Genomic and phylogenetic perspectives on the evolution of prokaryotes

Abstract.—Prokaryoteshavebeenat the forefrontof the genomesequencing revolution.Manygenomes havebeencompletely sequenced, revealingmuchabout bacterial and archaeal genome content and or-ganization. Yet, a meaningful evolutionary picture of prokaryotes still eludes us. Much of the problem lies in understanding the mode and tempo of genome evolution. Here phenylalanyl-tRNA synthetase is used as an example of the complex interplay among lateral gene transfer, operon recombination, and gene recruitment in the evolution of some prokaryotic genes. Promising new approaches to genomic analyses, which could add to our understanding prokaryotic evolution and help in their classication, are discussed. [Archaea; comparative genomics; eubacteria; phenylalanyl-tRNA synthetase; universal tree.] An understanding of the evolutionary re-lationships among prokaryotes—the most abundant and diverse life forms on the planet—is essential. The important impact of prokaryotes on human health and economy as well as their key role in eukaryotic evolu