APHYS 237/BIO251: Quantitative evolutionary dynamics and genomics

The genomics revolution has fueled a renewed push to model evolutionary processes in quantitative terms. This course will provide an introduction to quantitative evolutionary modeling through the lens of statistical physics. Topics will range from the foundations of theoretical population genetics to experimental evolution of laboratory microbes. Course work will involve a mixture of pencil-and-paper math, writing basic computer simulations, and downloading and manipulating DNA sequence data from published datasets. This course is intended for upper level physics and math students with no biology background, as well as biology students who are comfortable with differential equations and probability.


Spring 2023

Course Meeting Schedule: TTh 10:30am – 11:50am
Course Meeting Location: Wallenberg Hall (Bldg 160) Rm 127
Instructor: Prof. Benjamin Good, Office: Clark S244, Email: bhgood@stanford.edu
Office Hours: Tu 1pm-2pm or by appointment.

Syllabus
Mathematical Background

Problem Sets

Data files for problem sets

Problem Set 1
Problem Set 2
Problem Set 3
Problem Set 4

Lecture Notes

Lectures 1 & 2 (Overview, Math Background, Bio Background)
Lectures 3 & 4 (PDF); Old version (PDF)
Lecture 4 & 5 (PDF); Old version (PDF)
Lectures 5 & 6 (PDF); Old version (PDF)
Lectures 7, 8, & 9 (PDF); Old versions (Part 1 PDF, Part 2 PDF, Part 3 PDF )
Lectures 10 & 11 (PDF); Old versions (Part 1 PDF, Part 2 PDF)
Lecture 12 & 13 (PDF); Old version (PDF)
Lecture 13 & 14 (PDF); Old version (PDF)
Lecture 14 (PDF); Old version (PDF)
Lecture 15 (PDF); Old version (PDF)
Lecture 16 (PDF); Old version (PDF)
Lecture 17 & 18 (PDF); Old version (PDF)
Lecture 18 & 19 (PDF); Old version (PDF)

Virtual Whiteboards from Winter 2021

(i.e. what we actually covered in class last time)

Overview Slides (1/12/21) PDF
Lecture 01 (1/12/21) PDF
Lecture 02 (1/14/21) PDF
Lecture 03 (1/19/21) PDF
Lecture 04 (1/21/21) PDF
Lecture 05 (1/26/21) PDF
Lecture 06 (1/28/21) PDF
Lecture 07 (2/02/21) PDF
Lecture 08 (2/04/21) PDF
Lecture 09 (2/09/21) PDF
Lecture 10 (2/11/21) PDF
Lecture 11 (2/16/21) PDF
Lecture 12 (2/18/21) PDF
Lecture 13 (2/23/21) PDF
Lecture 14 (2/25/21) PDF
Lecture 15 (3/02/21) PDF
Lecture 16 (3/04/21) PDF
Lecture 17 (3/09/21) PDF
Lecture 18 (3/11/21) PDF
Lecture 19 (3/16/21) PDF
Lecture 20 (3/18/21) PDF
Summary Slide (3/18/21) PDF

Other materials

1. BH Good (2016), Molecular evolution in rapidly evolving populations, Chapter 1
2. SF Levy, JR Blundell, et al (Nature 2015), Quantitative evolutionary dynamics using high-resolution lineage tracking, Supplementary Information
3. DS Fisher (Les Houches Course 11, 2007), Evolutionary dynamics
4. Korolev et al (Rev Mod Phys, 2010), Genetic demixing and evolution in linear stepping stone models
5. Neher and Shraiman (Rev Mod Phys, 2011), Statistical genetics and evolution of quantitative traits

Previous years

Winter 2021
Winter 2020