Population Genetics

Ecology and Evolutionary Biology 348

Tentative Lecture Schedule

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W Jan. 24 Class organization; Genetic transmission in populations
F
26 Hardy-Weinberg, Estimating allele frequencies
An example of the EM algorithm java
Notes on estimating allele frequencies (including some homework problems) disk
M
29 Testing Hardy-Weinberg
W
31 Inbreeding: Self-fertilization

Lab
Introduction to WinBUGS and Bayesian statistics
Allele frequencies in the ABO blood group WinBUGS
Problem 1: Estimating mating system parameters disk
F Feb. 2 Estimating selfing rates, Identity by descent
Estimating inbreeding coefficients with partial dominance (sample code for WinBUGS)
M
5 Wahlund effect, Wright's F-statistics



Examples of the Wahlund effect java
W
7 Genetic structure: Nei's Gst
Analyzing the genetic structure of populations

Lab
GDA and Arlequin
Genetic data for Isotoma petraea
Nexus (for GDA)
ARP (for Arlequin)
F
9 Genetic structure: Weir & Cockerham's Theta
Genetic data for Isotoma petraea with populations artificially grouped for illustrating a multi-level hierarchy
Nexus (for GDA)
ARP (for Arlequin)
Project 1: Analyzing genetic structure disk
Genetic data for Amblyomma dissimile
Problem 1 due
Solutions disk
M
12 No class
W
14 Two-locus population genetics
F
16 Viability selection: One locus with two alleles
M
19 Viability selection at one locus with two alleles (continued)
Simulations of natural selection java
Population mean fitness with viability selection java
W
21 Estimating viability, selection at one locus with multiple alleles
F
23 Fertility selection & sexual selection
Problem 2: Analyzing viability selection
Project 1 Due
M
26 Selection component analysis
W
28 Genetic drift (1)
F Mar. 2 Genetic drift (2)
Simulation of genetic drift java
Problem 2 due
Solution disk
WinBUGS code for the solution (as a plain ASCII text file)
M
5 Class canceled due to threatened winter storm
W
7 Mutation, migration, and drift
Simulation of mutation and genetic drift java
Simulation of migration and genetic drift java
F
9 Introduction to migration
Problem 3: Inferring migration
M
12 Migration (concluded)
W
14 The coalescent
F
16 Natural selection and genetic drift
Simulation of selection and genetic drift java
Simulation of the t-allele polymorphism java
Problem 3 due
M
19 No class, spring break
W
21 No class, spring break
F
23 No class, spring break
M
26 Introduction to quantitative genetics: the genetic components of variance PDF
W
28 Quantitative genetics: estimating variance components (1)
Resemblance among relatives PDF

Lab
Estimating variance components
Partitioning variance components with WinBUGS PDF
Sample WinBUGS code and data
F
30 Quantitative genetics: estimating variance components (2)
Problem 4: Estimating variance components
Offspring data offspring-data.txt
Fitness data fitness-data.txt
Examples of WinBUGS analyses introductory-examples.odc
M Apr. 2 Fisher's Fundamental Theorem of Natural Selection PDF
W
4 Quantitative genetics: response to selection
Response to selection in quantitative traits java
F
6 Selection on multiple characters PDF
Cumulative selection gradients PDF
Drift in quantitative traits PDF
M
9 Norms of reaction
Mapping quantitative trait loci: principles PDF version of notes disk
Problem 4 due
W
11 Mapping quantitative trait loci: applications

Lab
Mapping QTLs with QTL Cartographer
PDF version of the notes PDF
Map data (realdatm.inp)
Cross data (realdatc.inp)
User Manual for QTL Cartographer
F
13 Evolutionary quantitative genetics
M
16 Introduction to molecular population genetics
Project 2: Mapping QTLs
Data for mapping project (simulated.mcd)
W
18 No class
F
20 No class
M
23 The Neutral Theory of Molecular Evolution
W
25 Patterns of nucleotide and amino acid substitution
Divergence of DNA sequences java

Lab
Arlequin and analysis of selection on nucleotide sequences
F
27 Detecting selection on nucleotide sequences
Analysis of synonymous vs. non-synonymous substitutions: HIV Sequence Database
M
30 Patterns of selection on single-copy genes
Problem 5: Detecting selection on nucleotide sequences
Data in PHYLIP interleaved format
Data in Arlequin format
Project 2 due
W May 2 Evolution in multigene families

Lab
AMOVA and nested clade analysis
F
4 Divergence of populations
M
7 Phylogeography
Problem 5 due



Project 3: Phylogeography of Hawaiian damselflies
Data in Arlequin format
Data in nucleodi format
Map of the Big Island showing locations of population samples
Tu
15 Project 3 due


kent@darwin.eeb.uconn.edu
Last modified: Fri May 11 11:55:50 Eastern Daylight Time 2001