Forschungspraktikum: winter and summer semester


Forschungspraktikum: in silico Evolutionsgenetik von Pflanzen und Pathogenen

Practical course: in silico Evolutionary Genetics of Plants and Pathogens

Topics for forschungspraktikum:

1) Computer-based evolutionary genetics

Modern research in evolutionary biology demands the integration of sequence data with theoretical tools of simulations. This requires solid computational skills, including knowledge of various biological data resources, and usage of simulation softwares. During the course, students will 1) practice with some common data analysis methods of high throughput technology, such as next generation sequencing and whole genome sequencing, 2)  learn how to make use of existing biological databases and 3) perform coalescent simulations to tests evolutionary scenarios.

For whom? Master students interested in fundamental aspects of plant or pathogen evolution with desire to learn state of the art population genomics tools

 

2) Applied evolutionary genetics

Modern research in evolutionary biology demands the integration of sequence data with phenotypic measurements. Using the wild tomato species as a model system, several experiments on different populations of S. chilense will be performed. Experiments will include 1) infection of plants with bacteria, oomycete and fungal pathogens, and 2) measuring the response of plants to abiotic stresses (drought, cold). The results of these experiments will be connected to sequence data analysis using population genetics approaches.

For whom? Master students interested in fundamental aspects of plant evolution with desire to learn population genetics and experimental approaches in evolutionary biology.

 

If you are interested, please contact Prof. Dr. Aurelien Tellier

 

 

 


Summer semester

Description:

This course will provide examples and understanding of evolutionary processes occuring in agriculture and comparisons with wild plant populations. The stress will be put on how understanding theoretical aspects of evolutionary theory allows to understand the evolution of plant and pathogen species. The aim is to use such knowledge to derive more sustainable disease management strategies in agriculture, and understand the evolution of plant-pathogen systems in the wild.

Content:
1) Plant pathology and epidemiology

2) Host-parasite coevolution
3) Evolution of pesticide/fungicide resistance
4) Evolution of aggressiveness of pathogens in the field

For whom? Master students interested in plant and parasite evolution, especially how these species (co)evolve in agricultural systems or in natural habitats.

 

 

Summer semester

We will look at key questions in evolution using short lecture and reading of book chapters or articles (2 weeks on each topic).

Content:
1) Epigenetics and Evolution: return of Lamarckism? ;
2) Evolution of cooperation and society: game theory, kin selection and inclusive fitness ;
3) Ecology and evolution: levels of selection, metagenomics and holobionts ;
4) Experimental evolution in real time in the lab;
5) Origin of evolutionary innovations.

For whom? Master students interested in understanding evolution, and recent unsanswered questions in the field.

 

 


Winter semester

Description:

This course will cover fundamental aspects of evolutionary genetics. Namely we will study how populations evolve and the processes involved. Examples will be taken from the plant kingdom and from various species of plant pathogens: Arabidopsis thaliana, wild tomato species (our own studies) and rice for plants, and rusts or mildews for pathogens.
A seminar part will deal with studying the evolutionary processes occuring during domestication of crops (maize, wheat, tomato, barley, rice).
This course will provide bases for understanding statistical tests used in animal, plant and parasite evolutionary genomics.

Content:

1) Molecular Evolution: Hardy-Weinberg equilibrium, neutral model of evolution, mutation-drift equilibrium, natural selection, speciation models, molecular clock, sexual reproduction and recombination (Red Queen hypothesis).
2) Population Genetics and application to Genomic analyses in plants and micro-organisms: coalescent models, Muller’s ratchet, Genomic applications of the coalescent: tests of selection, Spatial structure of populations.
3) Population genetics and plant domestication:history of plant domestication, examples of domestication processes, genomic signatures of domestication.

For whom? Master students interested in understanding evolution and the molecular bases of adaptation, i.e. how populations and species adapt to diverse physical environments and coevolve with other species.

 

 

Winter semester

Description:

This course will provide examples and understanding of speciation processes. The stress will be put on how understanding evolutionary genetics allows us to understand the evolution and appearance of species.

The course is done with Prof. Hanno Schäfer and consists of five parts:

1) Population genetics of recent speciation: speciation models, DM incompatibilities, data analysis of sister species
2) Phylogenetics: BEST, Maximum Parsimony, Maximum Likelihood, Bayesian Methods (with/without relaxed clock) - BEAST
3) Structure software to analyse recent divergence
4) Network analysis
5) Analysis of selection over phylogenetic time scales (PAML)


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