[BBC] [Gtpb] PGDH18 Course announcement / Reminder

[GTPB Administration]

                        Course Announcement / Reminder
PGDH18
Population Genetics and Demographic History:
model-based approaches

with Mark Beaumont, Lounès Chikhi, Willy Rodriguez and Vitor Sousa

Key terms: Model-based Population Genetics

    IMPORTANT DATES for this Course
    Deadline for applications: May 4th 2018
    Course date: May 14th - May 18th 2018


The GTPB is proud to announce that the above referenced hands-on  
training course is open for applications


Admission:
Candidates with adequate profile will be accepted in the next 72 hours  
after the application until we reach 20 participants.

Course description:
Genetic and genomic 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 and genomic 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 five-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. We will also introduce  
methods that have been recently developed to analyse genomic data such  
as the PSMC method of Li and Durbin that reconstructs the demographic  
history of a species or population with the genome of a single  
individual.

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  
infer demographic history. We will learn how to perform coalescent  
simulations of genetic/genomic data (using mainly Richard Hudson's ms  
program). We will also show how to simulate data for PSMC analyses.  
This will allow users to compare the PSMC obtained with real data to  
those obtained for the models they used. We will also look at how  
habitat fragmentation can be simulated using an in-house program. 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.


More information at the GTPB website,
http://gtpb.igc.gulbenkian.pt/bicourses/2018/PGDH18/

Hoping that this course meets your interests,

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

-- 
The Gulbenkian Training Programme in Bioinformatics
General Office
Rua da Quinta Grande, 6
2780-156 OEIRAS
Portugal

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