolving the evolutionary relationships of molluscs with phylogenomic tools
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA
    Nature 480:364-7. 2011
  10. 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

Detail Information

Publications16

  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 An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants
    Stephen A Smith
    National Evolutionary Synthesis Center, Durham, NC 27705, USA
    Proc Natl Acad Sci U S A 107:5897-902. 2010
    ..g., the early radiation of herbaceous clades within angiosperms) may still be biasing our inferences...
  3. pmc Life history influences rates of climatic niche evolution in flowering plants
    Stephen A Smith
    National Evolutionary Synthesis Center, 2024 W Main Street A200, Durham, NC 27705, USA
    Proc Biol Sci 276:4345-52. 2009
    ..The consistent differences in the rate of climatic niche evolution also emphasize the need to incorporate models of phenotypic evolution that allow for rate heterogeneity when examining large datasets...
  4. 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...
  5. doi request reprint The origins of C4 grasslands: integrating evolutionary and ecosystem science
    Erika J Edwards
    Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
    Science 328:587-91. 2010
    ....
  6. 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...
  7. 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...
  8. doi request reprint Understanding angiosperm diversification using small and large phylogenetic trees
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA
    Am J Bot 98:404-14. 2011
    ..Mega-phylogenetic studies of diversification hold great promise for revealing new patterns, but we will need to focus more attention on properly specifying null expectation...
  9. doi request reprint Resolving the evolutionary relationships of molluscs with phylogenomic tools
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA
    Nature 480:364-7. 2011
    ..This well-resolved tree will constitute a framework for further studies of mollusc evolution, development and anatomy...
  10. 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
    ....
  11. pmc Phylogenetic analyses reveal the shady history of C4 grasses
    Erika J Edwards
    Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
    Proc Natl Acad Sci U S A 107:2532-7. 2010
    ..Furthermore, we argue that the evolution of cold tolerance in certain C(3) lineages is an overlooked innovation that has profoundly influenced the patterning of grassland communities across the globe...
  12. 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...
  13. doi request reprint treePL: divergence time estimation using penalized likelihood for large phylogenies
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Bioinformatics 28:2689-90. 2012
    ..We compare this approach with existing software including r8s, PATHd8 and BEAST...
  14. doi request reprint Phyutility: a phyloinformatics tool for trees, alignments and molecular data
    Stephen A Smith
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
    Bioinformatics 24:715-6. 2008
    ..Its simple command-line interface allows for easy integration into scripted analyses, and is able to handle large datasets with an integrated database...
  15. 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...
  16. pmc Optimizing de novo assembly of short-read RNA-seq data for phylogenomics
    Ya Yang
    Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University Ave, Ann Arbor, MI 48109 1048, USA
    BMC Genomics 14:328. 2013
    ..By doing so we evaluate strategies for optimizing total gene coverage and minimizing assembly chimeras and redundancy...