Stephen A. Smith

Publications

2011

  • Izquierdo-Carrasco F, S. A. Smith, A. Stamatakis. 2011. Algorithms, Data Structures, and Numerics for Likelihood-based Phylogenetic Inference of Huge Trees. BMC Bioinformatics. 12(1):470. link
  • Smith, S. A., N. G. Wilson, F. E. Goetz, C. Feehery, S. C. S. Andrade, G. W. Rouse, G. Giribet, C. W. Dunn. 2011. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature pdf
  • Soltis, D. E., S. A. Smith, N. Cellinese, et al. 2011. . American J. of Botany.98:704.
  • Smith, S. A., J. Beaulieu, A. Stamatakis, and M. J. Donoghue. 2011. Understanding angiosperm diversification using large and small phylogenies. American J. of Botany. 98: 404-414. pdf
  • S. Siebert, M. Robinson, S. Tintori, F. Goetz, R. Helm, S. A. Smith, N. Shaner, S. Haddock, C. Dunn. 2011. Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows. PLoS ONE link

2010

  • Smith, S. A. and M. J. Donoghue. 2010. Combining Historical Biogeography with Niche Modeling in the Caprifolium Clade of Lonicera (Caprifoliaceae, Dipsacales). Syst. Biol. 590: 322-341. pdf
  • E. E. Goldberg,1 J. R. Kohn, R. Lande, K. A. Robertson, S. A. Smith, and B. Igic. 2010. Species Selection Maintains Self-Incompatibility. Science. 328: 587-591. pdf
  • Edwards, E.J., C. P. Osborne, C. A. E. Strömberg, S. A. Smith, and C4 Grasses Consortium. 2010. The origins of C4 grasslands: integrating evolutionary and ecosystem science. Science. 328: 587-591. pdf
  • Smith, S. A, J. M. Beaulieu and M. J. Donoghue. 2010. An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants. PNAS. 107: 5897-5902. pdf (F1000)
  • E. Edwards and S. A. Smith. 2010. Phylogenetic analyses reveal the shady history of C4 grasses. PNAS. 107: 2532-2538. pdf

2009

  • Smith, S. A. and J. Beaulieu 2009. Life history influences rates of climatic niche evolution in flowering plants. Proc Roy Soc B. 276: 4345-4352. pdf
  • Smith, S. A. and B. C. O’Meara 2009. Morphogenera, monophyly, and macroevolution. PNAS. 106: E97-E98. pdf
  • Smith, S. A., J. Beaulieu, and M. J. Donoghue. 2009.  Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evol Biol. . 9: 37.link (listed as “Highly accessed”) (F1000)
  • Smith, S. A. 2009. Taking into account phylogenetic and divergence-time uncertainty in a parametric biogeographic analysis of the Northern Hemisphere plant clade Caprifolieae. Journal of Biogeography. pdf
  • Cellinese, N., S. A. Smith, E. J. Edwards, S. T. Kim, R. C. Haberle, M. Avramakis and M. J. Donoghue. 2009. Historical biogeography of the endemic Campanulaceae of Crete. Journal of Biogeography. 36: 1253-1269. link
  • Evans, M. E., S. A. Smith, R. E. Flynn and M. J. Donoghue. 2009. “Climate, niche evolution, and diversification of the “bird-cage” evening primroses (Oenothera, sections Anogra and Kleinia). American Naturalist. 173: 225-240. pdf

2008

  • Smith, S. A. and M. J. Donoghue. 2008. Rates of Molecular Evolution are Linked to Life History in Flowering Plants. Science. 322: 86-89.pdf (F1000)
  • Smith, S. A. and C. Dunn. 2008. Phyutility: a phyloinformatics utility for trees, alignments, and molecular data. Bioinformatics. 24: 715-716. pdf
  • Ree, R. H. and S. A. Smith. 2008. Maximum-likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis. Systematic Biology. 57: 4-14. pdf
  • Smith, S. A. et al. 2008. Bioactive endophytes warrant intensified exploration and conservation. PLoS ONE. 3: e3052. pdf
  • Dunn, C. W., A. Hejnol, D. Q. Matus, K. Pang, W. E. Browne, S. A. Smith, et al. 2008. Broad taxon sampling improves resolution of the Animal Tree of Life in phylogenomic analyses. Nature. 452: 745-749. pdf

before 2008

  • Roulston, T. H., S. A. Smith and A. L. Brewster. 2007. Comparison of Pan Trap and Intensive Net Sampling Techniques for Documenting a Bee (Hymenoptera: Apiformes) Fauna. Journal Kansas Entomological Society.
  • Moore, B. R., S. A. Smith, M. J. Donoghue. 2006. Increasing Data Transparency and Estimating Phylogenetic Uncertainty in Supertrees: Approaches Using Nonparametric Bootstrapping. Systematic Biology 55:4. 662 – 676. pdf
  • Donoghue, M.J. and S. A. Smith. 2004. Patterns in the Assembly of Termperate Forests Around the Northern Hemisphere. Philosophical Transactions of the Royal Society of London B. 359(1450):1633-44 pdf