General Biology Seminar

The advances of comparative genomics and phylogenomics call for replacement of the key models of molecular evolution by a new generation of more general models. The dominance of horizontal gene transfer (HGT) in the evolution of prokaryotes undermines the classical Tree of Life (TOL) concept.  The notion of a single TOL is giving way to the model of a phylogenetic network that, however, is shown to encompass a tree-like central trend. Genome-wide comparison of phylogenetic trees also bears on the Molecular Clock model. It has been long known that the Molecular Clock is substantially overdispersed. I will show that the new model of Universal Pacemaker of genome evolution that only requires the conservation of relative rates of gene evolution, in contrast to the conservation of absolute rates inherent in Molecular Clock, yields a better fit to the phylogenomic data for diverse organisms. Finally, I will present the pangenome concept that replaces the traditional notion of a species genome. A mathematical model of pangenome evolution resulting in robust estimates of the pangenome size for prokaryotes will be presented. The results of the pangenome evolution modeling indicate that the entire gene universe of prokaryotes might include only about one million genes. The new, general models of evolution do not refute the classic models but include them as extreme cases, in a pattern that appears common in the history of science.