[BBC] [Gtpb] PGDH18 Course announcement / Reminder
GTPB Administration
bicourses at igc.gulbenkian.pt
Mon Apr 2 10:41:35 CEST 2018
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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