Download The genetics and bioinformatics of haploid selection We are looking

The genetics and bioinformatics of haploid selection
We are looking for an MSc/project student with a strong interest in population
genetics and bioinformatics to perform a project under the supervision of Simone
Immler (http://www.ieg.uu.se/evolutionary-biology/immler/) and Douglas Scofield at
the Department of Ecology and Genetics/Evolutionary Biology.
Project background: Evolutionary conflicts resulting from genetic differences
between units of selection across different levels of biological organisation (e.g.
species, sexes, individuals, cells, organelles and genes form the basis of most fields of
evolutionary biology. The biphasic life cycle with alternating diploid and haploid
phases is one of the consequences of the evolution of sex in eukaryotes. The
occurrence of selection during both phases has far reaching consequences for many
evolutionary processes. In plants, the importance of a biphasic life cycle is well
established, but in animals, long-standing dogma favouring the diploid genome has
resulted in haploid selection having been largely discarded. However, there is
growing evidence that genetic and epigenetic effects transferred through gametes may
affect the fitness of offspring, as exemplified by very recent results produced in our
lab which show provide striking evidence for an effect of sperm phenotypes on
offspring fitness and establish links between these sperm phenotypes and the
underlying sperm genotypes.
Despite many other recent developments in population genetics and
bioinformatics, we are lacking a theoretical framework that would allow us to
establish null hypotheses and make predictions in the context of natural and
experimental haploid selection. The primary reason for this is that the structure of
genetic transmission within such datasets is not equivalent to ‘population’ structure as
traditionally studied. Hence, existing theory is suboptimal at best.
Project aim: The aim of this project is to begin to develop just this theoretical
framework, using population genetics and bioinformatics tools. With the help of the
NGS and experimental data produced in our lab, we aim to develop and test
theoretical models of genetic transmission within pools of haploid gametes. It is clear
that even with pervasive haploid selection, nonselective sampling must occur among
gametes in nature. Therefore, it is important that the theory includes sampling effects
from the start.
The first goal of the project is to develop null expectations for allele frequency
spectra (AFS) and linkage disequilibria (LD) between loci within pools of gametes, to
establish baseline expectations in the absence of selection. One example question that
could be addressed is, how genomically unique are gametes within a pool?
Project size and requirements: This project is suitable for MSc students or 15 hp
research project students. The student should have a good knowledge of bioinformatics
and ideally some population genetics (but that can be acquired during the project).
If you are interested, please send an email to Simone Immler
([email protected]).