The question of whether prokaryotes represent a single evolutionary lineage is central to modern biological classification. Historically, life was divided into two structural categories: organisms that lack a nucleus and internal compartments, known as prokaryotes, and those that possess them, called eukaryotes. Phylogenetic classification requires a group to be monophyletic—meaning it must contain a common ancestor and all of its descendants. The historical grouping of all non-nucleated cells into the “Prokaryota” suggests a single, unified evolutionary history, but this simple structural division does not align with the complex genetic evidence that has been uncovered.
The Traditional Classification of Prokaryotes
The initial classification of prokaryotes stemmed almost entirely from observing their cellular structure, or morphology. These organisms, which include the familiar bacteria, were defined primarily by the absence of features found in eukaryotes, such as a membrane-bound nucleus, mitochondria, or Golgi apparatus. Their genetic material is typically a single, circular chromosome located in the nucleoid region.
This historical approach grouped organisms based on shared negative characteristics, assuming that all life lacking a nucleus formed a cohesive, distinct evolutionary branch. Scientists used criteria like cell shape, staining properties (Gram-positive or Gram-negative), and metabolic differences to categorize them. However, the morphological classification system was a practical tool for identification but failed to capture the true, deep evolutionary relationships required for a monophyletic group.
Molecular Evidence for Two Distinct Domains
A paradigm shift occurred in the late 1970s with the work of Carl Woese and his colleagues, who began using molecular data to map evolutionary distance. Instead of relying on physical traits, they focused on the sequence variations in the gene that codes for the small subunit of ribosomal RNA (rRNA), specifically the 16S rRNA component. This molecule is present in all forms of life and changes very slowly over vast evolutionary timescales, making it an excellent “chronometer” for comparing distant relatives.
The 16S rRNA analysis revealed that the organisms traditionally classified as prokaryotes fell into two fundamentally distinct, deeply divergent evolutionary lineages. Woese proposed a new classification system, the “Three Domains of Life,” to reflect this genetic reality. The two prokaryotic groups were named Bacteria and Archaea, with the third domain being Eukarya.
The genetic differences between Bacteria and Archaea are immense, often exceeding the genetic differences between Archaea and Eukarya. Archaea possess unique cell membrane lipids, different cell wall compositions, and transcription and translation machinery that is remarkably similar to that of Eukarya. This molecular evidence demonstrated that the two groups of non-nucleated cells had been evolving separately for billions of years.
Why Prokaryotes Are Not a Monophyletic Group
The definitive answer lies in the precise definition of a monophyletic group and the evolutionary position of the three domains. For a group to be monophyletic, it must include an ancestor and all of its descendants. The group “Prokaryotes,” which includes Bacteria and Archaea, deliberately excludes the Eukarya.
The phylogenetic tree constructed from molecular data shows that Archaea and Eukarya share a more recent common ancestor with each other than either group shares with Bacteria. This means that if you trace back to the common ancestor of Bacteria and Archaea, the Eukarya are also descendants of that ancestor. By excluding Eukarya, the grouping of Bacteria and Archaea is incomplete in an evolutionary sense.
Therefore, the term “Prokaryote” describes a paraphyletic group, which includes a common ancestor and some, but not all, of its descendants. While the term “prokaryote” remains useful for describing a cell lacking a nucleus, it is an inaccurate descriptor for a formal evolutionary group.