Learning objectives | Introduction | Genetic drift: qualitative expectation | Genetic drift: building intuition | Dissecting the variability in outcomes | Genetic drift and heterozygosity decay | Effective population size | Some food for thought: | Historical note | References:

Learning objectives | Introduction | R basics | R as a vector calculator | Objects in R | Appending elements | Indexing | Time for a pause and ponder | Matrices | Logical tests | Data frames | Functions | Installing and running packages | Scripts | File paths and directories | Getting help | Generation of random numbers | Plotting (and plot annotation) | Loops | Last remarks | References

Learning objectives | Introduction | Exploring sequence data | A simple measure of genetic distance | The Poisson correction | Some food for thought: | Building a molecular clock | Molecular clocks and inferences about deep-time | The Jukes-Cantor correction | The uncertainty of your molecular clock | Brief introduction to intervals derived from log-likelihood | References

What is R and how can I install it? | What is RStudio and how can I install it? | Starting R and RStudio: | Working Routine in R | Step 1: Setting work directory | Step 2: Checking working directory | Step 3: Saving files | Step 4: Compiling/knitting your RMarkdown | Step 5: Sourcing R scripts | Step 6: Loading external data | Step 7: Debbuging one specific strange behavior some students found | What is RMarkdown and how can I install it (optional)? | More on RMarkdown | RMarkdown advantages | An example of why RMarkdown is so neat: | RMarkdown practice (part I) | RMarkdown practice (part II)

Learning objectives | Introduction | Simulating phylogenetic trees | What affects speciation and extinction? | Shifts in diversification rates | References:

The fossil record: | Comparing molecular patterns

Learning objectives | Introduction | Exploring fossil occurrences | A brief introduction to temporal ranges | The K-Pg mass extinction | Something to think about: | The pull of the recent | Diversity patterns in deep time | The spatial distribution of the record | Drawing conclusions from the fossil record | Technical note: Dating fossils in absolute time | References:

Learning objectives | Introduction | Breeding effective population size | Mutation-drift equilibrium | Selection | The case of the peppered moths | References

Learning objectives | Introduction | The birth-death (BD) model | Glossary: | Deterministic expectations of the BD model | Estimation under the simplest BD | Effects of variation on the net diversification rate | The birth-death model is a stochastic process | Adding in extinction | Age-richness models and empirical richness through time | Some food for thought: | References:

Molecular phylogenies: | Diversification

Learning objectives | Introduction | Simple math notation | Probability of independent events | Random number generators and density/mass probability functions | Malthusian growth | Calculating and visualizing exponential growth in R | Mendelian genetics and Hardy-Weinberg Equilibrium (HWE) at a single locus | Kermode bear from British Columbia | Calculating allele frequencies from genotypes | A statistical approach to test for HWE and a given allele frequency | Heterozygosity | HWE, deleterious alleles, and mutation | Mendelian genetics at multiple loci | Describing genetic variation in DNA segments | References:

Hardy-Weinberg equilibrium | Genetic drift | Natural selection | References: