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Course Syllabus - Special Topics: Macroevolution

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: [email protected]
Office hours: By appointment

Textbooks

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.

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:

  1. 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.
  2. 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.
  3. 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.

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 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)

Final Project Description

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.

Technology

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.

Services for Students with Disabilities (SSD)

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, [email protected], 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.

Course Schedule

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

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Macroevolution & Phylogenetics Course

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