[BBC] [Gtpb] GTPB Bioinformatics Training Course Announcement

[Pedro Fernandes]

ANNOUNCEMENT / REMINDER


Dear Research

Applications are open for


PGDH15
Population Genetics and Demographic History: model-based approaches

with Mark Beaumont, Lounes Chikhi, Willy Rodriguez and Barbara Parreira

    IMPORTANT DATES for this Course
    Deadline for applications: June 28th 2015
    Latest notification of acceptance: July 1st 2015
    Course date: July 6th - July 9th 2015

Details are available at:
http://gtpb.igc.gulbenkian.pt/bicourses/PGDH15/

Course description
Genetic data are increasingly used by ecologists and evolutionary  
biologists in general. It has thus become important for many  
biologists with different levels of experience to produce and analyse  
genetic (and genomic) data. In this course we will take a practical  
approach to the analysis of genetic data, but we will also provide  
some of the theoretical background required to understand the outputs  
of the software used. This course will be organised so as to mix  
lectures where important notions are introduced with practicals where  
freely available software will be used. While this will not be the  
focus of the course, we will also introduce and discuss genealogical  
(coalescent-based) simulation methods and those based on  
forward-in-time simulations. Altogether this will allow to discuss the  
potentialities and limitations of the tools available to the community.

In this four-day course we will introduce the main concepts that  
underlie many of the models that are frequently used in population  
genetics. We will focus on the importance of demographic history (e.g.  
effective sizes and migration patterns) in shaping genetic data. We  
will go through the basic notions that are central to population  
genetics, insisting particularly on the statistics used to measure  
genetic diversity and population differentiation. The course will also  
cover a short introduction to coalescent theory, Bayesian inference in  
population genetics and data simulation, as they are connected to what  
makes landscape genetics today on the basis of multilocus data. We  
will also introduce two methods that have been recently developed to  
analyse genomic data. The PSMC of Li and Durbin reconstructs the  
demographic history of a species or population with the genome of a  
single individual. The Rehh package is an R implementation of the  
Extended Haplotype Homozygosity (EHH) test for selective sweeps and  
looks for signals of selection based on the analysis of genomic regions.

Most theory will be put into practice in practical sessions, analyzing  
real and/or simulated datasets. In these sessions, we will look at  
measures of genetic diversity and differentiation and use methods to  
detect population structure as implemented in the program STRUCTURE  
and discuss related programs such as FastSTRUCTURE. We will learn how  
to perform coalescent simulations of genetic data (using SPAms and  
ms). Some exercises will make use of R scripts (R being a freely  
available statistical program). Basic R knowledge is a pre-requisite  
but we will provide a short introduction to R. The R statistical  
package is a very powerful tool to analyse data outputs from many  
population genetics software, and can also be used to simulate genetic  
data under simple demographic scenarios.

Thanks for your interest,
Pedro

-- 
Pedro Fernandes
GTPB Coordinator
Instituto Gulbenkian de Ciência
Apartado 14
2781-901 OEIRAS
PORTUGAL
Tel +351 21 4407912
http://gtpb.igc.gulbenkian.pt


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