A mammalian tree drawn on the basis of myoglobin sequences from some species and hemoglobin sequences from others would be accurate as far as the molecules (which are all homologues) are concerned, but would be seriously wrong for the organisms. A third possibility, formally identical to paralogy in its baleful consequence for tree construction, is lateral (horizontal) gene transfer. Certainly such transfer has occurred within and between domains, early and late in their evolution (Smith et al., 1992). Zillig and Sogin (Zillig et al., 1993; Sogin, 1991) have drawn (quite different) scenarios in which extensive lateral transfer is invoked to explain the multiplicity of trees shown in Figure 7, each of which can then be taken at face value.
What renders all such attempts to resolve the current dilemma unnecessary and dangerously premature is the certainty that we will soon have enormously many more data. Total genome sequencing projects are under way for several eubacteria (E. coli, B. subtilis, a mycoplasma, and two mycobacteria), several archaebacteria (including Sulfolobus solfataricus ), and, of course, a number of "crown" eukaryotes seen as more direct models for the human genome. Instead of at most three dozen data sets with representative gene sequences from all three domains, we should have 3000. If the data in aggregate favor a single tree, this should be apparent. If there have been lateral transfers of related or physically linked genes, then we might be able to see them. If transfer has so scrambled genomes that we can no longer talk sensibly about the early evolution of cellular lineages but only of lineages of genes, then that too should be apparent, as would the need to change the very language with which we address an evolutionary process so radically different in both tempo and mode.
We should not allow our current confusion about the root to discourage us, and it is heartening to remember how far we have come. The prokaryote-eukaryote distinction has replaced that between animals and plants, and although we may no longer see that distinction as clearly as Stanier and van Niel thought they did, it is because we know more about the diversity of microbes; we will never go back to a world of just animals and plants. Similarly, the endosymbiont hypothesis for the origin of mitochondria and chloroplasts is as firmly established as any fact in biology; we will not return to the belief in direct filiation (bacteria -> cyanobacteria -> algae -> all other eukaryotes) which preceded it. As for the archaebacteria, although there remains some doubt as to their "holophyly" (thermophiles may be especially close to eukaryotes) and legitimate debate over the philosophical and biological implications of their existence for the meaning of the word "prokaryote," we will never again see these fascinating creatures scattered