Reconstructing the Tree of Life

U. Chicago BIOS 23404 / EVOL 35401 – Autumn 2021


This course is an introduction to the “tree of life” (phylogeny): its conceptual origins, methods of discovery and analysis, and importance to evolutionary biology and other areas of science. Topics include sources of data, optimality criteria, strategies for searching tree space, methods for studying the tempo and mode of trait evolution and lineage diversification, and applications to coevolution, biogeography, conservation, epidemiology, and forensics.


Office hours: by appointment

Time and place

  • Lectures: Tuesdays and Thursdays, 2:00 - 3:20 pm in BSLC 324

  • Computer laboratories: Tuesdays, 3:30 – 5:30 pm in BSLC 018


Baum, D. A. & Smith, S. D. 2013. Tree Thinking: An Introduction to Phylogenetic Biology. Roberts and Company.

Additional books that may be useful:

  • Felsenstein, J. 2003. Inferring Phylogenies. Sinauer Associates, Inc.

  • Hall, B.G. 2007. Phylogenetic Trees Made Easy: A How To Manual. Third Edition. Sinauer Associates, Inc.

  • Lemey, P., M. Salemi & A.-M. Vandamme (Eds.). 2009. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing. Second Edition. Cambridge University Press.

  • Quammen, D. 2018. The Tangled Tree: A Radical New History of Life. Simon & Schuster.


  • Midterm exam: 30% of final grade

  • Final exam: 30%

  • Labs: 20%

  • Pre-lecture assignments: 20%