Course information

University of Chicago BIOS23404/EVOL35401 – Autumn 2019

Reconstructing the Tree of Life - Introduction to systematics and phylogenetics
Course web site:


This course is an introduction to the “tree of life” (phylogeny): its conceptual origins, how it is discovered, and its importance in evolutionary biology and other areas of science. Topics include sources of data, methods of phylogenetic inference, relevance to systematics, and uses of phylogenies to study the tempo and mode of trait evolution, lineage diversification, coevolution, biogeography, conservation, epidemiology, and other fields.


    Office hours: by appointment

Time and place

  • Lectures: Tuesdays and Thursdays, 2:00 - 3:20 pm in BSLC 324
  • Computer laboratories: Thursdays, 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%
  • 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 (2019)
 LectureTopics and Textbook chapters/pages
Required discussion readings
Tu Oct 1
 1Course overview; introduction to “tree thinking”; conceptual origins (Chapter 1) None
Th Oct 3  2Evidence for common ancestry; anatomy of a tree; steps of tree inference (Chapters 2, 3, 7 in part)
Gould, S. J. (1983) What, if anything, is a zebra? in Hen's Teeth and Horse's Toes. Norton, New York.
Tu Oct 8  3Characters; homology; parsimony (Chapters 4, 7 in part)Silverton, J. (2005). The tree of trees. In: Demons in Eden: The Paradox of Plant Diversity, ch. 2. University of Chicago Press, Chicago.
Th Oct 10  4Heuristic search of tree space; estimating confidence in the tree (bootstrapping)
Sober, E. (2016-05-03). Why is simpler better? Aeon. URL: [accessed 2019-10-07].
Tu Oct 15  5Inferring phylogeny using likelihood; models of character evolution (Chapter 8)Felsenstein (2001) The Troubled Growth of Statistical Phylogenetics
Th Oct 17  6Likelihood, continued; nomenclature and taxonomy (Chapter 5)Hibbett et al. (2011) Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences
Tu Oct 22  7Bayesian inference; confidence intervals in tree space (Chapters 8 in part, 9 in part)
Th Oct 24  8Molecular clocks and divergence-time estimation (Chapter 11, second half) Prum RO, Berv JS, Dornburg A, Field DJ, Townsend JP, Lemmon EM, Lemmon AR. 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526: 569–573.

[Appendix: supplemental methods]
Tu Oct 29  Midterm None
Th Oct 31  9Diversification
Tu Nov 5  10Gene trees and population trees; the coalescentMaddison W. 1997. Gene trees in species trees. Systematic Biology 46: 523-536.
Th Nov 7  11Inferring the population ("species") tree
Tu Nov 12  12Other causes of gene tree discordance; reticulation and networks
Th Nov 14 13Species: part 1, part 2 Baum (2009) Species as ranked taxa. Syst. Biol.

Tu Nov 19 14Character evolution on a tree I - categorical states Whiting et al. (2003) Loss and recovery of wings in stick insects.
Goldberg and Igic (2008) On phylogenetic tests of irreversible evolution
Th Nov 21  15Trees within trees: gene duplication, cospeciation, biogeography Reed at al. (2007) Pair of lice lost or parasites regained: the evolutionary history of anthropoid primate lice
Tu Nov 26  16Character evolution on a tree II - continuous states
Th Nov 28  No class – Thanksgiving None
Tu Dec 3 17Epidemiology and forensics; conservationGonzález-Candelas et al. (2013) Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source
Th Dec 5 18Review 
Th Dec 12  FINAL EXAM     BSLC Rm. 324 1:30pm-3:30pm

Computer lab schedule

See here for more information: Lab Schedule and Exercises

 Date (2019)
Oct 3
Introduction to phylogenetic trees
 2 Oct 10 Homology and sequence alignment; tree inference using parsimony
 3 Oct 17 Tree inference using likelihood; concatenation; bootstrapping
 4 Oct 24 Divergence time estimation
 5 Oct 31Diversification rate estimation
 6 Nov 7 Gene trees and deep coalescence
 7 Nov 14 Species tree estimation; reticulation
 8 Nov 21 Ancestral state estimation; independent contrasts
 9Nov 28Open lab to work/consult on final project

Final projects

Due Monday, Dec 9, 2019 by 5 pm via email to Richard Ree ( and Andrew Hipp (  See here for details.