Ribosomal genes are used to construct evolutionary hypotheses regarding prokaryotic relationships. These relationships are then used to guide taxonomic classification. Central to the use of ribosomal genes in this capacity are the assumptions that these genes evolve in a tree-like manner and never undergo horizontal gene transfer. Various examples within the body of published research contradict these assumptions, suggest that horizontal transfer does occur and furthermore results in mosaic ribosomal RNA genes. The research that is presented in this dissertation was undertaken in order to document the incidence and gauge the extent of horizontal transfer of ribosomal genes among a particular group of organisms, the hyperthermophilic archaebacterial eocytes (Crenarchaeota).

Horizontal transfer of ribosomal RNA genes was inferred from detecting recombination between ribosomal RNA genes from different taxa. For a small case example, it was shown that the spatial partition of the alignment corresponds to unique and well-supported phylogenetic signals. Bulk analyses provided evidence that extensive horizontal transfer has occurred during the evolutionary history of the ribosomal RNA genes possessed by the majority of cultivated archaebacterial eocytes. Ribosomal proteins were also shown to undergo frequent horizontal transfer, with at most five out of twenty eight ribosomal proteins sharing a pathway through the ancestral population that gave rise to the modern day eocytes.

These results make it clear that the ribosome as a whole does not evolve according to a strict tree-like process. Instead, frequent exchange of ribosomal components gives rise to a population structure for this ubiquitous and essential molecular machine. As such, care should be undertaken when interpreting phylogenies calculated using ribosomal genes. Rather than providing evidence of relatedness by vertical descent, these phylogenies may instead be placing taxa together that have undergone recent ribosomal gene exchange.