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: Introduction (Overview,
Math Preliminaries,
Bio Background)
Lecture 3: A Simple Model of Evolution (PDF); Old version (PDF)
Lecture 4 & 5: Microscopic Models and the
Diffusion Limit (PDF)
Lectures 5 & 6: Working with the
single-locus diffusion model (PDF)
Lectures 7, 8, & 9: Dynamics of linear
branching processes (PDF)
Lecture 10 & 11: DNA sequencing &
genomics (PDF)
Lecture 11 & 12: Multi-locus models of
evolution (PDF)
Lecture 12 & 13: The successive mutations regime (PDF); Old version (PDF)
Lecture 13 & 14: Neutral theory and the
coalescent (PDF)
Lecture 14 & 15: Genealogies with selection
and recombination (PDF)
Lecture 16: The independent sites
approximation (PDF)
Lecture 17: Genetic hitchhiking from
classic selective sweeps (PDF)
Lecture 18 & 19: Linked selection and clonal
interference (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