All readings are from “An Introduction to Molecular Evolution and Phylogenetics” 2nd Ed. by Bromham, L.
*Schedule contains links to tutorials for Weeks 9-13.
Week 1
Introduction and DNA
Ch. 1: 2-30; Ch. 2: 31-60
- Reading the story in DNA
- Overview of textbook
- Review of genetics and heredity
- DNA extraction
Activity: Alien eggs on Dee-Why beach
What on earth is Xenoturbella?
Week 2
Mutation
Ch. 3: 61-94
- Overview of mutation
- SNPs
- Estimating mutation rates
Activity: DNA repair
Week 3
DNA Replication
Ch. 4: 95-130
- Overview of DNA replication
- DNA amplification and PCR
- DNA sequence evolution
Activity: Copy errors
Week 4
Exam 1 (Chapters 1-4)
Genome
Ch. 5: 131-166
- Evolution of genome size
- Repeat sequences
- Transposable elements
Activity: Assembling DNA sequence reads
Week 5
Gene
Ch. 6: 167-196
- Molecular properties of genes
- Review of transcription and translation
- Regulation of gene expression
- Gene sequence evolution
Activity: Decoding DNA
Week 6
Natural Selection
Ch. 7: 197-228
- Variation in natural populations
- Fitness, linkage, and human evolution
Activity: Signatures of selection in umami genes
Week 7
Genetic Drift
Ch. 8: 229-261
- The neutral theory of evolution
- Drift and effective population size
- Inbreeding and homozygosity
- Substitution patterns
Activity: Taking a chance
Week 8
Exam 2 (Chapters 5-8)
Species
Ch. 9: 262-294
- Taxonomy and classification
- Divergence, speciation, and hybrid incompatibility
- Defining species through DNA-based methods
Activity: Battle of the species concepts
Week 9
Alignment
Ch. 10: 295-328
- Homology vs. analogy/homoplasy
- DNA homology vs. morphological homology
- Indels and gaps
- Manual and automated multiple sequence alignment
Activity: Databases and alignment (AliView)
Week 10
Phylogeny
Ch. 11: 329-368
- Tree-based thinking in evolutionary biology
- Principles and characteristics of phylogenetic trees
- Methods of phylogenetic inference
- Phylogenetic networks
Activity: ML analysis (IQ-TREE)
Week 11
Hypotheses
Ch. 12: 369-402
- Evaluating and comparing phylogenetic trees
- Models of molecular evolution
- Maximum likelihood and Bayesian inference of trees
- Statistical methods of tree support
Activity: Bayesian inference (MrBayes)
Week 12
Exam 3 (Chapters 9-12)
Substitution rates
Ch. 13: 403-437
- Rate variation across sites and branches of trees
- Potential causes of evolutionary rate variation
- Testing for rate variation
Activity: Divergence time estimation (BEAST)
Week 13
Dates/Divergence Time Estimation
Ch. 14: 438-483
- The importance of the fossil record
- Estimation of divergence times
- Gene divergence vs. population/species divergence
- Strict vs. relaxed molecular clocks
Activity: Species tree analysis (SVDquartets)
Week 14
- Discussion of Case Studies
- Finish any computer exercises
- Term papers due by 11:59 pm
Activity: TBD
Week 15
- Discussion of Case Studies
- Finish any computer exercises
Activity: TBD
