I have been working on methods 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. I have built trees of flowering plant clades to examine rates of evolution and how they relate to life history and have built a 13,533 species tree of green plants.
Relevant publications
- 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
- Smith, S. A. et al. 2008. Bioactive endophytes warrant intensified exploration and conservation. PLoS ONE. 3: e3052. 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
- 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
