The primary, if not the only, objects of evolutionary biology were multicellular eukaryotes, primarily animals and plants, when Charles Darwin formulated the fundamental ideas of evolutionary biology in The Origin of Species, and the architects of the Modern Synthesis integrated these ideas with population genetics almost a century later. All attempts to apply evolutionary studies to bacteria had been fruitless prior to the development of effective genome sequencing. The development of the three-domain "ribosomalttree ofllife," which was widely believed to have clarified the evolutionary links between the cellular life forms, was made possible by the sequencing of the rRNA genes in thousands of microorganisms. The most fundamental of these are pervasive Horizontal Gene Transfer (HGT), which shapes the genomes of bacteria and archaea and requires a radical revision (if not abandonment) of the Tree of Life concept; Lamarckian-type inheritance, which appears to be crucial for antivirusddefense; and other types of adversity. Phylogenomics and metagenomics of virusesaand theirtheird associated selfish genetic elements in the noncellular portion of the microbial world have shown vast genetic and molecular diversity as well as an extraordinarily high abundance of viruses, which appear to be the dominant biological entities on earth. Furthermore, one of the key characteristics of evolution is the ongoing competition between viruses and their hosts. Thus, even while Darwin's discovery of the principle of descent with modification and the principles of population genetics remain at the foundation of evolutionary biology, microbial phylogenomics expands on the basic picture of evolution
