Genetic Analysis and the Three-Domain Classification System

As technology developed, scientists became able to compare the base sequences in organisms’ DNA and RNA. A base sequence is the order of the chemical bases in these molecules. Comparing equivalent sequences across organisms provides evidence about their evolutionary relationships.

Generally, the more similar the sequences, the more closely related the organisms are, and the more recently they shared a common ancestor. For example, a mammal’s DNA sequences are generally more similar to those of other mammals than to those of birds or fish.

Genetic analysis therefore adds evidence that cannot be obtained simply by looking at organisms or examining their cells. Classification can be revised when this evidence reveals relationships that were previously hidden.

Why one prokaryote kingdom became two domains

Genetic comparisons revealed major differences between two groups that had both been placed in the prokaryote kingdom. Although both groups lack a nucleus, the evidence showed that they were less closely related than scientists had previously thought.

This supported separating them into Bacteria and Archaea. Along with the eukaryotes, they form the three-domain system proposed by Carl Woese in 1990:

• Bacteria: prokaryotic organisms, including E. coli and Staphylococcus.
• Archaea: a genetically distinct group of prokaryotic organisms. Many live in extreme environments, such as hot springs and very salty lakes.
• Eukaryota: organisms with a nucleus, including protists, fungi, plants and animals.

Domains sit above kingdoms

A domain is a broader classification group than a kingdom. In the three-domain system, the four eukaryotic kingdoms are grouped within Eukaryota, while organisms formerly grouped together as prokaryotes are separated into Bacteria and Archaea.

The change is therefore not simply replacing five group names with three names at the same level. It introduces a higher level of classification that better reflects the relationships revealed by genetic evidence. It also shows how scientific models can change when new methods provide new evidence.

Five kingdoms → three domains

Traditional kingdoms: prokaryotes, protists, fungi, plants and animals.

Three domains:

• Bacteria: prokaryotes, such as E. coli.
• Archaea: genetically distinct prokaryotes; many inhabit extreme environments.
• Eukaryota: protists, fungi, plants and animals.

Domain is above kingdom. Genetic evidence supported separating prokaryotes into Bacteria and Archaea, while grouping the four eukaryotic kingdoms within Eukaryota.