Lectures

Section I: Foundations
Topic 1: Introduction [same as slides]
Topic 2: History

Topic 3: Mutation and recombination

Topic 4: Review of probability and likelihood

Section II: Population genetics

Topic 1: Introduction and Hardy-Weinberg equilibrium
Topic 2: Linkage disequilibrium
Topic 3: Inbreeding
Topic 4: Assortative mating

Topic 5: Mutation
Topic 6: Natural Selection
Topic 7: Genetic Drift

Topic 8: Transient and equilibrium polymorphism

Section III: Phylogenetics
Topic 1: Introduction

Topic 2: Phylogenetic homology

Topic 3: Methods

Section IV: Neutral evolution
Topic 1&2: Genetic load and neutral theory

Topic 3: Macroevolution

~~Topic 4: Molecular Clock~~

Section V: Functional divergence

Topic 1: FFTNS and shifting balance

Topic 2A: Review the structure and function of genes

Topic 2B: Review the structure and function of proteins

Topic 3/4: Evolution of new genes and functions

Topic 3: Appendix I

~~Topic 4: Genes to diversity: evolution of the "molecular tool box"~~

~~Topic 5: Statistical tests~~

~~Topic 6: Case studies of molecular adaptation~~

Section VI: Fun stuff [no notes]

Topic 1: Ancient DNA

Topic 2: Will the real Neanderthal stand up?
~~Topic 3: Paleomolecular biochemistry~~

[Slides only: see links above for slides in PDF format]

Supplemental notes

Supp 1: Genetic code evolution

Supp 2: Maximum likelihood phylogeny reconstruction
Supp 3a: Estimating the rate of DNA evolution

Supp 6: Statistical tests of adaptive [macro] evolution

Supp 3b: Estimating the rate of DNA evolution

Supp 4: Molecular clock binder from 2004

Supp 5: Testing populations for non-neutral evolution

Supp 7: Genomics binder from 2004

Supp 8: Genomics to Metabolomics

Supp 9: Introduction to the coalescent

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Old stuff:

Sect III: Methods

Current set of slides:

Sect V: FunctDiv-T2AB

Sect V: FunctDiv-T3T4

Reviews:

Exam 3:

Tuesday

December 6th

2:35-3:55