3. Phylogenetics: Evolution of microbial diversity

• Mutations, horizontal gene transfer (conjugation, transformation, transduction) , selection, symbioses, cellular compartmentalization.
• Consequences of lateral gene transfer on phylogeny, plasmid structures and plasmid propagation, transposable elements.
• Prerequisits for rapid expression of new traits: haploid chromosome, plasmids, DNA-exchange and insertion mechanisms, small genome size (500kb to 10mb), rapid growth rate.
• Evolutionary experiments with microbes.
• Ecology of spreading genes and selection of microbes that carry them.
• The role of high temperatures for early evolutionary processes.
• Evolution of microbial symbioses, incl. symbioses in eukaryotic cells.

• Biological databases for the study of microbial evolution: physiology, genomics, phylogeny.
• Molecular records of the biosphere: databases containing genome and protein sequences.
• Evolutionary models based on functional bioinformatics.
• How large is the essential genome ?

• The three domains (kingdoms) of organisms: Bacteria, Archaea and Eukarya.
• What are the forces that select for differentiated cells and not for the unified cell ?
• Criteria defining evolutionary relatedness: what distignuishes the three domains (kingdoms) of life ?
• Phylogenetic trees based on 16S-rRNA, backgrounds and construction.
• Phylogeny and taxonomy: metabolic genomics beyond phylogenetic trees.
• Metabolic phylogeny in the Archaea domain (kingdom), in the Bacteria domain (kingdom).
• Phylogeny of microbial eukaryotes from anoxic environments.
• Environmental evolutionary driving forces: effects of mass extinction phases, new radiations in the tree.

• Strategies and methods to analyze mixed population DNA.
• DNA/DNA hybridization for analyses of microbial communities: FISH and Checkerboard-Hybridization.
• Environmental genomics, novel organisms.