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 http://dsa.indiana.edu/ethics.html . 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)
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.
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.
A Statistical Test for Host-Parasite Coevolution by Pierre Legendre, Yves Desdevises, and Eric Bazin in Systematic Biology, 2002 51:217-234
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
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
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--
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
None
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.
No HW
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
No HW
Wednesday, November 16
Phylogenetic Comparative Methods
Chapter 25 and
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.
Monday, November 21
Help with projects day
--
No HW
Wednesday, November 23
Thanksgiving Break
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Friday, November 25
Thanksgiving Break
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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.
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
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Final Project due by 12:15 p.m., Wednesday December 14.
Final Project Grading Rubric