Population genomics of natural hybridization
Over decades biologists have debated what a species is. How are species being
formed and which evolutionary forces maintain species? The biological species
concept predicts that gene flow between species is rare. Nevertheless, in plants but
also in animals there is solid evidence that species boundaries are not complete. In
particular in geographic areas where species meet hybridization can be observed.
Genetic analyses of such hybrid zones indicated that genes could be exchanged
between species. While recent studies were restricted to a small number of genes or
neutral markers, the recent advances in sequencing technology provide for the first
time the opportunity to study the patterns of genetic exchange on the genome scale.
Using a combination of experimental and theoretical approaches students of the PhD
program have the exciting opportunity to apply the latest sequencing technology
(massive parallel sequencing) to hybrid zones in hares and Drosophila.
Prospective students could either have a background in theoretical, computational or
experimental biology. The nature of the PhD program requests a strong desire for
interdisciplinary and interactive research.
Available PhD projects
Development of new sequence alignment algorithms for massive parallel sequencing
data
With the advent of modern sequencing techniques, like the 454 sequencing machines,
a very large number of short sequence reads from the genome is accumulating. To
render a further process such data it is necessary to generate a consensus sequences
and to ensure high confidence in the determination of e.g. genetic differences. While
such approaches exist for typical large-scale genome approaches, we want to adapt
them to fit the needs for special population genetics questions. The project aims to
develop statistical tool distinguishing, for example, sequence artifacts and true
polymorphisms in a population sample. We also develop tools that account for the
technical glitches of the new technology to obtain unbiased population parameter
estimates.
Further questions should be addressed to Arndt v. Haeseler
Bayesian approaches to estimate population parameters from incomplete population
genomic data
Hybrid zones offer an opportunity for evolutionary biologists to explore concepts and
methods. These days, the number of selected loci that maintain a hybrid zone is
controversial: do only few, strongly selected loci maintain species identity, while the
rest of the genome is leaky, or does essentially the whole genome contribute, albeit
only weakly? It is proposed to model the genomic distribution of hybridization loci
(in analogy to quantitative trait loci,i.e. QTL),or segregation distorting loci, i.e., SDL)
and analyze genomic data of species in hybrid zones. Importantly, variable numbers
of loci will be modeled in a bayesian framework. As outcome, either few strongly
distorted regions or many mildly distorted regions are expected. Hence, an important
controversy in evolutionary biology can be approached cleanly.
Further questions should be addressed to Claus Vogl
Measuring gene flow between Drosophila/hare species by massive parallel
sequencing (2 positions)
Taking advantage of the latest technological advances in massive parallel sequencing
these two projects will develop new experimental approaches to measure gene flow in
hybrid zones by sequencing a large part of the genome. While the Drosophila project
takes full advantage of the available genome sequences and a very compact genome,
the hare project will develop new approaches to focus on the evolutionary important
genomic regions.
Further questions should be addressed to Christian Schlötterer (Drosophila) or Franz
Suchentrunk (hares)
The genomic signature of adaptive trait introgression
The aim of this project is to model adaptation in a recently diverged species pair.
Given a new environmental challenge for both species, there are two scenarios for an
adaptive response: The first possibility is that one of the species adapts first, and the
adaptation is then introgressed into the other one. Alternatively, each species develops
its own adaptive response. In the first scenario, selection locally enhances gene-flow,
in the second scenario it inhibits gene flow and can contribute to the species barrier if
both adaptations are incompatible (adaptive Dobzhansky-Muller incompatibilities).
We will use analytical methods based on coalescent theory and computer simulations
to analyze how the probability of each scenario depends on factors like selection
coefficients, mutation rates and hybrid fitness. We will further study the molecular
signature of inter-specific adaptations and compare our findings with molecular data.
Hybridization in camels
Microsatellites will be used to infer the degree of admixture between domestic and
wild camels.
Further questions should be addressed to Chris Walzer