Biol Z620 - Phylogenetics

Section: 7039
Class Day and Times: MWF 10:10-11:00
Class Location: SW 221
WEB Page:
Text: The Phylogenetic Handbook edited by Lemey, Salemi, and Vandamme
Instructor: Elizabeth Housworth
Office and Office Hours: 371 Rawles Hall, Tentatively Mondays 1:15-2:45 and Thursdays 2-3:30 and by appointment

Important Dates: Last day for Automatic Withdrawal: Wednesday, October 23. Project idea due on Wednesday, November 6. Prelimary project report due on Wednesday, December 4. Final Project due by 12:30 p.m., Wednesday December 18.

Religious Holiday Policy: If you will miss class, especially a class during which there will be an exam or other required work, for a religious holiday, you must inform me during the first two weeks of the semester.

Cheating: It is not possible to cheat on homeworks. However, all final project work must be your own and no cheating will be tolerated. Also, you cannot combine this project with that of another class (past, present, or future) unless you get the permission of both instructors. All suspected cases of cheating will be handled in accordance with University procedures found at . If you do cheat, you will receive an F* in the course - the star informs the registar that the F is due to cheating. Additional sanctions may be imposed by the Dean.

Homework: The homework is designed to help you learn how to use relevant software and to help you get a feel for the issues that come up when you conduct a phylogenetic analysis. However, by keeping the homework reasonable by limiting the number of species and by considering only one gene, there is no way that the homework reflects a deep phylogenetic analysis. You may work with each other on the homework assignments.

Projects: Half your grade will be based on a final project. I am imagining that your project will be of one of the following types:
(1) You can use original sequence data (yours or someone else's) to conduct an original, careful phylogenetic analysis. You should describe what you are looking for in the data and why it is important.
(2) You can discuss and critique two or more different approaches in the literature to an issue in phylogenetics. The topic can be biological (such as the placement of a group on a phylogeny) or theoretical (such as two different phylogenetic comparative methods).
If your imagination takes you elsewhere, just run your idea by me to get my approval.

You will turn in your project idea and a rough draft before you turn in your final project. This is designed to keep you on schedule and to give you feedback so that you can address any problems in a timely manner.

Project idea: Due Wednesday, November 6. Give a brief description of what you intend to do for your final project. If you have your own data to work with, provide a copy of your data. If you have data from another source provide the data or the reference. If you are comparing two different approaches to an issue in phylogenetics, briefly describe the topic and provide copies of the references you are using.

Preliminary report: Due Wednesday, December 4. Provide a rough draft of your final project report.

Grades: Grades are calculated as 20% participation (attendance and questions), 30% homeworks, and 50% the final project.

Database Links:     NCBI GenBank     UniProt (contains SwissProt)     Ensembl     European Nucleotide Archive     DNA Databank of Japan    

Software Links:     Clustal Omega online from EMBL-EBI     Coffee programs     DNA sequence manipulation     Tree View     jModeltest     PHYLIP     MEGA     Tree Puzzle     MrBayes     PAUP     R (statistical software)     PhyML Online     SplitsTree4     Others (Felsenstein's list)

Links to other Phylogenetics Learning Resources:     David Baum's Phylogenetics Course     NCBI Phylogenetics Primer     Software Learning Activities     Welcome to a Little Book of R for Bioinformatics!   


