Schedule
The class meets twice a week from 10:15–11:30 AM on Tuesday and Thursday (3 credit hours). Lecture materials and activities will be posted at this site if possible, but some materials may only be available through Moodle. Discussions usually fall on Thursdays, 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; the readings are meant to generate questions and discussion. There will also be active computer activities in class that require submission for points and are graded on participation.
Fall 2026 Schedule
The schedule is still in progress and subject to change until class begins. The draft schedule and readings are provided below. Please note there are some deadlines for project-related assignments 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 | course information on moodle | slides on moodle |
| 20 August | Introduction | Random variables, probability theory, and stochastic processes | Poisson Processes | slides |
| 25 August | Population Genomics | Genetic Diversity | Estimating Genetic Diversity and answers | slides on moodle |
| 27 August | Population Genomics | Population Structure | NA | slides on moodle |
| 01 September | Population Genomics | Structure applied | NA | computer activity |
| 03 September | Population Genomics | Structure and life history | McAllister and Miller 2016 | class discussion |
| 08 September | Population Genomics | Selection and Demography | The Site Frequency Spectrum | slides on moodle |
| 10 September | Population Genomics | Selection continued and Local Adaptation | NA | slides on moodle |
| 15 September | Population Genomics | Local Adaptation and Environmental Associations | NA | computer activity |
| 17 September | Population Genomics | Environmental Associations: GEA | Dauphin et al. 2020 | class discussion |
| 22 September | Exams | Exam 1: 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 | Phylogenetics: Theory and Overview | NA | slides |
| 08 October | Speciation Genomics | Speciation Delimitation with Adaptive Introgression | NA | slides |
| 09 October | Project (595) | 595 Research Proposal: One-Pager Due | NA | Project Guidelines |
| 13 October | Speciation Genomics | Speciation and rapid radiations through pollinator syndrome | NA | computer activity |
| 15 October | Speciation Genomics | Speciation with gene flow | Stone and Wessinger 2024 | 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 | Exam 2: Speciation Genomics | NA | NA |
| 29 October | Macroevolution | Species-level diversity: More than population-level processes? | NA | slides |
| 03 November | Macroevolution | State-dependant diversification | NA | slides |
| 04 November | Class Project | Poster Help Session (optional, outside class time) | Gardner 2212 (14:00-16:00) | workshop |
| 05 November | Macroevolution | Diversification rates and selfing syndrome | Goldberg et al. 2010 | computer activity and discussion combined |
| 06 November | Project (595) | 595 Research Proposal: First Draft Due | NA | Project Guidelines |
| 10 November | Macroevolution | Biogeography: Diversifying in new spaces | NA | slides |
| 11 November | Class Project | Poster Help Session (optional, outside class time) | Gardner 2212 (16:00-18:00) | workshop |
| 12 November | Macroevolution | Guest Lecture: Dr. Acer VanWallendael | NA | TBD |
| 16 November | Class Project | Class Project 3: Final, Print-Ready Draft Due | NA | Project Guidelines |
| 17 November | Macroevolution | The rise of pathways and key innovations | NA | slides |
| 19 November | Macroevolution | Duplication and polyploidy: Revisited | NA | slides |
| 20 November | Project (595) | 595 Research Proposal: Peer Reviews Returned | NA | Project Guidelines |
| 24 November | Macroevolution | The genome as a trait | TBD | computer activity and discussion combined |
| 26 November | No Class! | Thanksgiving Holiday | NA | NA |
| 01 December | Class Project | Class Project 4: Presentations | NA | Project Guidelines |
| 03 December | No Class! | Exam is scheduled 08 December | NA | NA |
| 04 December | Project (595) | 595 Research Proposal: Final Proposal Due | NA | Project Guidelines |
| 08 December | Exams | Exam 3: Macroevolution (university final examination period) | NA | NA |
Grading
Grading will consist of three exams, a class project, paper discussions, and computer activities. 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.
