Clades and the molecular clockSpec A3.2.4, A3.2.5
In short
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.
- Clade
- A group of organisms with common ancestry and shared characteristics: a common ancestor and all of its descendants.
- Molecular clock
- A method of estimating when clades diverged from a common ancestor, using the number of differences in base or amino acid sequences.
Evidence for clades
The most objective evidence for placing organisms in the same clade comes from base sequences of genes or amino acid sequences of proteins. Sequences can be compared position by position and the differences counted, so the evidence is quantitative.
Morphological traits can also be used to assign organisms to clades, but they are less reliable. Similar structures can evolve separately in unrelated groups (convergent evolution), as in the wings of bats and birds.
The molecular clock
After two lineages split, mutations build up in each independently. Differences in sequence therefore accumulate gradually: the more differences between two species, the longer ago they shared a common ancestor. If the rate of change is known, for example calibrated using a fossil of known age, the number of differences can be used to estimate when the clades diverged.
The molecular clock can only give estimates, because mutation rates are affected by:
- the length of the generation time (more generations per year means more DNA replication and more chances of mutation);
- the size of the population;
- the intensity of selective pressure on the gene;
- other factors, such as differences between genes in how freely their sequence can change.
Using a molecular clock
Two species differ at 18 positions in the amino acid sequence of a protein. A fossil-calibrated rate for this protein is 1 difference per 4 million years (a practice value). Estimate when the species diverged.
- Time since divergence = number of differences × time per difference
- = 18 × 4 million years
- = 72 million years
Answer: About 72 million years ago. This is only an estimate, as the rate of change may not have been constant.
Linking question: how can similarities between distantly related organisms be explained? By convergent evolution, which is why sequence data is preferred to morphology for defining clades.
Written and checked against the IB Biology HL specification · Updated October 2026