Course: BIOL 6014
Time: Tuesday & Thursday; 11:00am - 12:15pm
Professor: Prof. Josef Uyeda (Yo-sef Weh-duh/Oo-weh-duh)
Office: 4076 Derring Hall
Email: juyeda@vt.edu
Office hours: By appointment
None are required to be purchased; readings will be provided from the primary literature, as well as from the following texts. Purchase of these texts is optional, though they are great reference material for those interested in macroevolution.
- Revell, Liam J., and Luke J. Harmon. Phylogenetic comparative methods in R. Princeton University Press, 2022.
- 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.
Phylogenetic trees are the map by which we understand evolutionary history and ultimately, all of biology. The goals of this course are threefold:
- 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.
- 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.
- 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 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.
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.
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.
- Exams: 2 exams, 100 points each (200 points total)
- Participation: In discussions of primary literature (50 points)
- Exercises: 5 assignments, each worth 10 points (50 points total)
- Final Project: Final project presentation (100 points)
All course participants will conduct a final research project that will analyze phylogenetic data using the methods and techniques learned in class. This project is largely open-ended and up to the student. 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 10/1) 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 on final presentations in the form of 15-minute talks on the results of these independent research projects.
All material will be posted on Canvas and GitHub, except for recorded lectures/discussions, which will only be posted on Canvas. The provided Slack channel is available for students to connect to their instructor and each other to work on projects, develop ideas, discuss topics, complete assignments, and otherwise build our virtual community. The code of conduct and University principles of community extend to this virtual setting.
Virginia Tech welcomes students with disabilities into the University’s educational programs. The University promotes efforts to provide equal access and a culture of inclusion without altering the essential elements of coursework. If you anticipate or experience academic barriers that may be due to disability, including but not limited to, chronic medical conditions, Deaf or hard of hearing, learning disability, mental health, or vision impairment, please contact the Services for Students with Disabilities (SSD) (540-231-3788, ssd@vt.edu, or visit www.ssd.vt.edu). If you have an SSD accommodation letter, please meet with me privately during office hours as early in the semester as possible to discuss implementing your accommodations. You must give me reasonable notice to implement your accommodations, which is generally 5 business days and 10 business days for final exams.
| Date | Topic | Reading | Assignments |
|---|---|---|---|
| T 8/27 | 1. Introductions & intro to macroevolution | Baum & Smith Ch. 1-3 | |
| Th 8/29 | 2. History of phylogenetic methods | Baum & Smith Ch. 1-3 | |
| T 9/3 | 3. Probability, likelihood, & Rev. Bayes | Baum & Smith Ch. 4 & 7 | Assignment I (Self-Test) |
| Th 9/5 | 4. Lab: Likelihood | ||
| T 9/10 | 5. Felsenstein & the birth of statistical phylogenetics | Baum & Smith | |
| Th 9/12 | 6. Discrete character evolution | O'Meara 2012 | |
| T 9/17 | 7. Discrete character evolution II | ||
| Th 9/19 | 8. Inferring phylogenies from molecular data | ||
| T 9/24 | 9. Bayesian methods of inference | ||
| Th 9/26 | 10. Exam I | ||
| T 10/1 | 11. Dating phylogenetic trees | ||
| Th 10/3 | 12. Biogeographic models | ||
| T 10/8 | 13. Revbayes lab: Biogeography | ||
| Th 10/10 | 14. Discrete traits - correlations, integration, & dependency | ||
| T 10/15 | 15. Brownian Motion & continuous trait evolution | ||
| Th 10/17 | 16. The comparative method & PICs | Felsenstein 1985 | Assignment II: Project proposal |
| T 10/22 | 17. Modeling adaptation | Hansen 1997 | |
| Th 10/24 | 18. Ornstein-Uhlenbeck models II | Butler and King 2004 | |
| T 10/29 | 18. Finding evolutionary shifts | ||
| Th 10/31 | 19. Hidden state models | Beaulieu et al. 2013 | |
| T 11/5 | 20. Exam II | ||
| Th 11/7 | 21. Species selection - SSE models | ||
| T 11/12 | 22. SSE Models | ||
| Th 11/14 | 23. Linking micro & macroevolution | ||
| T 11/19 | 24. Punctuated equilibrium | Eldredge and Gould, 1972 | |
| Th 11/21 | No Class - Thanksgiving Holiday | ||
| T 11/26 | No Class - Thanksgiving Holiday | ||
| Th 11/28 | 25. Grand challenges | ||
| T 12/3 | 26. Presentations | ||
| Th 12/5 | 27. Presentations |