This is a graduate-level course in phylogenetics, emphasizing primarily maximum likelihood and Bayesian approaches to estimating phylogenies, which are genealogies at or above the species level. A primary goal is to provide an accessible introduction to the theory so that by the end of the course students should be able to understand much of the primary literature on modern phylogenetic methods and know how to intelligently apply these methods to their own problems. The laboratory provides hands-on experience with several important phylogenetic software packages (PAUP*, IQ-TREE, RevBayes, BayesTraits, and others) and introduces students to the use of remote high performance computing resources to perform phylogenetic analyses.

Semester: Spring 2024
Lecture: Tuesday/Thursday 11:00-12:15 (Paul O. Lewis, office hours Tu 1-2 or by appointment in Gant w421)
Lab: Thursday 1:25-3:20 (Analisa Milkey, office hours: Mo 1:30-2:30, Fr 12-1 in Gant W420)
Room: Torrey Life Science (TLS) 181, Storrs Campus
Text: Lewis, P. O. 2024. Getting Rooted in Bayesian Phylogenetics (unfinished, but some chapters are ready)


Warning: This schedule will most likely change quite a few times during the semester.

Date Lecture topic Lab/homework
Tuesday Jan. 16 Introduction Homework 1 Splits due 2024-01-23
Thursday Jan. 18 Optimality criteria, search strategies, consensus trees Lab 1 Using the Xanadu cluster, Introduction to PAUP*, and NEXUS file format
Tuesday Jan. 23 The parsimony criterion Homework 2 Parsimony due 2024-01-30
Thursday Jan 25 Distance methods Lab 2 Searching
Tuesday Jan. 30 Substitution models Homework 3 Distances Python primer due 2024-02-06
Thursday Feb. 1 Substitution models (cont.) Lab 3 Estimating parameters using likelihood
Tuesday Feb. 6 Maximum likelihood criterion Homework 4 Transitions and transversions due 2024-02-15
Thursday Feb. 8 Rate heterogeneity Lab 4 Simulating sequence data
Tuesday Feb. 13 SNOW DAY (no class) Homework 5 Site likelihood due 2024-02-20
Thursday Feb. 15 Rate het. (finish up), Bootstrapping, bootstrap demo in R, Simulation Lab 5 Maximum likelihood analyses with IQ-TREE
Tuesday Feb. 20 Bayes’ Rule and Bayesian statistics Homework 6 Rate heterogeneity due 2024-02-27
Thursday Feb. 22 Markov chain Monte Carlo (MCMC) Lab 6 Using R to explore probability distributions (Through Exponential, questions 1-19)
Tuesday Feb. 27 MCMC (cont.) Homework 7 MCMC due 2024-03-05
Thursday Feb. 29 Model selection Lab 7 Using R to explore probability distributions (start with Lognormal, questions 20-29)
Tuesday Mar. 5 Priors Homework 8 Bloodroot due 2024-03-19
Thursday Mar. 7 Coalescence Lab 8 MrBayes
Tuesday Mar. 12 SPRING BREAK  
Thursday Mar. 14 SPRING BREAK  
Tuesday Mar. 19 Species trees Homework 9 Taking a step in treespace
Thursday Mar. 21 Discrete morphological models Lab 9 RevBayes
Tuesday Mar. 26 rjMCMC and Polytomies; Evolutionary Correlation Homework 10 Conditioning on variability
Thursday Mar. 28 Stochastic character mapping] Lab 10 Discrete Morphology in RevBayes
Tuesday Apr. 2 Bloodroot revisited; Independent Contrasts; PGLS regression Homework 11 Simulating a character using the Brownian motion model
Thursday Apr. 4 PGLS (cont.); Phylogenetic signal in continuous traits Lab 11 BayesTraits
Tuesday Apr. 9 Dirichlet Process Priors Homework 12 Maddison and Fitzjohn (2015)
Thursday Apr. 11 Codon and amino acid models; Relaxed clock models Lab 12 Comparative methods and diversification in R
Tuesday Apr. 16 Relaxed clocks (cont.); Confidence vs. credible intervals Homework 13 Dirichlet process prior
Thursday Apr. 18 Heterotachy, and Covarion models; Lab 13 Divergence Time Estimation with RevBayes
Tuesday Apr. 23 Diversification no homework assignment
Thursday Apr. 25 Species delimitation and information Lab 14 Divergence Time Estimation with RevBayes (finish); Plotting trees in R with ggtree (optional)

Index to major topics

Index for 2024

Literature cited

Literature cited in 2024


Grading info

Books (and book chapters) on phylogenetics

This is a list of books that you should know about, but none are required texts for this course. Listed in reverse chronological order.

LJ Revell and LJ Harmon. 2022. Phylogenetic comparative methods in R. Princeton University Press. ISBN:978-0-691-21903-5

L Harmon. 2019. Phylogenetic comparative methods. (Version 1.4, released 15 March 2019). Published online by the author.

AJ Drummond and RR Bouckaert. 2015. Bayesian evolutionary analysis with BEAST, Cambridge University Press. ISBN:978-1-139-09511-2

Z Yang. 2014. Molecular evolution: a statistical approach. Oxford University Press. ISBN:978-0-199-60261-0

LZ Garamszegi. 2014. Modern phylogenetic comparative methods and their application in evolutionary biology: concepts and practice. Springer-Verlag, Berlin. ISBN:978-3-662-43549-6 (Well-written chapters by current leaders in phylogenetic comparative methods.)

DA Baum and SD Smith. 2013. Tree thinking: an introduction to phylogenetic biology. Roberts and Company Publishers, Greenwood Village, Colorado. ISBN:978-1-936-22116-5 (This book is a useful companion volume for this course, introducing the methods in a very accessible way but also providing lots of practice interpreting phylogenies correctly.)

BG Hall. 2011. Phylogenetic trees made easy: a how-to manual (4th edition). Sinauer Associates, Sunderland. ISBN:978-0-878-93606-9 (A guide to running some of the most important phylogenetic software packages.)

P Lemey, M Salemi, and AM Vandamme. 2009. The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing (2nd edition). ISBN:978-0-511-81904-9 Cambridge University Press, Cambridge, UK (Chapters on theory are paired with practical chapters on software related to the theory.)

J Felsenstein. 2004. Inferring phylogenies. Sinauer Associates, Sunderland. ISBN:978-0-878-93177-4 (Comprehensive overview of both history and methods of phylogenetics.)

R Page and E Holmes. 1998. Molecular evolution: a phylogenetic approach. Blackwell Science. ISBN:978-0-865-42889-8 (Very accessible pre-Bayesian-era introduction to the field.)

D Hillis, C Moritz, and B Mable. 1996. Molecular systematics (2nd ed.). Sinauer Associates, Sunderland. ISBN:978-0-878-93282-5 (Still a very valuable compendium of pre-Bayesian-era phylogenetic methods.)

DL Swofford, GJ Olsen, PJ Waddell, and DM Hillis. 1996. Chapter 11: Phylogenetic inference. Pages 407-514 in Molecular Systematics (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer Associates, Sunderland, Massachusetts. ISBN:978-0-878-93282-5 (Excellent reference for pre-Bayesian phylogenetics; original description of the SOWH topology test)