Visual guide to concepts in population genetics.

Introduction

Classic models of selection and drift at a single locus

Drift and selection in haploids
Drift and selection in diploids
Fixation in a diploid population

The Kingman coalescent

The structure of a tree
A model for data
Trees
Trees with recombination
Variation in diversity along a recombining genome (interactive Python)
Mutation frequencies
Theoretical expectations
Theoretical distributions

Diffusion models

Mutation frequencies under selection (interactive Python)

Linked selection

Selective “sweeps” (from new mutations)

Appendix

Interactive Python notebooks
Using interactive Python applets in slideshow presentations
Using Observable content in Jupyter presentations
Python dependencies
Acknowledgements
Literature cited

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Theoretical expectations¶

Time to most recent common ancestor

Total time on the tree

Allele frequency spectrum

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Theoretical distributions

By Kevin R. Thornton
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