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Course information

University of Chicago BIOS23404/EVOL35401 – Autumn 2015

Reconstructing the Tree of Life - An introduction to systematic and phylogenetic biology
Course web site:


This course is an introduction to the “tree of life” (phylogeny): its conceptual origins, methods for discovering its structure, and its importance in evolutionary biology and other areas of science. Topics include historical context and concepts, sources of data, methods of phylogenetic analysis, and the use of phylogenies to study the tempo and mode of phenotypic and genetic evolution, lineage diversification, coevolution, biogeography, conservation, molecular biology, development, and epidemiology.


Time and place

  • Lectures: Tuesdays and Thursdays, 1:30 – 2:50 pm in BSLC 313.
  • Computer laboratories: Thursdays, 3:00 – 5:00 pm in BSLC 228.

Office Hours

  • Richard Ree: by appointment
  • Benjamin Blanchard: by appointment


Available at the UChicago Bookstore:

Baum, D. A. & Smith, S. D. (2013). Tree Thinking: An Introduction to Phylogenetic Biology. Roberts and Company Publishers, Greenwood Village, Colorado pp.1-476.

Additional books that may be useful for this course are also on reserve in Crerar Library.  Currently the list includes:
  • 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.


  • Midterm exam: 20% of final grade
  • Final exam: 30%
  • Lab + Discussion: 20%
  • Final project: 30%

Schedule of lectures and readings - updated throughout the quarter

Required discussion readings are assigned for each lecture and are intended to review and provoke curiosity about the material covered to date.  The final 15-20 minutes of each lecture will be dedicated to discussing the reading, and participation will be considered in your final grade.

Date (2015)
Topic(s) and Textbook pages/chapters
Required discussion readings
Tu Sep 29 Course overview; introduction to “tree thinking” (Ch 1) None
Th Oct 1 Brief history of systematics; conceptual origins of phylogeny (Ch 2) Gould, S. J. (1983) What, if anything, is a zebra? in Hen's Teeth and Horse's Toes. Norton, New York.
Tu Oct 6 Anatomy of a tree; terminology; branch lengths; uncertainty; trait evolution; homology/homoplasy(Chs 3, 4, & 5) Baum et al. (2005) Science 310:979-980  -AND- vonHoldt et al. (2010) Nature 464: 898-902 (note two readings for this class meeting)
Th Oct 8 Gene trees vs. species trees; speciation; species concepts (Ch 6) Baum, D. A. (2009) Syst. Biol. 58:74-86
Tu Oct 13 Parsimony; long branch attraction (Ch 7) Halanych, K. (2015) J. Experimental Biology 218, 592-597
Th Oct 15 Models of evolution; likelihood (Ch 8: pages 217 – 247) Feinberg et al. (2014) Plos ONE and Newman et al. (2012). MPE
Tu Oct 20 Tree search strategies; Bayesian inference (Ch 8: pages 247 – 258) Organ et al. (2007) Nature 446:180-184
Th Oct 22 Midterm
Tu Oct 27 Measuring clade support; concordance analysis; species tree methods (Ch 9) Forsberg et al. (2014) Nature
Th Oct 29 Phenotypic evolution; ancestral states; single-trait hypothesis tests (Ch 10: part) Whiting et al. (2003) Nature 421:264-267 -AND- Goldberg and Igic (2008) Evolution 62:2727-2741
Tu Nov 3 Adaptation; natural selection; comparative method (Ch 10: part) Felsenstein, J. (1985) American Naturalist 125:1--15
Th Nov 5 Molecular clocks; diversification; key innovations (Ch 11: pages 363 – 381) Meredith et al. (2011) Science 334: 521-524.
Tu Nov 10 Biogeography; cospeciation (Ch 11) Reed et al. (2007) BMC Ev. Biol.
Th Nov 12 Next-generation sequencing; phylogenomics Wagner et al. (2013) Molecular Ecology
Tu Nov 17 Nomenclature; conservation; community ecology (Ch 11) Cavender-Bares et al.  (2004) American Naturalist
Th Nov 19 Human origins; epidemiology; forensics Gonzales-Candelas et al. (2013) BMC Biology 11: 76.
Tu Nov 24 Final exam None
Th Nov 26 No class – Thanksgiving None

Computer lab schedule

Date (2015)
Oct 1 Intro - GenBank - TreeBase - Terminal/Linux
Oct 8 Homology and sequence alignment
Oct 15 Tree reconstruction (parsimony; likelihood); bootstrap
Oct 22 Model selection; Bayesian inference; posterior probabilities
Oct 29 Character evolution (reconstructing ancestral states; correlated evolution)
Nov 5 Consult on final projects – individual meetings
Nov 12 Molecular clocks; lineage through time plots
Nov 19 Open lab to work on projects
Nov 26 No lab – Thanksgiving
Dec 6 Final projects due by 5pm via email

Final projects

Due Dec 6, 2015 by 5 pm via email to Richard Ree (  See here for details.

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