The research in the lab covers a wide range of topics from genomics and transcriptomics to large dataset and large phylogenetic analyses. Primarily, we are broadly interested in the evolution of innovation and complexity across plants and how these events intersect with heterogeneity in molecular and phenotypic evolution. A brief description for some of the major research projects is provided below.

Plant evolution

Although people in the lab work on a wide range of organisms, we generally always come back to plants at some point. Some of the subjects we are always interest in genomics, biogeography and the evolution of particular ecological niches, rates of evolution, and the evolution of particular adaptations and innovations.

Some relevant publications

  • Allen, J., C. C Germain-Aubrey, N. Barve, K. M. Neubig, L. C. Majure, S. W. Laffan, B. D. Mishler, H. L. Owens, S. A Smith, W. M. Whitten, J. R. Abbott, D. E. Soltis, R. Guralnick, P. S. Soltis. 2019. Spatial Phylogenetics of Florida Vascular Plants: The Effects of Calibration and Uncertainty on Diversity Estimates. iScience. 11:57-70.
  • Grass Phylogeny Working Group II. 2012. New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins. New Phytologist. 193: 304-312.
  • Soltis, D. E., S. A. Smith, N. Cellinese, et al. 2011. Angiosperm phylogeny: 17 genes, 640 taxa. 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
  • 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)
  • 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. Edwards and S. A. Smith. 2010. Phylogenetic analyses reveal the shady history of C4 grasses. PNAS. 107: 2532-2538. pdf
  • 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
  • Ree, R. H. and S. A. Smith. 2008. Maximum-likelihood Inference of Geographic Range Evolution by Dispersal, Local Extinction, and Cladogenesis. Syst. Biol. 57: 4-14. pdf
  • 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. pdf
  • Cellinese, N., S. A. Smith, E. J. Edwards, S. T. Kim, R. C. Haberle, M. Avramakis and M. J. Donoghue. in press. Historical biogeography of the endemic Campanulaceae of Crete. Journal of Biogeography.

Genomics and transcriptomics

Recently we have started developing methods and building and analyzing phylogenetic datasets with sequences generated by next generation sequencing techniques.

  • Cheng, S., M. Melkonian, S. A. Smith, S. Brockington, J. M. Archibald, P. Delaux, F. Li, B. Melkonian, E. V. Mavrodiev, W. Sun, Y. Fu, H. Yang, D. E. Soltis, S. W. Graham, P. S. Soltis, X. Liu, X. Xu, G. K. Wong. 2018. 10KP: A phylodiverse genome sequencing plan. GigaScience
  • Wang, N., Y. Yang, M. J. Moore, S. F. Brockington, J. F. Walker, J. W. Brown, B. Liang, T. Feng, C. Edwards, J. Mikenas, J. Olivieri, V. Hutchinson, A. Timoneda, T. Stoughton, R. Puente, L. C. Majure, U. Eggli, S. A. Smith. 2018. Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments. Molecular Biology and Evolution
  • Yang, Y. and S. A. Smith. 2013. Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. BMC Genomics. 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
  • 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
  • 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

The origins of innovation and complexity

In the lab, we use genetic information and new methods to better understand the evolution of complex traits and adaptations. For these studies, we take a holistic view, examining potential correlates in geographic movements, niche expansion and shifts, morphological evolution, and molecular evolution.

  • Wang, N., Y. Yang, M. J. Moore, S. F. Brockington, J. F. Walker, J. W. Brown, B. Liang, T. Feng, C. Edwards, J. Mikenas, J. Olivieri, V. Hutchinson, A. Timoneda, T. Stoughton, R. Puente, L. C. Majure, U. Eggli, S. A. Smith. 2018. Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments. Molecular Biology and Evolution
  • Walker, J., J. W. Brown, and S. A. Smith. 2018. Analyzing contentious relationships and outlier genes in phylogenomics. Systematic Biology. 67:916–924. link
  • Lopez-Nieves, S., Y. Yang, T. Feng, S. A. Smith, S. F. Brockington, and H. A. Maeda. 2017. Relaxation of Tyrosine Pathway Regulation Underlies the Evolution of Betalain Pigmentation in Caryophyllales. New Phytologist
  • 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. link
  • 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. link

Large phylogenetics

We develop methods and software for assembling large datasets with an emphasis on both large numbers of taxa and with large numbers of genes. In particular we have an interest in showing how large phylogenies can illuminate problems that we have not been able to address adequately with smaller phylogenies. We have also been developing methods, in relation to the opentree of life grant that place trees into a common graph. This allows for interesting ways to synthesize and analyze sets of trees.

  • Smith, S. A. and J. F. Walker. 2018. PyPHLAWD: A python tool for phylogenetic dataset construction. Methods in Ecology and Evolution link
  • Smith, S. A., J. F. Walker, and J. Brown. 2018. So many genes, so little time: rate variation in phylogenomic datasets. PLoS One link
  • Smith, S. A. and J. W. Brown. 2018. Constructing a comprehensive seed plant phylogeny. American Journal of Botany link
  • Pease J.B., J. W. Brown, J. F. Walker, C. E. Hinchliff, S. A. Smith. 2018. Quartet Sampling distinguishes lack of support from conflicting support in the plant tree of life. American Journal of Botany link
  • 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
  • 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., 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
  • 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)