Reductive evolution of microbial genomes
We study the evolutionary links between the three cellular domains: Archaea, Bacteria and Eukaryotes. In contrast to conventional wisdom, all the available phylogenomic, proteomic and paleontological data suggest that Eukaryotes are the ancestors of both Archaea and Bacteria. The embarrassing fact is that the characteristic features of eukaryotic cells cannot be explained by the traditional endosymbiotic theory, which postulates the evolution of eukaryotes from a fusion of Archaea and Bacteria. Rather, it appears that stringent selection for maximal growth rates has supported the metabolic specializations and correlated reductive evolution of Archaea and Bacteria from their Eukaryote ancestors.
The data demonstrate that the intensity of that reductive selection depends on large population sizes, but this same selective pressure is inversely proportional to the complexity of proteomes. As a consequence small populations of complex Eukaryotes in general are less intensively driven by stringent reductive pressure than are the large populations of Archaea and Bacteria, with their numerically simpler proteomes. In addition to minimization of proteome complexity (genome coding capacity) reductive evolution in Archaea and Bacteria is expressed at the level of individual protein sequences, which are shorter than their eukaryote homologues.
Our current research focuses on large-scale phylogenomic methods to further define the deep phylogenetic relationships between domains of organisms. We also explore the ecological adaptations of modern organisms that support reductive evolution among some eukaryotes such as fungi and protozoa.