Tentative Syllabus

Date Lecture Reading Assignment
Monday, August 26 Basic concepts of molecular evolution Chapter 1
Wednesday, August 28 Getting data Chapter 2
Friday, August 30 Aligning the data Chapter 3
Homework 1     Due: Friday, September 6
Monday, September 2 Labor Day Holiday --
Wednesday, September 4 Aligning the data Chapter 3
BaliBASE Kinase alignment
Friday, September 6 Genetic distances and Jukes Cantor Chapter 4
Homework 2     Due: Friday, September 13
Monday, September 9 More complicated models of DNA evolution Chapter 4
Wednesday, September 11 Even more complicated models Chapter 4
Primate mitochondrial DNA [Hayasaka, K., T. Gojobori, and S. Horai. 1988. Molecular phylogeny and evolution of primate mitochondrial DNA. Mol. Biol. Evol. 5:626-644.]
R code for getting pairwise distances from 'ape'
Friday, September 13 Log det distances Recovering Evolutionary Trees under a More Realistic Model of Sequence Evolution by Peter Lockhart, Michael Steel, Michael Hendy, and David Penny in Molecular Biology and Evolution (1994) 11:605-612.
Evolutionary Distance Estimation Under Heterogeneous Substitution Pattern Among Lineages by Koichiro Tamura and Sudhir Kumar in Molecular Biology and Evolution (2002) 19:1727-1736.
Algae data from the Lockhart et al. paper
Some R code for roughly checking the equidistribution of base frequencies
Homework 3     Due: Friday, September 20
Monday, September 16 Model selection procedures Chapter 10
Algae data from the Lockhart et al. paper in MEGA format
Some R code for roughly checking the equidistribution of base frequencies
Wednesday, September 18 Distance based methods using clustering Chapter 5
Friday, September 20 Minimum evolution and neighbor joining Chapter 5
Homework 4     Due: Friday, September 27
Monday, September 23 Bootstrapping - nonphylogenetic examples Introduction to the Bootstrap Lecture Notes by Michael Eichler
Bootstrap Methods: Another Look at the Jackknife by Bradley Efron in The Annals of Statistics (1979) 7:1-26.
The bootstrap: a tutorial by Ron Wehrens, Hein Putter, and Lutgarde Buydens in Chemometrics and Intelligent Laboratory Systems (2000) 54:35-52.
Some simple R code demonstrating the bootstrap for the silly example given in class.
Wednesday, September 25 Bootstrapping in phylogenetics Chapters 5 and 12
R code for bootstrapping and for Felsenstein's and Kishino's example.
Friday, September 27 Correcting the bootstrap Bootstrap support is first-order correct (Efron, Halloran, and Holmes)
Bootstrap support is not first-order correct (Susko)
How to make phylogenetic bootstrap values first order correct (Susko)
The additional problem of post-hoc analyses.
Homework 5     Due: Friday, October 4
Monday, September 30 Maximum likelihood theory Chapter 6
Wednesday, October 2 Maximum likelihood in phylogenetics Chapter 6
R code for phylogenetic maximum likelihood analyses
Friday, October 4 Maximum likelihood in phylogenetics Chapter 6
Homework 6     Due: Friday, October 11
Monday, October 7 Searching tree space Chapter 6
Wednesday, October 9 Bayesian theory An Introduction to Bayesian Statistics Without Using Equations by Eguchi
Introduction to Bayesian Statistics (with some equations) by Brynjarsdottir and Li
Friday, October 11 Bayesian phylogenetics Chapter 7
Mr. Bayes User Manual
Primate Data Nexus file plus code
Monday, October 14 Using Mr. Bayes Chapter 7
Wednesday, October 16 Parsimony theory Chapter 8
Friday, October 18 Fall Break --
Homework 7     Due: Friday, October 25
Monday, October 21 Parsimony and phylogenetics Chapter 8
Wednesday, October 23 Branch and bound Chapter 8
Friday, October 25 Parsimony example Chapter 8
Homework 8     Due: Friday, November 1
Monday, October 28 Consensus methods and total evidence Cladistics: Consensus trees by Peter Forey, posted by Thomas R. Holtz, from The Palaeontology Newsletter (2007) 64:28-34.
War and Peace in Phylogenetics: A Rejoinder on Total Evidence and Consensus by Claudine Levasseur and Francois-Joseph Lapointe in Systematic Biology (2001) 50:881-891.
R Code for creating a consensus phylogeny
A collection of Bayesian Posterior Primate Trees
Wednesday, October 30
Split networks Chapter 21
