Schedule
The lecuture meets two times a week from 10:15-11:30 on Tuesday and Thursday (3 credit hours). Lectures materials and activies will be posted at this site if possible, but some materials may only be available through moodle. Discussions will usually try to fall on Thursdays, and will draw from current literature and require active participation. There are a number of required journal articles that should be read for class. They will typically be written beyond the scope of class materials at the time, so you will be expected to be, in part, confused. Perfection is not expected in this class, this is meant to generate questions and discussion. There will also be active computer activities in class which will require submission for points and are graded on participation.
Fall 2026 Schedule
The schedule is still in progress and subject to changes until class begins. The draft schedule and readings are provided below. Please note there are some deadlines for project-related assgnments that do not fall on a class day. This is done to provide some spacing between exams and time for feedback. Slides or activity pages will be made available the day of class.
| Date | Module | Topic | Assigned Reading | Slides and Resources |
|---|---|---|---|---|
| 18 August | Introduction | Why Plants? An overview of early plant evolution | Syllabus | slides |
| 20 August | Introduction | Random variables, probability theory, and stochastic processes | Poisson Processes | slides |
| 25 August | Population Genomics | Genetic Diversity | Estimating Genetic Diversity | slides |
| 27 August | Population Genomics | Population Structure | NA | slides |
| 01 September | Population Genomics | Outcrossing, Selfers, and Apomicts | NA | slides; computer activity |
| 03 September | Population Genomics | Structure across the Genome | Rivera-Rodríguez et al. 2023 | class discussion |
| 08 September | Population Genomics | Selection and Demography | The Site Frequency Spectrum | slides |
| 10 September | Population Genomics | Local Adaptation and Environmental Associations | NA | slides; computer activity |
| 15 September | Population Genomics | Gene Flow and Polyploidy | NA | slides |
| 17 September | Population Genomics | Environmental Associations: GEA | Dauphin et al. 2020 | class discussion |
| 22 September | Exams | First Exam: Population Genomics | NA | NA |
| 24 September | Speciation Genomics | What are species? Rules and resources for naming and synonymizing botanical species. | De Queiroz 2007 | slides |
| 25 September | Class Project | Class Project 1: Proposal Due | NA | Project Guidelines |
| 29 September | No Class! | Wellness Day | NA | NA |
| 01 October | Speciation Genomics | Plant Speciation Mechanisms | NA | slides |
| 06 October | Speciation Genomics | Species Delimitation: Integrative Taxonomy | Mayo 2022 | slides |
| 08 October | Speciation Genomics | Speciation with Adaptive Introgression | NA | slides; computer activity |
| 13 October | Speciation Genomics | Phylogenetics: Theory and Overview | NA | slides |
| 15 October | Speciation Genomics | Species complexes and species networks: Examples from blueberries | TBD | class discussion |
| 20 October | No Class! | Fall Break | NA | NA |
| 22 October | Speciation Genomics | Estimating the timescale and rate of evolution | NA | slides |
| 23 October | Class Project | Class Project 2: First Draft Due | NA | Project Guidelines |
| 27 October | Exams | Second Exam: Speciation | NA | NA |
| 29 October | Macroevolution | Species-level diversity: More than population-level processes? | NA | slides |
| 03 November | Macroevolution | Comparative Methods: Theory and Overview | NA | slides |
| 05 November | Macroevolution | Comparative Methods: Evolution of Nodulation and Nitrogen Fixation | Zhao et al. 2021 | class discussion |
| 10 November | Macroevolution | Plant Genome Architecture: Polyploidy-revisited | Tang et al. 2008 | slides |
| 11 December | Class Project | Extended Poster Help Sesssion | NA | |
| 12 November | Macroevolution | Plant Genome Architecture: Reconciling Gene Families | NA | slides; computer activity |
| 17 November | Macroevolution | The rise of pathways and key innovations | NA | slides |
| 18 November | Class Project | Extended Poster Help Sesssion | NA | |
| 19 November | Macroevolution | Trait-dependent diversification | NA | slides; computer activity |
| 24 November | Macroevolution | Biogeographic Models | Pérez-Escobar et. al. 2017 | class discussion |
| 24 November | Projects | Class Project 3: Final Draft Due | NA | Project Guidelines |
| 26 November | No Class! | Thanksgiving Holiday | NA | NA |
| 01 December | Class Project | Class Project 4: Presentations | NA | Project Guidelines |
| 03 December | Exams | Final Exam: Macroevolution | NA | NA |
Grading
Grading will consist of three exams, a class project, and paper discussions. The class project will be a poster on an assigned clade and topic done in small groups. Guidance on poster projects is available on the projects page. The point distribution for the 495 version and dates for project phases are below:
| Assignment | Points | Dates |
|---|---|---|
| Exam 1 | 100 | 22 September |
| Exam 2 | 100 | 27 October |
| Exam 3 | 100 | 03 December |
| Project 1 | 25 | 25 September |
| Project 2 | 25 | 23 October |
| Project 3 | 50 | 24 November |
| Project 4 | 50 | 01 December |
| Discussion 1 | 10 | 03 September |
| Discussion 2 | 10 | 17 September |
| Discussion 3 | 10 | 22 October |
| Discussion 4 | 10 | 05 November |
| Discussion 5 | 10 | 24 November |
| Computer Activity 1 | 10 | 01 September |
| Computer Activity 2 | 10 | 10 September |
| Computer Activity 3 | 10 | 06 October |
| Computer Activity 4 | 10 | 12 November |
| Computer Activity 5 | 10 | 19 November |
| Total | 500 |
Grading is based on the cumulative score and a ten-point scale with +/- grades are used. Here is the point-to-letter distribution for the 495 version:
| Percentage (x) | Points (x) | Letter Grade |
|---|---|---|
| x >= 97 | x > 485 | A+ |
| 93 <= x < 97 | 465 <= x < 485 | A |
| 90 <= x < 93 | 450 <= x < 465 | A- |
| 87 <= x < 90 | 435 <= x < 450 | B+ |
| 83 <= x < 87 | 415 <= x < 435 | B |
| 80 <= x < 83 | 400 <= x < 415 | B- |
| 77 <= x < 80 | 385 <= x < 400 | C+ |
| 73 <= x < 77 | 365 <= x < 385 | C |
| 70 <= x < 73 | 350 <= x < 365 | C- |
| 67 <= x < 70 | 335 <= x < 350 | D+ |
| 63 <= x < 67 | 315 <= x < 335 | D |
| 60 <= x < 63 | 300 <= x < 315 | D- |
| x < 60 | x < 300 | F |
What makes the 595 version different from 495?
Graduate students enrolled in the 595 version of the course will have an additional expectation to write a research proposal in evolutionary biology that builds off of your current research projects or interests. Research proposals should provide a plausible basis for a graduate student or postdoc fellowship proposal, or at least, help develop some background for manuscripts you are working on. 495 students are assigned a plant family of interest for their projects to research and present. The 595 project topics should be proposed by you. The proposal is worth an additional 100 points and has a separate ruberic and template available here. Guidance on research proposal projects is available on the projects page.