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 Notes on estimating allele frequencies (including some homework problems)
M		29	Testing Hardy-Weinberg
W		31	Inbreeding: Self-fertilization
	Lab		Introduction to WinBUGS and Bayesian statistics Allele frequencies in the ABO blood group Problem 1: Estimating mating system parameters
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
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 Genetic data for Amblyomma dissimile Problem 1 due Solutions
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 Population mean fitness with viability selection
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 Problem 2 due Solution 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 Simulation of migration and genetic drift
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 Simulation of the t-allele polymorphism 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
W		28	Quantitative genetics: estimating variance components (1) Resemblance among relatives
	Lab		Estimating variance components Partitioning variance components with WinBUGS 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
W		4	Quantitative genetics: response to selection Response to selection in quantitative traits
F		6	Selection on multiple characters Cumulative selection gradients Drift in quantitative traits
M		9	Norms of reaction Mapping quantitative trait loci: principles PDF version of notes Problem 4 due
W		11	Mapping quantitative trait loci: applications
	Lab		Mapping QTLs with QTL Cartographer PDF version of the notes 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
	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

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