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| W | Jan. | 20 | Class organization; Genetic transmission in populations | pp. 72-79 |
| F | 22 | Estimating allele frequencies | pp. 20-25 | |
| An example of the EM
algorithm
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| Notes on estimating allele
frequencies (including some homework problems)
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| Solutions to allele frequency estimation problems | ||||
| M | 25 | Testing Hardy-Weinberg | pp. 79-88 | |
| W | 27 | Inbreeding: Self-fertilization | ||
| Homework problems
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| F | 29 | Estimating mating system parameters | ||
| Problem #1
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| Estimating inbreeding coefficients with WinBUGS | ||||
| M | Feb. | 1 | Wahlund effect, Wright's F-statistics | pp. 111-135 |
| Examples of the
Wahlund effect
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| W | 3 | Genetic structure: Nei's Gst | ||
| Genetic data for Isotoma petraea | ||||
| F | 5 | Genetic structure: Weir & Cockerham's Theta | ||
| Project #1: Analyzing genetic
structure
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| Genetic data for Amblyomma dissimile | ||||
| Problem #1 due | ||||
| M | 8 | Two-locus population genetics (Steinbachs) | pp. 95-106 | |
| W | 10 | Review of statistical estimation and inference | ||
| Estimating selfing rates with WinBUGS | ||||
| F | 12 | Viability selection: One locus with two alleles (1) | pp. 211-236 | |
| Simulations of
natural selection
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| Population mean fitness with
viability selection
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| Notes and examples on selection at one
locus with two alleles
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| M | 15 | Viability selection: One locus with two alleles (2), Estimating viability | pp. 250-251 | |
| Project #1 Due | ||||
| W | 17 | Viabilty selection with multiple alleles; Fertility selection & sexual selection | pp. 255-256 | |
| Problem #2: Analyzing viability
selection
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| Analyzing viability selection with WinBUGS | ||||
| F | 19 | Fertility selection, sexual selection, and an introduction to genetic drift | ||
| Simulation of
genetic drift
|
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| M | 22 | Genetic drift (1) | pp. 267-277 | |
| Notes on genetic drift: fixation time,
selection, mutation, and migration
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| W | 24 | Genetic drift (2) | pp. 277-294 | |
| Problem #2 due | ||||
| F | 26 | Mutation, migration, and drift | pp. 294-296 | |
| Simulation of
mutation and genetic drift
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| Simulation of
migration and genetic drift
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| M | Mar. | 1 | Selection and drift | |
| W | 3 | The coalescent | pp. 304-310 | |
| Problem #3: Inferring
migration
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| F | 5 | No class | ||
| M | 8 | The coalescent and Fst | ||
| W | 10 | Wright's shifting balance theory | pp. 259-262 | |
| The t-allele polymorphism in Mus musculus | ||||
| Simulation of the t-allele
polymorphism
|
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| F | 12 | Temporal and spatial variation in selection | ||
| Problem #3 due | ||||
| M | 15 | No class, spring break | ||
| W | 17 | No class, spring break | ||
| F | 19 | No class, spring break | ||
| M | 22 | Quantitative genetics: the genetic components of variance | pp. 424-434 | |
| The genetic components
of variance
|
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| W | 24 | Quantitative genetics: estimating variance components (1) | pp. 442-445 | |
| Resemblance between
relatives
|
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| Estimating migration rates with WinBUGS | ||||
| F | 25 | Computer lab on variance components (Steinbachs) | ||
| Partitioning variance
with S-Plus
|
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| M | 29 | Quantitative genetics: estimating variance components (2) | ||
| W | 31 | Fisher's Fundamental Theorem of Natural Selection | ||
| Fisher's Fundamental Theorem;
Response to selection
|
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| Partitioning variance
with WinBugs
|
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| Problem #4: Estimating variance components -- Description, Data
(WinBUGS), Data (S-Plus) |
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| F | Apr. | 2 | Quantitative genetics: response to selection | pp. 461-467 |
| Response to selection
in quantitative traits
|
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| Beak size in Darwin's Finches | ||||
| M | 5 | Selection on correlated characters | pp. 448-460 | |
| Selection on multiple
characters
|
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| Cumulative selection
gradients in a garter snake
|
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| W | 7 | Norms of reaction | pp. 448-452 | |
| F | 9 | Mapping quantitative trait loci: principles | pp. 467-476 | |
| Mapping quantitative trait
loci
|
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| Problem #4 due | ||||
| M | 12 | Mapping quantitative trait loci: applications | ||
| Mapping quantitative trait
loci with Mapmaker/QTL
|
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| Project #2: Mapping QTL's -- Description, Data (in
Mapmaker RAW format) |
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| W | 14 | The Neutral Theory of Molecular Evolution | pp. 315-338 | |
| F | 16 | Patterns of nucleotide and amino acid substitution (1) | pp. 338-349 | |
| Divergence of nucleotide
sequences, diversity within and among populations
|
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| Divergence of DNA
sequences
|
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| M | 19 | Patterns of nucleotide and amino acid substitution (2) | pp. 349-368 | |
| W | 21 | Detecting selection on nucleotide sequences (1) | ||
| F | 23 | Detecting selection on nucleotide sequences (2) | ||
| Analysis of synonymous vs. non-synonymous substitutions: Local, HIV Sequence Database | ||||
| Project #2 due | ||||
| M | 26 | Evolution in multigene families | pp. 374-390 |
|
| Problem #5: Detecting selection on nucleotide sequences | ||||
| W | 28 | Reconstructing phylogenetic history: principles | pp. 368-374 | |
| F | 30 | Reconstructing phylogenetic history: applications (Steinbachs) | ||
| S-RNAse sequences (example) | ||||
| PHYLIP documentation (in HTML) | ||||
| PHYLIP server | ||||
| M | May | 3 | Joint analysis of selection and phylogenetic history | |
| Problem #5 due | ||||
| Project #3: Molecular evolution and phylogeny | ||||
| Project #3: Molecular evolution and phylogeny -- Data and additional instructions | ||||
| M | 10 | Project #3 due |
