Microbial evolution: The new synthesis

Over the last two decades, molecular phylogeneticists have built up an understanding of relationships within and between prokaryotic and eukaryotic microbial organisms which seems to have explanatory and predictive power. There is at the moment general confidence in the distinctness and coherence of the Archaea and Bacteria, in the notion that eukaryotic cells arose by an increase in internal complexity from an archaea-like ancestor, in the (a-proteobacterial) endosymbiotic origin of mitochondria and in the primitive status of certain deeply diverging lineages of protists. Come the millennium, however, we are likely to see our confidence shaken, as more genome sequences appear and are compared. Archaeal and eukaryotic genomes are unexpectedly chimeric. It is not clear whether there are any genes whose products are so tightly integrated in cellular function that they cannot be replaced. The concept of genomic lineages may be inappropriate for understanding cellular evolution, but it is not obvious what will replace it.