I have launched a new page for my class EEB 491 in phylogenetic methods and theory. It will have code and algorithms for many of the procedures and will continue to grow. It is for the class, but anyone can comment, or contribute.

You can see it here hackingtrees.net

Graduate students

University of Michigan is currently accepting graduate students (see link here) and I am always looking for good students interesting in computational molecular evolution, large scale plant evolution, biogeography, and phylogenetics. If you are interested in joining the lab, check out some recent publications and drop me an email. Here is my faculty page for my email (don’t want to post it here for spam).

old news

Moved the news from the sticky front piece. They will now be posts. Here is what I removed:


  • 10/25/11 — article published in Nature – Resolving the evolutionary relationships of molluscs with phylogenomic tools link pdf
  • 10/22/10 — article published in Science with a crew from Illinois – Species Selection Maintains Self-Incompatibility pdf
  • 5/01/10 — article published in Systematic Biology with Michael Donoghue – Combining Historical Biogeography with Niche Modeling in the Caprifolium Clade of Lonicera (Caprifoliaceae, Dipsacales) pdf
  • 4/29/10 — article published in Science with a bunch of collaborators – The origins of C4 grasslands: integrating evolutionary and ecosystem science pdf
  • 3/16/10 — article published in PNAS with Jeremy Beaulieu and Michael Donoghue – An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants pdf
  • 3/1/10 — article “The Botanist Hacker” published in the magazine The Scientist with corresponding YouTube video
  • 2/9/10 — article published in PNAS with Erika Edwards – Phylogenetic analyses reveal the shady history of C4 grasses pdf
  • 9/23/09 — article published in Proc Roy Soc B with J. Beaulieu — S. A. Smith and J. Beaulieu 2009. Life history influences rates of climatic niche evolution in flowering plants. pdf
  • 8/31/09 — letter published in PNAS with B. O’Meara — S. A. Smith and B. C. O’Meara 2009. Morphogenera, monophyly, and macroevolution. pdf
  • 7/13/09 — paper published in J. of Biogeography — S. A. Smith 2009. Taking into account phylogenetic and divergence-time uncertainty in a parametric biogeographical analysis of the Northern Hemisphere plant clade Caprifolieae. pdf