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 2024

Course Meeting Schedule: TTh 10:30am – 11:50am
Course Meeting Location: Lane History Corner (Bldg 200) Rm 105
Instructor: Prof. Benjamin Good, Office: Clark S244, Email: bhgood@stanford.edu
Office Hours: Fri 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 Preliminaries, Bio Background)
Lecture 3 (PDF); Old version (PDF)
Lecture 4 & 5 (PDF)
Lectures 5 & 6 (PDF)
Lectures 7, 8, & 9 (PDF)
Lecture 10 & 11 (PDF)
Lecture 11 & 12 (PDF) Lecture 12 & 13 (PDF); Old version (PDF)
Lecture 13 & 14 (PDF)
Lecture 14 & 15 (PDF)
Lecture 16 (PDF)
Lecture 17 (PDF)
Lecture 18 & 19 (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 2023
Winter 2021
Winter 2020