Stephen A. Smith

Phylogenetic dataset construction

I develop methods and software for assembling large datasets with an emphasis on both large numbers of taxa (mega-phylogenies) and with large numbers of genes (supermatrices). I have an interest in showing how large phylogenies can illuminate problems that we have not been able to address adequately with smaller phylogenies. Until recently, I have focused on building phylogenies that have large numbers of tips but have recently started developing methods and building datasets with 454 and Illumina sequences. Although these analyses and tools are in their infancy, preliminary results are promising and provide tools from de novo assembly of the data to the construction of the dataset.

Relevant publications

  • 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
  • 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
  • E. Edwards and S. A. Smith. 2010. Phylogenetic analyses reveal the shady history of C4 grasses. PNAS. 107: 2532-2538. 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. link
  • Smith, S. A. and M. J. Donoghue. 2008. Rates of Molecular Evolution are Linked to Life History in Flowering Plants. Science. pdf
  • Smith, S. A. and C. Dunn. 2008. Phyutility: a phyloinformatics utility for trees, alignments, and molecular data. Bioinformatics. 24: 715-716. 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

Software