Your lowest paper discussion score and your lowest computer activity score are dropped. Five of each are scheduled, but only your best four in each category count. Discussions and in-class activities cannot be meaningfully reconstructed after the fact, so instead of adjudicating make-ups, everyone gets one of each to spend on illness, travel, or a day that simply did not go well.
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 | 20 | 25 September |
| Project 2 | 20 | 23 October |
| Project 3 | 50 | 16 November |
| Project 4 | 50 | 01 December |
| Discussion 1 | 20 | 03 September |
| Discussion 2 | 20 | 17 September |
| Discussion 3 | 20 | 15 October |
| Discussion 4 | 20 | 05 November |
| Discussion 5 | 20 | 24 November |
| Computer Activity 1 | 20 | 01 September |
| Computer Activity 2 | 20 | 10 September |
| Computer Activity 3 | 20 | 08 October |
| Computer Activity 4 | 20 | 12 November |
| Computer Activity 5 | 20 | 19 November |
| less lowest discussion | -20 | |
| less lowest computer activity | -20 | |
| Total | 600 |
Grading is based on the cumulative score and a ten-point scale with +/- grades. Here is the point-to-letter distribution for the 495 version:
| Percentage (x) | Points (x) | Letter Grade |
|---|---|---|
| x >= 97 | x >= 582 | A+ |
| 93 <= x < 97 | 558 <= x < 582 | A |
| 90 <= x < 93 | 540 <= x < 558 | A- |
| 87 <= x < 90 | 522 <= x < 540 | B+ |
| 83 <= x < 87 | 498 <= x < 522 | B |
| 80 <= x < 83 | 480 <= x < 498 | B- |
| 77 <= x < 80 | 462 <= x < 480 | C+ |
| 73 <= x < 77 | 438 <= x < 462 | C |
| 70 <= x < 73 | 420 <= x < 438 | C- |
| 67 <= x < 70 | 402 <= x < 420 | D+ |
| 63 <= x < 67 | 378 <= x < 402 | D |
| 60 <= x < 63 | 360 <= x < 378 | D- |
| x < 60 | x < 360 | F |
The 595 version adds a 100-point research proposal for a total of 700 points, distributed across four stages:
| Proposal Stage | Points | Date |
|---|---|---|
| One-pager | 20 | 09 October |
| First draft | 30 | 06 November |
| Peer reviews returned | 20 | 20 November |
| Final proposal | 30 | 04 December |
| Total | 100 |
The peer review is graded on the quality of the review you give, not the one you receive. A central goal of the proposal is to help you anticipate the criticisms a reviewer would raise about your own work, and that skill is exercised by writing a review rather than by receiving one.
The point-to-letter distribution for the 595 version:
| Percentage (x) | Points (x) | Letter Grade |
|---|---|---|
| x >= 97 | x >= 679 | A+ |
| 93 <= x < 97 | 651 <= x < 679 | A |
| 90 <= x < 93 | 630 <= x < 651 | A- |
| 87 <= x < 90 | 609 <= x < 630 | B+ |
| 83 <= x < 87 | 581 <= x < 609 | B |
| 80 <= x < 83 | 560 <= x < 581 | B- |
| 77 <= x < 80 | 539 <= x < 560 | C+ |
| 73 <= x < 77 | 511 <= x < 539 | C |
| 70 <= x < 73 | 490 <= x < 511 | C- |
| 67 <= x < 70 | 469 <= x < 490 | D+ |
| 63 <= x < 67 | 441 <= x < 469 | D |
| 60 <= x < 63 | 420 <= x < 441 | D- |
| x < 60 | x < 420 | F |
What makes the 595 version different from 495?
If you are enrolled in the 595 version, you have one additional expectation: a research proposal in evolutionary biology that builds on your current research projects or interests. A proposal should provide a plausible basis for a graduate student or postdoctoral fellowship application, or at minimum help develop background for a manuscript you are working on. 495 students are assigned a plant family to research and present; you propose your own 595 topic. The proposal is worth an additional 100 points and has its own rubric and template. Guidance, deadlines, and the point breakdown are on the projects page.