How often were housekeeping genes transferred between divergent organisms? It appears that these events were infrequent enough to extract the organismal evolution from the simultaneous analyses of different molecular markers. The transfer of housekeeping genes can be used to correlate the evolution in different parts of the tree of life.

By which mechanisms are transferred genes incorporated into the recipient genome?

What are the units of gene transfer? (Single genes, gene clusters, gene fragments)

Are most gene transfers neutral or nearly neutral to the recipient? Is gene loss the most common fate of recently acquired genes?

Inteins are intervening sequences that are transcribed and translated into protein. Only at the level of the protein do they self-splice themselves out of the host protein. Inteins are found in pro- and eukaryotes. Usually they are located in the most conserved (and most important) part of the host protein. Do inteins confer any benefit to the organism? How do they spread between organisms?

Genes that adapt an organism to an ecological niche (which could be temporary) can be acquired through horizontal gene transfer (antibiotic or heavy metal resistance, genes that allow access to a new food source). Are the genes, and not the species, the most important factor in the ecological system?

Develop tools to reliably assess the frequency of genes within populations (inteins and other molecular parasites // genes that reflect a within population division of labor) from metagenomic data.

What is the function of rare genes in microbial populations? How can these be maintained over long periods of time?

How can one avoid artifacts due to small genomes, compositional bias and changing substitution rates? Under which conditions are Super-tree or Super-matrix approaches more reliable?

What were the properties of the early eukaryotes? How did the different parts of the eukaryotic cell originate? Using V-ATPase A-subunits as molecular markers, we try to identify early branching eukaryotic lineages. This V-ATPase subunit appears more appropriate than other proteins and RNAs, because it contains many sites that are slow to undergo substitutions, and because the outgroup (archaeal ATPase catalytic subunits) is connected to the ingroup by a comparatively short branch. Some frequently encountered artifacts (e.g. microsporidia as a deep branching lineage) are not encountered when analyzing V-ATPase catalytic subunits.

How do enzymes with new properties (regulation of expression, enzyme properties) arise?
How is selection pressure maintained on nearly identical gene copies?

Different sites in proteins experience substitution events with different probability. This process, called 'among site rate variation', and 'substitution bias' greatly influence the velocity with which sequences accumulate observable differences. Accurate correction for multiple substitutions is necessary to precisely reconstruct the evolutionary history of proteins, and to date the early evolution with respect to time.

Do changes in the quaternary structure of ATPases correlate to changes in physiologic function? (proton pumping ATPase versus ATPsynthase?)
Did early eukaryotes use their V-ATPase for ATPsynthesis?
Was the eukaryotic ancestor an acidophile?
Is the subunit stoichiometry related to the ATP/proton ratio?