Biol Z620 - Phylogenetics

Section: 7967
Class Day and Times: MWF 10:10-11:00
Class Location: SW 221
WEB Page:
Text: Inferring Phylogenies by Joseph Felsenstein
Instructor: Elizabeth Housworth
Office and Office Hours: 371 Rawles Hall, 1-4 pm Sundays and by appointment

Important Dates: Last day for Automatic Withdrawal: Wednesday, October 26. Project idea due on Wednesday, November 2. Prelimary project report due on Wednesday, November 30. Final Project due by 12:15 p.m., Wednesday December 14.

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: There is one homework problem given for each lecture for the first part of the course. The purpose of the homework is to make sure you basically understood the lecture for that day. The homework will not be turned in or graded, but you should do it before the next class and come to see me if you have any trouble with it.

Projects: The bulk of your grade will be based an 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.

Project idea: Due Wednesday, November 2. 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, November 30. Provide a rough draft of your final project report.

Grades: Grades are calculated as 40% participation (attendance and questions) and 60% the final project.

Software Links:     PHYLIP     R (statistical software)     jModeltest     MrBayes     Tree View     PAUP     Others (Felsenstein's list)    

Tentative Syllabus

Date Lecture Reading Homework
Monday, August 29 Trees: rooted vs. unrooted, bifurcating vs. multifurcating, ordered vs. unordered, phylogenies vs. pedigrees, labeled vs. unlabeled Chapter 3 HW 1
Wednesday, August 31 Computing the parsimony score for data on a given tree Chapter 2 HW 2
Friday, September 2 Finding the best tree for data Chapter 4 HW 3

Monday, September 5 Labor Day Holiday -- --
Wednesday, September 7 Branch and bound methods Chapter 5 HW 4
Friday, September 9 Computer demonstrations Example data set The data comes from: Adenylate Kinase Intron 5: A New Nuclear Locus for Avian Systematics by Leo H. Shapirp and John P. Dumbacher, The Auk 118:248-255, 2001. HW 5

Monday, September 12 Ancestral states and branch lengths in parsimony Chapter 6 HW 6
Wednesday, September 14 Compatibility with binary characters Chapter 8 HW 7
Friday, September 16 Compatibility with DNA (4-states) Chapter 8 HW 8

Monday, September 19 Models for DNA evolution: Jukes-Cantor and calculating the likelihood of a phylogeny under using the Jukes Cantor model Chapter 11 (p. 156) HW 9
Wednesday, September 21 The Kimura 2-parameter model Chapter 16 HW 10
Friday, September 23 Other models for DNA evolution: GTR + Gamma + I. Discussion of independence of sites assumption. Chapter 13 HW 11

Monday, September 26 Calculating the likelihood of a tree given a model for DNA evolution and searching tree space. Model selection. Chapter 16 HW 12
Data for homework: [Hayasaka, K., T. Gojobori, and S. Horai. 1988. Molecular phylogeny and evolution of primate mitochondrial DNA. Mol. Biol. Evol. 5:626-644.]
Primate data in nexus format from PAUP developers
Primate data in MEGA format
Primate data in Phylip format
Wednesday, September 28 Computer demonstrations Chapter 16 HW 13
Friday, September 30 Rooting a tree and computer demonstrations Chapter 16 HW 14
Link to the original primate paper cited above.

Monday, October 3 Rooting a tree and molecular clocks with computer examples in PHYLIP and MEGA Chapter 16 HW 15
Wednesday, October 5 Testing molecular clocks Chapters 16 and 19 HW 16
Friday, October 7 Statistical consistency - None

Monday, October 10 Statistics of bootstrapping; Parametric vs. nonparametric bootstrapping -- HW 17
Wednesday, October 12 Bootstrapping to indicate confidence in phylogenetics with computer demonstration Chapter 20 HW 18
Friday, October 14 Problems with bootstrapping in phylogenetics Chapter 20
Bootstrap support is first-order correct
Bootstrap support is not first-order correct

Monday, October 17 Bayesian philosophy Chapter 18 HW 19
Wednesday, October 19 Bayesian phylogenetics Chapter 18 None
Friday, October 21 Mr. Bayes computer demonstration Chapter 18 HW 20

Monday, October 24 Mr. Bayes and comparison to bootstrapping Chapters 18 and 20 HW 21
Wednesday, October 26 Distance methods: distances and trees Chapter 11 No HW
Friday, October 28 Distance methods: Neighbor-joining Chapter 11 No HW

Monday, October 31 Distance methods: UPGMA and computer demonstrations Chapter 11 No HW
Wednesday, November 2 Phylogenetic invariants Chapter 22
Project idea due
HW 22
Friday, November 4 Combining data: consensus vs. total evidence vs. ? Chapter 30 No HW

Monday, November 7 LogDet Distances Chapter 13 p.211-213
Sequence Evolution by Peter Lockhart, Michael Steel, Michael Hendy, and 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.
Wednesday, November 9 Summary of phylogenetic reconstruction techniques --
Friday, November 11 Additional issues in constructing phylogenies Gene Tree Distributions Under the Coalescent Process by James Degnan and Laura Salter in Evolution 2005 59:24-37
Chapter 25 and Phylogenies and the Comparative Method by Joseph Felsenstein in The American Naturalist, 1985 125:1-15.

Monday, November 14 Phylogenetic Comparative Methods Chapter 25 and

The Quantitative Assessment of Phylogenetic Constraints in Comparative Analyses: Sexual Dimorphism in Body Weight Among Primates by James M. Cheverud, Malcolm M. Dow, and Walter Leutenegger in Evolution, 1985 39:1335-1351.

Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data by Thomas F. Hansen and Emilia P. Martins in Evolution, 1996 50:1404-1417.

Comparative Methods for the Analysis of Continuous Variables: Geometric Interpretations by F. James Rohlf in Evolution, 2001 55:2143-2160.

R Code and Data for Examples

Wednesday, November 16 Phylogenetic Comparative Methods Chapter 25 and

The Phylogenetic Mixed Model by Elizabeth Housworth, Emilia Martins, and Michael Lynch in The American Naturalist, 2004 163:84-96.

Conducting Phylogenetic Comparative Studies When the Phylogeny is not Known by Emilia Martins in Evolution 1996, 50:12-22.

Friday, November 18 Uses of phylogenies: Host-Parasite evolution 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

Monday, November 21 Help with projects day -- No HW
Wednesday, November 23 Thanksgiving Break --
Friday, November 25 Thanksgiving Break --

Monday, November 28 Uses of phylogenies: Ferns Ferns diversified in the shadow of angiosperms by Harald Schneider, Eric Schuettpel, Kathleen M. Pryer, Raymond Cranfill, Susana Magallon, and Richard Lupia in Nature 2004 428: 553-557 No HW
Wednesday, November 30 Uses of phylogenies: Resolving controversies (or not...) Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm by V. V. Goremykin, K. I, Hirsch-Ernst, S. Wolfl, F. H. Hellwig in Molecular Biology and Evolution, 2003 20:1499-1505.

Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots? by Sasa Stefanovic, Danny W Rice, and Jeffrey D Palmer in BMC Evolutionary Biology, 2004 4:35
Preliminary project report due

Friday, December 2 Experimental design issues 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.

Monday, December 5 Computing distances between trees Chapter 30 and Geometry of the Space of Phylogenetics Trees by Louis Billera, Susan Holmes, and Karen Vogtmann in Advances in Applied Mathematics 2001 27:733-767 No HW
Wednesday, December 7
Friday, December 9 Summary and evaluations --
Final Project due by 12:15 p.m., Wednesday December 14. Final Project Grading Rubric