Friday, November 1 Phylogenies and the coalescent process Gene Tree Distributions Under the Coalescent Process by James Degnan and Laura Salter in Evolution (2005) 59:24-37
Homework 9     Due: Friday, November 8 (Skipped due to accidental deletion)
Monday, November 4 Phylogenetic networks NETGEN: generating phylogenetic networks with diploid hybrids by M. M. Morin and B. M. E. Moret in Bioinformatics (2006) 22:1921-1923.
Wednesday, November 6
Project idea due
Testing the molecular clock Chapter 11
Friday, November 8 Testing the molecular clock Chapter 11
Homework 10     Due: Friday, November 15
Monday, November 11 Synonomous and nonsynonymous substitutions Chapter 13 and Handout on dN/dS ratios by Rausher
Li's method Unbiased estimation of the rates of synonymous and nonsynonymous substitution. Journal of Molecular Evolution (1993) 36:96-99.
R code for reverse.align and kaks.
Parul's DNA data set for input into R
Parul's protein alignment for input into R
Wednesday, November 13 McDonald-Kreitman test Standard and generalized McDonald–Kreitman test: a website to detect selection by comparing different classes of DNA sites by Raquel Egea, Sonia Casillas, and Antonio Barbadilla in Nucleic Acids Research (2008) 36(suppl. 2): W157-W162.
McDonald-Kreitman Test software
Partial gnd locus in strains of E. coli.
Frequent adaptation and the McDonald-Kreitman Test by Philipp Messer and Dmitri Petrov in PNAS (2013) 110:8615-8620.
Friday, November 15 Other methods for detecting selection Chapter 14 and Datamonkey Tutorial
Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection by Sergei L. Kosakovsky Pond and Simon D. W. Frost in Molecular Biology and Evolution (2005) 22:1208-1222.
Inferring Selection and Mutation from DNA Sequences: The McDonald-Kreitman Test Revisited by Stanely Sawyer in Non-Neutral Evolution, Brian Golding, Editor, Springer (1994) 77-87.
Homework 11     Due: Friday, November 22
Monday, November 18 Host-parasite coevolution tests Disparate Rates of Molecular Evolution in Cospeciating Hosts and Parasites by Mark Hafner, Philip Sudman, Francis Villablanca, Theresa Spradling, James Demastes, and Steven Nadler in Science (1994) 265:1087-1090
Statistical Tests of Host-Parasite Cospeciation by John P. Huelsenbeck; Bruce Rannala; Ziheng Yang in Evolution (1997) 51:410-419.
A Statistical Test for Host-Parasite Coevolution by Pierre Legendre, Yves Desdevises, and Eric Bazin in Systematic Biology (2002) 51:217-234
Wednesday, November 20 Distances between trees Geometry of the Space of Phylogenetics Trees by Louis Billera, Susan Holmes, and Karen Vogtmann in Advances in Applied Mathematics (2001) 27:733-767
Friday, November 22 Experimental design issues: taxa and data Experimental design criteria in phylogenetics: where to add taxa by K. Geuten, T. Massingham, P. Darius, E. Smets, and N. Goldman in Systematic Biology (2007) 56:609-22.
Thanksgiving Break
Monday, December 2 Phylogenetic Comparative Methods Phylogenies and the Comparative Method by Joseph Felsenstein in The American Naturalist (1985) 125:1-15.
Salmon data from Crespi and Teo (2002)
Salmon phylogeny approximation from Crespi and Teo (2002)
Sample R code for conducting Independent Contrasts
Wednesday, December 4
Rough draft of final project due
Phylogenetic Comparative Methods Conducting Phylogenetic Comparative Studies When the Phylogeny is not Known by Emilia Martins in Evolution (1996) 50:12-22.
Sample R code for including phylogenetic uncertainty
Friday, December 6 Phylogenetic Comparative Methods Phylogenetic Analysis and Comparative Data: A Test and Review of Evidence by R. P. Freckleton, P. H. Harvey, and M. Pagel in The American Naturalist (2002) 160:712-726.
The Phylogenetic Mixed Model by Elizabeth Housworth, Emilia Martins, and Michael Lynch in The American Naturalist (2004) 163:84-96.
Monday, December 9 Phylogenetic comparative methods --
Wednesday, December 11 Phylogenetic meta-analysis/Evaluations General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters by J. D. Hadfield and S. Nakagawa in Journal of Evolutionary Biology (2010) 23:494-508.
A tree
Sample R code
Friday, December 13 Help with Projects Day --
Final Project due by 12:30 p.m., Wednesday December 18. Final Project Grading Rubric