Publications

Lab members in bold

2017

  • Smith, S. A. and J. W. Brown. accepted. Constructing a comprehensive seed plant phylogeny.
    American Journal of Botany
  • Pease J.B., J. W. Brown, J. F. Walker, C. E. Hinchliff, S. A. Smith. in press. Quartet Sampling distinguishes lack of support from conflicting support in the plant tree of life. American Journal of Botany
  • Fleischmann, A., J. Schlauer, T. Givnish, and S. A. Smith. In press. Evolution of carnivory in angiosperms. Chapter 3. in forthcoming book on Carnivory in angiosperms.
  • Lopez-Nieves, S., Y. Yang, T. Feng, S. A. Smith, S. F. Brockington, and H. A. Maeda. In press. Relaxation of Tyrosine Pathway Regulation Underlies the Evolution of Betalain Pigmentation in Caryophyllales. New Phytologist
  • Brown, J. W., N. Wang, and S. A. Smith. 2017. The development of scientific consensus: analyzing conflict and concordance among Avian phylogenies. Molecular Phylogenetics and Evolution https://doi.org/10.1101/123034
  • Brown, J. W. and S. A. Smith. 2017. The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates. Systematic Biology https://doi.org/10.1101/113720
  • Walker, J., Y. Yang, M. Moore, S. F. Brockington, and S. A. Smith. 2017. Conflict among carnivores: whole transcriptomes unable to resolve the carnivorous clade of Caryophyllales. American Journal of Botany. https://doi.org/10.1101/115741
  • Smith, S. A., J. W. Brown, Y. Yang, R. Bruenn, C. P. Drummond, S. F. Brockington, J. F. Walker, N. Last, N. A. Douglas, M. J. Moore. 2017.Disparity, diversity, and duplications in the Caryophyllales. New Phytologist. link
  • Yang, Y., M. J. Moore, S. F. Brockington, J. Mikenas, and S. A. Smith. 2017. Improved transcriptome sampling pinpoints widespread paleopolyploidy events in Caryophyllales New Phytologist. https://doi.org/10.1101/143529
  • Brown, J., J. Walker, and S. A. Smith. 2017. phyx: Phylogenetic tools for Unix. Bioinfor- matics. https://doi.org/10.1093/bioinformatics/btx063
  • Yang, Y., M. J. Moore, S. F. Brockington, A. Timoneda-Monfort, T. Feng, H. E. Marx, Joseph F. Walker, and S. A. Smith. 2017. An efficient field and laboratory workflow for plant phylotranscriptomic projects. Applications in Plant Sciences. https://doi.org/10.1101/ 079582

2016

  • Smith, S.A.* and J. Pease. 2016. Heterogeneous molecular processes among the causes of how sequence similarity scores can fail to recapitulate phylogeny Briefings in Bioinformatics link
  • O’Meara, B. C., S. D. Smith, W. S. Armbruster, L. D. Harder, C. R. Hardy, L. C. Hileman, Larry Hufford, Amy Litt, Susana Magallón, S. A. Smith, P. F. Stevens, C. B. Fenster, P. K. Diggle. Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity.Proc Roy Soc Blink

2015

  • C. E. Hinchliff*, S. A. Smith*+, J. F. Allman, J. G. Burleigh, R. Chaudhary, L. M. Coghill, K. A. Crandall, J. Deng, B. T. Drew, R. Gazis, K. Gude, D. S. Hibbett, L. A. Katz, H. D. Laughinghouse IV, E. J. McTavish, P. E. Midford, C. L. Owen, R. H. Ree, J. A. Rees, D. E. Soltis, T. Williams, and K. A. Cranston+. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. * Co-first authors, +corresponding authors. PNAS link
  • Smith, S. A., M. Moore, J. W. Brown, and Y. Yang (2015). Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. BMC Evolutionary Biology link
  • Brockington S.F.*, Y. Yang*, F. Gandia-Herrero, S. Covshoff, J.M. Hibberd, R.F. Sage, G.K.-S. Wong, M.J. Moore and S.A. Smith. Lineage specific gene radiations underly the evolution of novel betalain pigmentation in Caryophyllales. *Co-first author. New Phytologist. link.
  • Yang, Y. M.J. Moore, S.F. Brockington, D.E. Soltis, G.K.-S. Wong, E.J. Carpenter, Y. Zhang, L. Chen, Z.-X. Yan, Y.-L. Xie, R.F. Sage, S. Covshoff, J.M. Hibberd, M.N. Nelson, and S.A. Smith. Dissecting molecular evolution in the highly diverse plant clade Caryophyllales using transcriptome sequencing. Molecular Biology and Evolution. link.
  • McTavish, E. J., C. E. Hinchliff, J. F. Allman, J. W. Brown, K. A. Cranston, M. T. Holder, J. A. Rees, and S. A. Smith. Phylesystem: a git-based data store for community curated phylogenetic estimates. Bioinformatics Accepted

