“Nothing in biology makes sense except in the light of evolution.” T.H. Dobzhansky, 1973
“Nothing in evolution makes sense except in the light of population genetics.” Michael Lynch, 2007
“Nothing in population genetics makes sense except in the light of coalescent theory.”
Dr. Mike Hickerson Office: rm 835 Marshak; City College; Graduate Center (rm TBA) Office hours location: CUNY GC location TBA Office Hours: by appointment e-mail: mhickerson@ccny.cuny.edu
Lecture: Fridays 9:30am -12:30pm at the CUNY GC; room = 7395
Texts: Matthew Hahn - Molecular Population Genetics
This course will be a hybrid between a standard population genetic graduate course and a hands-on methodology course. Instead of working on and turning in homework problems each week about the associated material covered, you will design, implement and visualize population genomic data simulations related to each week’s topic. For example, one week we might be covering models of population subdivision whereby you could explore and summarize simulations of whole genomes sampled from a stepping stone model of population history over a period of 20,000 generations. The simulation program we’ll often be using is SLIM v3.x which enables rapid simulation of complex geographic demographic histories with and without selection at arbitrary levels of genomic sampling (i.e. whole chromosomes or SNP data). This capability offers an excellent pedagogical tool and opportunity to build intuition for patterns of genetic variation in complex (or simple!) phylogeographic scenarios. However, we will also explore with other simulation tools (e.g. PipeMaster), and for your final simulation project there is no one required simulation software (you can something else instead of SLIM). Beyond useful exploration, simulation methods are routinely used in statistical inference such as machine learning methods, or to compare between different mechanistic models using approximate Bayesian computation. Moreover, simulation-based inference has proved to be extremely useful for problems that may be analytically intractable.
| Item | note | points |
|---|---|---|
| Simulation Assignments | 5 assignments (30 pts each) | 150 pts |
| Leading Discussions | 5 discussions (20 pts each) | 100 pts |
| Midterm | 100 pts | |
| Final Simulation Project | 150 pts | |
| Total | 500 pts |
Requests for re-grades must be made within one week of the assignment being handed back to the student. Only assignments/exams done in pen can be submitted for a regrade. Midterms will only be regarded if it has the potential to affect your final grade.
An simulation assignment will sometimes be given during a lecture, due one week later at the start of class. You are free to work in groups, but each individual is responsible for designing and running simulation in addition to analyzing and/or visualizing the results. Late penalty will be 20% of the assignment’s value per week late. Each student can briefly demonstrate their simulation results at the start of class. The final project will involve a more extensive simulation-based inference of real data (your own or published data).
On some of the weeks, we will have a discussion in the 2nd half of the class. In this case, two randomly selected people will lead the discussion on the assigned chapter of Hahn (or paper, TBA). The actual paper assignment will be given the week before. After you lead two discussions, you are off the hook
Each student will Final project will involve a more extensive simulation-based inference of real data (your own or published data). Alternatively, one can conduct stand-alone simulation experiments that answer questions about observable predictions under different hypotheses/models of interest. This project can be modest in scope, but can lead to a downstream publication. Oral presentation of final project at the end of the semester (15 min, 3 min for questions)
| Date | Topic | Reading |
|---|---|---|
| Sept 6 | Models of Evolution (Lecture 1a) | Chapter 1 |
| Sept 13° | Genetic Variation (Lecture 1b) (Lecture 2) | Chapter 3 |
| Sept 20* | The Coalescent model (Lecture 3) | Chapter 6 |
| Sept 27 | (guest appearence by Marcelo Gehara - PipeMaster ) | PipeMaster Tutorial |
| Oct 4°* | Population Structure (Lecture 4) | Chapter 5 |
| Oct 11 | final project proposals, 5 min each & Take home midterm distributed | |
| Oct 18 | Direct Selection(Lecture 5); (ABCs Step by Step); Take home midterm due | Chapter 7 |
| Oct 25*° | Linked Selection | Chapter 8 |
| Nov 1*° | Demographic History part 1 (guest appearence by Ariadna Morales - phrapl ) | Chapt 9 (203-221) |
| Nov 4-8 | 5 day workshop by Ben Haller | SLiM |
| Nov 15 | Demographic History part 2 (Lecture 7) | Chapt 9 (222-248) |
| Nov 22*° | Special topics (Lecture 8 Space) | |
| Dec 6 | Project Presentations | N/A |
| Dec 13 | Project Presentations | N/A |
*Indicates simulation assignment due and briefly presented (assigned friday before). ° Indicates reading based discussion (assigned friday before)
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