The Evolution of the Three Domains


Genetic studies indicate that modern life descended from a common ancestor. The last universal common ancestor likely existed more than three billion years ago. Over the course of evolution, it appears that three main lines of descent—drawn as branches on the tree—have sprung from the last universal common ancestor and that all modern species would naturally fit into three large taxonomic groupings, called domains, based on these lineages.

Here we describe some of the reasons biologists group modern organisms into three domains. We also focus on a process called lateral gene transfer, in which one organism receives genetic information from another, without being the offspring of that organism. The evidence for lateral gene transfer has revealed surprising and complex webs of genetic relationships among the three evolving lineages.

  1. Based on molecular and morphological features, many biologists agree that all of Earth's diverse life forms naturally fall into three large taxonomic groups, called domains. These groups are the Bacteria, the Archaea, and the Eukarya.
  2. The Eukarya include all animals, plants, fungi, and protists. These organisms are eukaryotes, meaning they have membrane-enclosed nuclei within their cells. The Bacteria and Archaea are both considered prokaryotes, because their cells lack true nuclei, meaning a membrane does not enclose their genetic material.
  3. Although the Bacteria and the Archaea are all prokaryotes, they have many features that distinguish themselves from each other. One important feature that distinguishes many Bacteria from the Archaea is the molecule peptidoglycan. Most Bacteria have this molecule in their cell walls, whereas the Archaea do not.
  4. By these features alone, it may appear that Bacteria and Archaea are more closely related to each other than either is to Eukarya. However, this turns out not to be true. Recent evidence indicates that Archaea and Eukarya are more closely related to each other than either is to Bacteria.
  5. According to the evidence, all three domains of life share a common ancestor that probably existed more than 3 billion years ago (bya). Two lines of descent emerged from this ancestor. One line produced modern-day Bacteria. The other gave rise to a common ancestor (~2 bya) of both the Archaea and the Eukarya.
  6. The evidence of the close relationship between the Archaea and the Eukarya came when scientists analyzed the nucleotide sequences of molecules called ribosomal RNA (rRNA). All organisms tested from Eukarya and Archaea had a particular sequence in common, and none of those tested from Bacteria had this sequence.
  7. As scientists gather more data, a new layer of complexity is beginning to emerge. The clean lines of descent among the domains are becoming less clear. It appears that, through a process called lateral gene transfer, organisms over the course of evolution repeatedly swapped genes with each other.
  8. Usually genetic information is passed from parent to offspring, in a vertical transmission. However, in lateral gene transfer, an organism from one generation transfers DNA to another organism in the same generation. This lateral transfer can occur between two organisms of the same or different species.
  9. In this example, a cell from the domain Bacteria has taken up a gene from an Archaean cell. This Archaean gene is now incorporated into the Bacterial cell's own DNA, and is passed vertically from parent to offspring when the cell divides.
  10. Lateral gene transfer appears to have happened many times in evolution, such that two very different species may share very similar genes. Therefore, depending on the genes being compared to establish relationships, a researcher could find conflicting results about the apparent path of evolution.


In the past few years, scientists have sequenced the entire genomes of many different species from the domains Bacteria, Archaea, and Eukarya. This plethora of data has allowed scientists to compare how thousands of genes differ or are similar among organisms from the three domains.

Many of the comparisons corroborate the model of evolution that biologists currently hold: that Archaea and Eukarya diverged from the Bacteria long ago. However, many surprises have also emerged from the vast amount of collected data. For example, Archaean species have genes that have been recently derived from Bacteria, and Eukarya also have a number of genes that are of relatively recent Bacterial origin. This DNA sequence data has provided the evidence that lateral gene transfer occurred repeatedly throughout evolution.

Lateral gene transfer is a well-documented event that occurs today. It is clear that DNA can be transferred between organisms by vectors, such as viruses. Prokaryotes can also transfer DNA on circular pieces of vector DNA, called plasmids. Additionally, prokaryotes are also capable of taking up naked DNA through a process called transformation.

For scientists, the lateral transfer of genes has turned three relatively clean lines of descent into a vast and complex network of relationships. Yet it is debatable whether lateral gene transfer has seriously complicated attempts to resolve the tree of prokaryotic life. While it complicates studies in some individual species, it need not present problems at higher levels. Nucleotide sequence comparisons involving entire genomes are revealing a stable core of crucial genes that are uncomplicated by lateral gene transfer. Gene trees based on this stable core more accurately reveal relationships of the organismal phylogeny.