2014

  • Smith, S. A. and A. Stamatakis. 2014. Inferring and Postprocessing Huge Phylogenies. in Biological Knowledge Discovery Handbook: Preprocessing, Mining and Post-processing of Biological Data. Wiley, NY.
  • Yang, Y. and S. A. Smith. 2014. Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics MBE. link
  • Hinchliff, C. and S. A. Smith. 2014. Some Limitations of Public Sequence Data for Phylogenetic Inference (in Plants) Plos ONE. link
  • Izquierdo-Carrasco, F., J. Cazes, S. A. Smith, and A. Stamatakis. 2014. PUmPER: phylogenies updated perpetually. Bioinformatics. doi: 10.1093/bioinformatics/btu053 link
  • Cornwell, W. K., M. Westoby, D. S. Falster, R. G. FitzJohn, B. C. O’Meara, M. W. Pennell, D. J. McGlinn, J. M. Eastman, A. T. Moles, P. B. Reich, D. C. Tank, I. J. Wright, Lonnie Aarssen, J. M. Beaulieu, R. M. Kooyman, M. R. Leishman, E. T. Miller, U. Niinemets, J. Oleksyn, A. Ordonez, D. L. Royer, S. A. Smith, P. F. Stevens, L. Warman, P. Wilf, and A. E. Zanne. 2014. Functional distinctiveness of major plant lineages. Journal of Ecology. 102: 345-356 link
  • Drew, B. T., B. R. Ruhfel, S. A. Smith, M. J. Moore, B. G. Briggs, M. A. Gitzendanner, P. S. Soltis, and D. E. Soltis. 2014. Another look at the root of angiosperms reveals a familiar tale. Systematic Biology. doi: 10.1093/sysbio/syt108 link

2013

  • S. A. Smith, J. Brown, and C. Hinchliff. 2013. Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs. PLoS Computational Biology. link
  • Yang, Y. and S. A. Smith. 2013. Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. BMC Genomics. link
  • Rabosky, D. L., F. Santini, J. Eastman, S. A. Smith, B. Sidlauskas, J. Chang, and M. E. Alfaro. 2013 Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nat. Commun. 4:1958, doi: 10.1038/ncomms2958. link
  • Ryan, J., P. Pang, C. Schitzler, A. Nguyen, R. Moreland, D. Simmons, B. Koch, W. Francis, P. Havlak, NISC Comparative Sequence Program, S. A. Smith , N. Putnam, S. Haddock, C. Dunn, T. Wolfsberg, J. Mullikin, M. Martindale, A. Baxevannis. 2013. The genome of the Ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342 link
  • Zanne, A., D. C. Tank, W. K. Cornwell, J. M. Eastman, S. A. Smith, R. G. FitzJohn, D. J. McGlinn, B. C. OMeara, A. T. Moles, P. B. Reich, D. L. Royer, D. E. Soltis, P. F. Stevens, Mark Westoby, I. J. Wright, Lonnie Aarssen, R. I. Bertin, Andre Calaminus, R. Govaerts, F. Hemmings, M.
    R. Leishman, Jacek Oleksyn, P. S. Soltis, N. G. Swenson, L. Warman, J. M. Beaulieu. 2013. Three keys to the radiation of angiosperm into freezing environments. Nature. doi:10.1038/nature12872 link

2012

  • Smith, S. A. and B. O’Meara. 2012. treePL: Divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics. doi: 10.1093/bioinformatics/bts492. link
  • Stamatakis, A., A. Aberer, C. Goll, S. A. Smith, S. Berger, and F. Izquierdo-Carrasco. 2012. Raxml-light: a tool for computing terabyte phylogenies. Bioinformatics, 28(15):2064–2066. doi: 10.1093/bioinformatics/bts309. link
  • Grass Phylogeny Working Group II. 2012. New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins. New Phytologist. 193: 304-312.

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