Introduction to coalescence theory

5-8 September 2011 - CLOSED

Faculty:

Prof. J. Novembre, University of California, USA
Dr. M.G.B. Blum, University of Grenoble, France
Prof. L. Excoffier, University of Bern, Switzerland
Dr. M. Foll, University of Bern, Switzerland

A joint course with the doctoral program in Population Genomics

Organizer

Prof. Laurent Excoffier

Program Outline

Coalescent theory with practical applications

Day 1

* Refreshment on basic laws of probabilities
* Gene genealogies and coalescent in a stationary population
* Effect of demographic changes on the coalescent
* Mutation models
* Simulation of the coalescent process. Programming the coalescent in R

Day 2

* Coalescent in a structured population
* Coalescent models with recombination
* Coalescent models with selection
* Introduction to various coalescent-based simulation programs
   (e.g. ms, msms, MaCS, selSim, fastsimcoal, Splatche)

Day 3

* Use of coalescent simulations to estimate model parameters
   o Approximate Bayesian Computations (ABC)
   o Composite likelihoods
* Model choice under ABC
* Description of packages to perform ABC (DIY ABC, ABCtoolbox)

Day 4

* Coalescent processes during spatial expansions
* Relationships between coalescent times, summary statistics
   (e.g. F-statistics, linkage disequilibrium), and principal component analysis (PCA).
* Non-coalescent approaches for modeling demography and selection (diffusion theory,
   Poisson random fields models)
* Practical analysis of DNA sequence and microsatellite data

Prerequisites

Participants need to have followed some basic population genetics course, and need to have a basic knowledge of programming or R.

Bern

General information

Time: Course starts on Monday, 9 am; full day; exact hours tba
Location: University of Bern, Baltzerstrasse 6, Practical Room
Number of participants: max. 20

Participants need to bring their own laptop.

Contact

Ute Friedrich
Coordinator of the Doctoral Program
in Population Genomics
Le Biophore, UNIL-Sorge
University of Lausanne
1015 Lausanne
Phone: +41 (0)21 692 4276
Fax : +41 21 692 4165
Email: Ute.Friedrich[@]unil.ch

here

Priority is given to PhD students form the doctoral programs in Ecology & Evolution and Population Genomics.

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