Course information

University of Chicago BIOS23404/EVOL35401 – Autumn 2017

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.


    Office hours: by appointment

Time and place

  • Lectures: Tuesdays and Thursdays, 2:00 - 3:20 pm in BSLC 305.
  • Computer laboratories: Thursdays, 3:30 – 5:30 pm in BSLC 216


Available at the UChicago Bookstore:

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

Additional books that may be useful for this course are also on reserve in Crerar Library:
  • 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: 30% of final grade
  • Final exam: 30%
  • Lab + Discussion: 20%
  • Final project: 20%

Schedule of lectures and readings - updated throughout the quarter

Required discussion readings are assigned for most lectures 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 (2017)
 LectureTopics and Textbook chapters/pages
Required discussion readings
Tu Sep 26
 1Course overview; introduction to “tree thinking” (Chapter 1) None
Th Sep 28  2A brief history of systematics; Darwin; evidence for common ancestry (Chapter 2)
Gould, S. J. (1983) What, if anything, is a zebra? in Hen's Teeth and Horse's Toes. Norton, New York.
Tu Oct 3  3Anatomy of a tree (Chapter 3); inferring a tree (Chapter 7)Brown and Doolittle (1995). Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. PNAS 92:2441-2445
Th Oct 5  4Characters and character states; homology and homoplasy; parsimony (Chapter 4)
No reading; bead alignment exercise
Tu Oct 10  5Inferring the tree using parsimony; bootstrapping; long branch attraction (Chapter 7)Mathews and Donoghue (1999). The Root of Angiosperm Phylogeny Inferred from Duplicate Phytochrome Genes. Science 286(5441):947.
Th Oct 12  6Likelihood (Chapter 8)Lee and Camens (2009). Strong morphological support for the molecular evolutionary tree of placental mammals. J Ev Bio
Tu Oct 17  7Likelihood, continued; Bayesian inference (Chapter 8) from Oct 12
Th Oct 19  8Molecular clocks and divergence-time estimation; gene trees and population trees part 1 (Chapter 6) No reading; elastic gene tree exercise
Tu Oct 24  9Midterm None
Th Oct 26  10Gene trees and population trees, part 2; inferring the population treeHahn and Nakhleh (2015) Irrational exuberance for resolved species trees. Evolution
Tu Oct 31  Next-generation sequencing and genome-scale phylogenetics; species (Chapter 6)Baum (2009) Species as ranked taxa. Syst. Biol.
Th Nov 2  11Inferring character evolution on a tree (Chapter 10) No reading
Tu Nov 7  12Adaptation; correlated evolution (Chapter 10) Pollux et al. (2014) The evolution of the placenta drives a shift in sexual selection in livebearing fish. Nature
Th Nov 9 13Diversification: inferring the tempo of lineage birth and death (Chapter 11) No reading
Tu Nov 14 14Nomenclature; conservation; community ecology Weiblen et al. (2006) Phylogenetic dispersion of host use in a tropical insect herbivore community
Th Nov 16  15Biogeography; cospeciation; phylogenetic synthesis Reed at al. (2007) Pair of lice lost or parasites regained: the evolutionary history of anthropoid primate lice
Tu Nov 21  16Human evolution; epidemiology; forensics González-Candelas et al. (2013) Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source
Th Nov 23  No class – Thanksgiving None
Tu Nov 28 Final exam
Tu Dec 5 Final projects due 

Computer lab schedule

See here for more information: Lab Schedule and Exercises

Date (2017)
Sep 28 Introduction to phylogenetic data
Oct 5 Homology and sequence alignment
Oct 12 Maximum parsimony, maximum likelihood, and bootstrapping
Oct 19 Model selection and Bayesian inference
Oct 26 Molecular clocks, fossils, and lineage-through-time plots
Nov 2 Ancestral state reconstruction & independent contrasts
Nov 9 Diversification
Nov 16 Phylogenetic synthesis
Nov 28 Open lab to work/consult on final project

Final projects

Due Dec 5, 2017 by 5 pm via email to Richard Ree (  See here for details.