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


I am Stephen A. Smith, an evolutionary biologist and Assistant Professor at the University of Michigan, Ann Arbor. You can find out more information about the people in the lab here and the projects here. A lot of the research in the lab focuses on plant evolution, detecting and describing large scale patterns of evolution, examining differences in the rate of molecular evolution, and using new data sources like transcriptomes and genomes to address these questions. A great deal of this involves the development of new methods and new computational tools. My faculty page is here.