[BBC] [Gtpb] GTPB Bioinformatics Training Course Announcement
Pedro Fernandes
pfern at igc.gulbenkian.pt
Mon Jun 15 17:07:27 CEST 2015
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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