A great discovery in the past 30 years has been a tree of life based on the molecular histories of genes. Now our histories of microorganisms rival those of plant and animals, even though the time spanned is more than 30 times that of, for example, the diversification of mammals. Although this might seem of only academic interest, it has revolutionized our understanding of life, and has revealed that several previously-know types of organisms belong to a distinct domain, or urkingdom, of life that is as different from all other organisms as humans are from bacteria. This domain, the Archaea, includes the highest temperature limits of life, the most salt tolerant organisms, some of the most acid tolerant organisms, and the only known organisms to derive their energy by reducing carbon dioxide to methane. This tree-like history of life has provided a framework within which questions can be posed and hypotheses tested. For example, it was only this framework that led to the recognition that in spite of their diversity, Archaea have a number of shared molecular features.

The recent sequencing of complete microbial genomes has enriched our perspective. We can now study the history of all of the genes in each sequenced genome. The picture emerging includes massive quantities of gene transfer between lineages. Thus, in the long run, the genetic potential available to organisms is not just that of their own ancestors, but also (to an unknown extent) that of their contemporaries (their cousins many billion times removed). The shear abundance of microorganisms and the immense periods of time ensure that even rare events do happen. Further, even a small improvement can be propagated to billions of descendants in a year, and as they become more abundant, they too are available for transfer between lineages, not just to direct descendants. In this way, many of the great biological innovations (including photosynthesis, dinitrogen fixation, and oxygen-based respiration) have been distributed to diverse lineages.

I will examine some of the evidence for ancient and more recent gene transfers, discuss evidence that all is not chaos (in spite of staggering amounts of gene transfer), and touch on how this influences what organisms have been able to do in a world so full of diverse niches, even if we would not wish to live in most of them.