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You are hereDoctoral Program in Population Genomics > ACTIVITIES > Activities 2011 > Coalescent Theory

Introduction to Coalescent Theory

September 5 - 8, 2011, BERN


Prof. Laurent Excoffier

This is a joint course between the Population Genomics Program
and the Doctoral Program in Ecology and Evolution


Dr. Miguel Arenas, University of Berne, Switzerland
Dr. Michael G.B. Blum, University of Grenoble, France
Prof. Laurent Excoffier, University of Bern, Switzerland
Dr. Matthieu Foll, University of Bern, Switzerland
Prof. John Novembre, University of California, USA

Program Outline

Coalescent theory with practical applications

Day 1

08:45 Registration and coffee break
09:30 Introduction to the course
10:00 Refreshment on basic laws of probabilities and probability distributions
12:00 Lunch
13:30 Coalescent in a stationary population, effect of demographic changes, mutations, introduction to fastsimcoal and FigTree
15:30 Coffee break
16:00 Programming the coalescent in R, computing summary statistics with fastsimcoal
17:30 End

Day 2

08:30 Coalescent in a structured population, Coalescent processes during spatial expansions (Splatche)
10:00 Coffee break
10:30 Coalescent models with recombination
11:15 Coalescent models with selection
12:00 Lunch
13:30 Coalescent models with selection, part 2
14:00 Coalescent simulation of coding data
14:45 Introduction to various coalescent-based simulation programs
15:30 Coffee break
16:00 Use of various coalescent-based simulation programs
17:30 End

Day 3

08:30 Bayesian statistics, Approximate Bayesian Computations, parameter inference
10:00 Coffee break
10:30 Model selection, cross-validation, goodness of fit
12:00 Lunch
13:30 Estimation of demographic parameters from the (joint) site frequency spectrum using fastsimcoal
14:30 Practicals in ABC
15:30 Coffee break
16:00 Practicals in ABC
17:30 End

Day 4

08:30 Relation between the coalescent, summary statistics (molecular diversity indices, FST, linkage disequilibrium indices), and principal component analysis (PCA).
10:00 Coffee break
10:30 Non-coalescent approaches for modeling demography and selection (diffusion theory, Poisson random fields models, ∂a∂i)
12:00 Lunch
13:30 Practicals
15:30 Coffee break
16:00 Final address, evaluation, conclusion

General information

Date: September 5-8, 2011
Time: Course starts on Monday, 8.45 am
Location: University of Bern, Baltzerstrasse 6, Practical Room D010
Number of participants: 25

Participants need to bring their own laptop.


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



Priority is given to PhD students of the Doctoral Programs in Population Genomics & Ecology and Evolution until July 27, 2011. After this deadline, registration is open on a first-come, first served basis. The course is limited to 25 people.

Deadline for all applications is August 15, 2011, and confirmations will be sent shortly after.

Note that travel, lodging and meals have to be organized by the participants themselves, who also need to bring their own laptop. Members of the Doctoral Program Population Genomics and members of the CUSO Doctoral Program in Ecology and Evolution can ask for reimbursement of their expenses for travel, accommodation, and meals.


Ute Friedrich
Le Biophore, UNIL-Sorge
University of Lausanne
1015 Lausanne
Phone: +41 (0)21 692 4207
Email: Ute.Friedrich[@]unil.ch


Registration CLOSED

Biophore - CH-1015 Lausanne  - Switzerland  -  Tel. +41 21 692 42 76