**September 5 - 8, 2011, BERN **

### Organizer

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

### Faculty

**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.*

**Prerequisites**

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

### Registration

**CLOSED **

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. *

### Contact

Ute Friedrich

Coordinator

Le Biophore, UNIL-Sorge

University of Lausanne

1015 Lausanne

Phone: +41 (0)21 692 4207

Email: Ute.Friedrich[@]unil.ch