BIOL 5984
MW 4:00 - 5:15 PM
Professor: Prof. Josef Uyeda (Yo-sef Weh-duh)
Office: 4076 Derring Hall
Email: juyeda@vt.edu
Office hours: By appointment
Course Website: Canvas and https://github.com/uyedaj/macrophy_course
Textbooks: None are required, readings will be provided from the primary literature, as well as from the following texts. Purchase of these texts is optional, though both are great reference material for those interested in phylogenetics and phylogenetic methods.
Baum, David A. and Stacey D. Smith. Tree Thinking: An Introduction to Phylogenetic Biology (1st Edition). W.H. Freeman, 2012.
Felsenstein, Joseph. Inferring Phylogenies (2nd Edition). Sinauer, 2003.
Harmon, Luke. Phylogenetic Comparative Methods: Learning from trees. CC-BY-4.0,2018.
**Course Description: **
Phylogenetic trees are the map by which we understand evolutionary history and ultimately, all of biology. The goals of this course are threefold:
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Embrace tree-thinking: You will learn what a phylogeny represents, how to use them to interpret evolutionary history and importantly, how to estimate them from biological data. This is the study of phylogenetics.
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Unleash the power of the comparative method: Why should we estimate trees in the first place? We will use phylogenies as a map for studying macroevolutionary questions about trait evolution, the relationships between organisms and their abiotic and biotic environment, and the causes and consequences of diversification. This is the study of phylogenetic comparative methods.
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Think big - Macroevolutionary science: We will engage with the rich and exciting history of evolutionary thought which fundamentally sought to unite microevolutionary processes, genetics and development to explain macroevolutionary patterns across the tree of life. We will read and discuss about these “big ideas” in macroevolution, and discuss how recent advances in phylogenetics and comparative methods enable us to test these ideas in ways never before possible.
Course Policies
Attendance
You are expected to attend every class and be on time. You are expected to participate in all discussions, have completed all readings BEFORE class, and to fully engage with the material and your classmates.
Course Syllabus
The course syllabus is subject to change by the instructor. Changes will be announced in class and on Canvas. Exam dates are unlikely to be changed from their original version.
Student Evaluation
Exams (2 X 100 pts, 200pts)
Participation in discussions of primary literature (50 pts)
Exercises (5 assignments, each worth 10 pts, 50 pts)
Final Project: Final project presentation(100 pts)
Final Project Description. All course participants will conduct an final research project that will conduct an analysis of phylogenetic data using the methods and techniques learned in class. This project is largely open-ended and up to the student. However, suggested topics include: building a phylogeny of a group of taxa of interest using available sequence data on Genbank, analyzing existing phenotypic datasets and phylogenies with phylogenetic comparative methods, or conducting a simulation study of phylogenetic model behavior. One of the 5 assignments is to submit a project proposal (due 10/8) that outlines the research question under study, the proposed datasets to be used, the analyses to be conducted, and the expected results (No more than 2 pages, not including citations). The last two class periods will be spent for final presentations in the form of 15 minute talks on the results of these independent research projects.
Course Schedule
| Date | Topic | Reading | Assignments |
|---|---|---|---|
| M 8/20 | 1. NO CLASS An Introduction to Tree-Thinking | Baum&Smith Ch 1 & 2 | |
| W 8/22 | 2. NO CLASS An Introduction to Tree-Thinking | Baum&Smith Ch 3 & 4 | |
| M 8/27 | 3. Tree-thinking, parsimony & cladistics | Baum&Smith Ch 4 & 7 | Assignment I (Self-Test) |
| W 8/29 | 4. Probability, likelihood & Rev. Bayes | ||
| M 9/3 | No Class, Labor Day | ||
| W 9/5 | 5. Felsenstein & the birth of statistical phylogenetics | Felsenstein 1981 | |
| M 9/10 | 6. Discrete character evolution I | O’Meara 2012 | |
| W 9/12 | 7. Discrete character evolution II | No Reading | |
| M 9/17 | 8. Model selection, model adequacy & Hypothesis testing | Assignment II: Paup Lab | |
| W 9/19 | 9. Practical considerations: alignments, concatenation, partitioning etc. | ||
| M 9/24 | 10. EXAM I | ||
| W 9/26 | 11. Biogeography | Ree and Smith 2008, Landis et al. 2018 | |
| M 10/1 | 12. Lab: RevBayes | Turn in lab at end of period | |
| W 10/3 | 13. Dating phylogenetic trees | ||
| M 10/8 | 14. The multispecies coalescent | Assignment III:Project proposal | |
| W 10/10 | 15. Guest speaker (T. Pelletier, Radford U.) | Pelletier et al. 2014 | |
| M 10/15 | 16. Brownian Motion & continuous trait evolution | ||
| W 10/17 | 17. The comparative method & PICs | Felsenstein 1985 | |
| M 10/22 | 18. Modeling adaptation | Hansen 1997 | |
| W 10/24 | 19. Ornstein-Uhlenbeck models II | Butler and King 2004 | |
| M 10/29 | 20. Finding evolutionary shifts | ||
| W 10/31 | 21. Hypothesis testing vs. data-driven modeling | Uyeda et al. 2018 | |
| M 11/5 | 22. EXAM II | ||
| W 11/7 | 23. Diversification models & SSE models | Maddison et al. 2007 | |
| M 11/12 | 24. Species selection (Lab: Diversitree) | ||
| W 11/14 | 25. Punctuations, stasis & gradualism | Eldredge and Gould, 1972; Charlesworth et al. 1982 | |
| M 11/19 | No Class - Thanksgiving Holiday | ||
| W 11/21 | No Class - Thanksgiving Holiday | ||
| M 11/26 | 26. Connecting Micro & Macroevolution | Uyeda et al. 2011; Futuyma 2010 | |
| W 11/28 | 27. Grand challenges in phylogenetics and macroevolution | ||
| M 12/3 | Presentations | ||
| W 12/5 | Presentations |