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

Sequence Evolution "Lab"

Notes and Lab protocol

Slides

Cheat sheet

Project report guidelines (2019)

*LINK to visual Markov Chain*

* report guidelines updated 2019 *

* phylogenetic inference is optional *

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~~

Guest Lecture: Dr. Conor Meehan

Slides: HIV Molecular Evolution

Section VI: Fun stuff [no notes]

Topic 1: Ancient DNA (2013: not on exam)

Topic 2: Will the real Neanderthal stand up? (2013: not on exam)
Topic 3: Paleomolecular biochemistry (2013: not on exam)

[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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FIRST set of slides:

Sect I: Intro

Sect I: History

Sect I: Mutation

Sect I: Prob & Likelihood

Sect II: PopGen Intro & HWE

Sect II: Linkage

Sect II: Inbreeding

Sect II: Assortative mating

Sect II: mutation pressure

FIRST Exam: Oct 07

Review PopGen-T4 & T5

SECOND set of slides:

Sect II: Assortative mating

Sect II: mutation pressure

Sect II: Natural Selection

Sect II: Drift

Sect II: Equilibrium

Sect III: Introductiom

Sect III: Homology (old)
Sect III: Homology (NEW)

SECOND Exam: Nov 04

Review PopGen-T1

Review PopGen-T2

Review PopGen-T3

Review PopGen-T4 & T5

THIRD set of slides:

Sect III: Phylogenetics (skip)

Sect IV: Genetic Load (2019)
REDUCED: Neutral 2 (2019)

Sect IV:NeutralTheory (skip)
REDUCED: Macroevolution

Sect IV: Macroevol. (skip)

Sect V: FFTNS

Sect V: Topic 2A/B (skip)

Sect V: Topics 3&4 (2019)

HIV Molecular Evol

THRID Exam: Dec 03 (Ts)

Exam 3 review questions