All subjects · Biology · WBI12 (Unit 2)

Classification and the three domains

Classification sorts organisms into groups. New molecular evidence has changed those groups, and scientists debate and test such changes before accepting them.

Species and the hierarchy

A species is a group of organisms with similar characteristics that can interbreed to produce fertile offspring.

Organisms are grouped in a hierarchy: domain, kingdom, phylum, class, order, family, genus, species. Each species has a two-part (binomial) name: genus then species, for example Homo sapiens.

The species concept is hard to apply to fossils, organisms that reproduce asexually, and populations that never meet.

Phenotype and genotype

Traditionally organisms were classified by phenotype: visible features, anatomy and development. Similar features can evolve separately, though, so this can mislead.

Molecular evidence compares DNA base sequences, and amino acid sequences of proteins. The more similar the sequences, the more recently two species shared a common ancestor, so the more closely related they are.

The three-domain system

By comparing ribosomal RNA sequences, Carl Woese found that some prokaryotes, now called Archaea, are as different from bacteria as they are from eukaryotes. This led to the three-domain system: Bacteria, Archaea and Eukarya.

New ideas like this are accepted only after the scientific community has evaluated them: findings are published in peer-reviewed journals, discussed at conferences, and checked by other scientists repeating the work.

Worked example

Species A and B differ by 3 amino acids in a protein; A and C differ by 15. Which species is most closely related to A?

  1. Fewer differences mean a more recent common ancestor.
  2. B differs by only 3.

Answer: Species B.

Key idea: Species: can interbreed to give fertile offspring. Hierarchy: domain to species. Molecular evidence (DNA, protein, rRNA sequences) shows relationships; Woese's rRNA work gave three domains: Bacteria, Archaea, Eukarya. Peer review tests new ideas.

Check yourself

  1. Which best defines a species?
    • Organisms that look the same
    • Organisms that can interbreed to produce fertile offspring
    • Organisms living in the same habitat
    • Organisms in the same family
    Show answer

    Organisms that can interbreed to produce fertile offspring. Fertile offspring is the key test.

  2. What are the three domains?
    • Animals, Plants, Fungi
    • Prokaryotes, Protoctists, Plants
    • Bacteria, Viruses, Eukarya
    • Bacteria, Archaea, Eukarya
    Show answer

    Bacteria, Archaea, Eukarya. Woese's three domains.

  3. What evidence led to the three-domain system?
    • Comparisons of leaf shapes
    • Comparisons of ribosomal RNA sequences
    • The colour of cells
    • The number of legs
    Show answer

    Comparisons of ribosomal RNA sequences. Woese compared rRNA.

  4. Which list is in the correct order from largest group to smallest?
    • Phylum, kingdom, order, class
    • Class, order, phylum, kingdom
    • Kingdom, phylum, class, order
    • Order, class, kingdom, phylum
    Show answer

    Kingdom, phylum, class, order. Domain, kingdom, phylum, class, order, family, genus, species.

  5. Why is molecular evidence useful in classification?
    • Similar DNA or protein sequences show how recently species shared an ancestor
    • It shows what colour an organism is
    • It shows where organisms live
    • It replaces the need for a species concept
    Show answer

    Similar DNA or protein sequences show how recently species shared an ancestor. Sequence similarity reflects evolutionary relationships.

  6. How does the scientific community evaluate a new classification proposal?
    • Accepting it as soon as it is suggested
    • A public vote
    • Peer review, publication and discussion, and repeating the work
    • Only if a government approves it
    Show answer

    Peer review, publication and discussion, and repeating the work. Peer review and independent checking build confidence.

  7. For which organisms is the interbreeding definition of a species hardest to use?
    • Organisms known only from fossils
    • Large mammals in zoos
    • Common garden birds
    • Domestic cats
    Show answer

    Organisms known only from fossils. Fossils cannot be tested for interbreeding; asexual organisms are also a problem.

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Last updated 7 November 2026. Spotted a mistake? Tell us.