Darwin ended the Origin with the statement:

There is a grandeur to this view of life, with its several powers, having been originally breathed into a few forms or into one; and the, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

Implied within that statement is the view that all life is interrelated and could be traced back to an original form. Thus, life emerged as a tree, and the tree of life became one of his favorite metaphors.  That image was co-opted by Ernst Haekel who illustrated a very famous image of the Tree of Life in 1866 (see Figure 1).  That image remained the icon of evolutionary history for a century.  Among the scientists involved in the elucidation of phylogenies, there were experts in the fields and a few over-arching thinkers like Haeckel.  The problems that they had with determinations of phylogenies, though, had to do with the inability to differentiate between characters as innovations versus shared primitive states (Willmann 2003).  That, together with the 2 (or 3 or 4 or 5) Kingdom systems further muddled the efforts of morphologists to come up with a tree that reflected the real tree of life.  Finally, logical rules for the creation of phylogenies that distinguished between derived and primitive characters arrived with Hennig (many publications from 1950-1966) in the methodology that we now call cladistics.  Though morphological characters worked well for the construction of phylogenies within closely-related groups, the construction of the great tree of life was not possible because distantly-related organisms have very few characters in common.  That is when Zuckerkandl and Pauling (1965) suggested that more subtle trees might be generated by using the repeating elements of biological molecules that all living things have in common.


FIGURE 1. Haeckel's Tree of Life for the Pedigree of Man from Generelle Morphologie der Organismen (1866). This image is in the Public Domain.



Woese and Fox (1977), using the suggestions of Zuckerkandl and Pauling, reasoned that because all living things (prokaryotes and eukaryotes) have ribosomal RNA, especially the small subunit ribosomal RNA, they might be able to compare directly very different taxa.  In particular, they were interested in the relative positions of methanobacteria within the bacteria and relative to the eukaryotes.  Their analyses (e.g. Figure 2) showed that the bacteria they were working on were very different from bacteria like E coli.  The methanogens, etc. received the name Archaebacteria, meaning ancient bacteria.  Woese then reconsidered the name and the organization of life itself.  He noted that the Archaebacteria was as different from the Eubacteria as each one was different from the Eukaryota.  Thus, Woese et al. (1990) defined three Domains of Life that they called Bacteria, Archaea, and Eucarya.  Margulis and Schwartz (1998) challenged the idea and suggested that the better way to think of the organization is two superkingdoms: Prokaryota and Eukaryota.  

I agree that life is organized into two forms: the prokaryote form which is monogenomic (barring the occasional plasmid) and the eukaryotic form that exists as communities of genomes functioning together as a unit.  The monogenomic form, although a type, does not form a clade (Figure 2).  The two lines of existing bacterial groups are distinctly different.  So, I accept that life exists in three types or domains, and two of those domains are bacterial: the Archaea and Eubacteria, and I treat the domains as Superkingdoms. However, this is only the structure of life writ large.  The organization of those domains varies enormously depending on the source [e.g. Margulis and Schwartz (1998), Garrity et al. (2001 and 2003), and Daubin et al. (2002)] and the excitement of systematics is the on-going process of growing Darwin's Tree of Life.


FIGURE 2. An early tree of life by Woese et al. (1990) using SSUrRNA sequence comparisons.





Black, J. G. 2002. Microbiology, Principles and Explorations. 5th ed. John Wiley and Sons, Inc. New York.

Gao, B. and R. S. Gupta. 2007. Phylogenetic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis. BMC Genomics. 8:86. http://www.biomedcentral.com/1471-2164/8/86.

Garrity, G. M., M. Winters, and D. Searles. 2001. Bergey's manual of systematic bacteriology. 2nd ed. Springer-Verlag. New York.

Garrity, G. M., J. A. Bell, and T. G. Lilburn. 2003. Taxonomic Outline of the Prokaryotes. Bergey's Manual of Systematic Bacteriology. 2nd edition. Release 4.0. Springer-Verlag. New York.  pp. 1-397.

Haeckel, E. 1866.General Morphologie des Organismen. Allemeine Grundzuge der organischen Formenwissenschaft, mechanisch begrundet durch die von Charles Darwin reformierte Descendenz-Theorie. G. Reimer. Berlin.

Hennig, W. 1966. Phylogenetic Systematics. University of Illinois Press. Chicago.

Margulis, L. and K. Schwartz. 1988. Five kingdoms, an illustrated guide to the phyla of life on earth. 2nd Edition. W. H. Freeman and Co.  New York.

Margulis, L. and K. Schwartz. 1998. Five kingdoms, an illustrated guide to the phyla of life on earth. 3nd Edition. W. H. Freeman and Co.  New York.

Willmann, R. 2003. From Haeckel to Hennig: the early development of phylogenetics in German-speaking Europe.  Cladistics.19: 449-479.

Woese, C. R. and G. E. Fox. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences USA . 74: 5088-5090.

Woese, C. R., O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences. USA. 87: 4576-4579.


By Jack R. Holt.  Last revised: 02/27/2017