Classification and cladistics — IB Diploma Biology HL
IB Biology A3.2 (HL): why we classify, the traditional hierarchy, clades, molecular clocks, building and analysing cladograms, and the three domains.
Revision notes
4 short notes, in the order of the specification. Each one in short:
Classification is needed because of the immense diversity of species, and once organisms are classified a broad range of further study is easier. The traditional hierarchy of kingdom, phylum, class, order, family, genus and species does not always match evolutionary divergence. The ideal classification follows evolutionary relationships, so characteristics of group members can be predicted.
A clade is a group of organisms with common ancestry and shared characteristics: an ancestor and all of its descendants. The most objective evidence for clades comes from base sequences of genes or amino acid sequences of proteins. Sequence differences accumulate gradually, so they act as a molecular clock to estimate when clades diverged.
A cladogram is a tree diagram showing the most probable sequence of divergence in a group of clades. It is built from base sequences of genes or amino acid sequences of proteins, using parsimony to choose the tree needing the fewest sequence changes. Each node represents a hypothetical common ancestor; terminal branches end in the species compared.
Cladistics can test whether a traditional classification matches evolutionary relationships. In the figwort family, groups based on morphology included species that were only similar through convergent evolution, so many were moved to other families. Evidence from rRNA base sequences led in 1977 to classifying all organisms into three domains: Bacteria, Archaea and Eukarya.
Exam questions
7 exam-style questions (22 marks), each with its mark scheme.
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14 cards: flip them, mark what you knew, and practise the rest.
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The whole of organisms (unity and diversity) on one page, so you can see where this subtopic fits.
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Quick check questions
List the traditional hierarchy of taxa from largest to smallest.
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Kingdom, phylum, class, order, family, genus, species.
What does a node on a cladogram represent?
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A hypothetical common ancestor.
What is parsimony analysis?
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Choosing the cladogram that accounts for the observed sequence variation with the smallest number of sequence changes.
Name the three domains.
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Bacteria, Archaea and Eukarya.
Why can a molecular clock only give estimates?
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Mutation rates vary with generation time, population size, intensity of selective pressure and other factors.
Frequently asked questions
What is the difference between a clade and a traditional taxon?
A clade is a group of organisms with common ancestry and shared characteristics: an ancestor and all its descendants, with no fixed rank. A traditional taxon, such as a family or class, has a fixed rank in a hierarchy, and some traditional taxa, like the class Reptilia without birds, are not clades.
How does the molecular clock work?
Differences in base or amino acid sequences build up gradually after two lineages split, so more differences mean longer since the common ancestor. With a rate calibrated from fossils, the number of differences estimates the divergence time. It is only an estimate because mutation rates vary with generation time, population size and selection.
How do you construct a cladogram from DNA sequences?
Align the base sequences of a gene from each organism and count the differences between them. Group organisms that share changes, using an outgroup to root the tree. Parsimony analysis then picks the most probable cladogram: the one that explains the observed variation with the smallest number of sequence changes.
Why were organisms reclassified into three domains?
In 1977, comparisons of ribosomal RNA base sequences showed that prokaryotes form two very different groups, Bacteria and Archaea, each as distinct from the other as from eukaryotes. This led to three domains, Bacteria, Archaea and Eukarya, as a new taxonomic level above kingdoms.
Written and checked against the IB Biology HL specification · Updated October 2026