AP Syllabus focus:
‘Phylogenetic trees can show time or amount of change, whereas cladograms do not include a time scale.’
Understanding what branch lengths mean is essential for interpreting evolutionary diagrams. A tree’s shape (branching pattern) shows relatedness, but only some diagrams let you read evolutionary time or the amount of change.
Cladograms vs phylogenetic trees: what the diagram can tell you
Shared feature: branching pattern (topology)
Both cladograms and phylogenetic trees display a branching pattern that represents hypotheses about lineage splitting. The key interpretation that is always valid is:
More recent common branching points indicate closer evolutionary relationships (in terms of shared ancestry).
Rotating branches around a node does not change relationships; only the connections matter.
The critical difference: meaning of branch length
A diagram becomes more than a simple relationship map when branch length is scaled to something measurable.
Comparison of three common evolutionary diagram types: (A) a chronogram (branch lengths proportional to elapsed time), (B) a phylogram (branch lengths proportional to amount of evolutionary change), and (C) a cladogram (branch lengths not scaled). This makes it visually clear that the same branching pattern can be drawn with different meanings for branch length depending on the scaling convention. Source
Phylogenetic tree: A branching diagram in which the pattern of branches shows hypothesised relationships, and branch lengths may be scaled to represent time and/or the amount of evolutionary change.
In contrast, a cladogram is intentionally “not-to-scale” for branch length.
Cladogram: A branching diagram that shows relationships based on branching order only; branch lengths are not scaled to time or amount of change.
Reading “time” on a tree
Trees scaled to time (chronograms)
Some phylogenetic trees include a time scale (for example, millions of years ago).
Example of a chronogram (time-calibrated phylogenetic tree) with a labeled time axis in Ma and divergence-time estimates at nodes. The horizontal position of nodes and tips encodes timing, while the gray bars indicate uncertainty around inferred divergence times. Source
On these trees:
Longer branch length corresponds to more elapsed time.
Nodes can be interpreted as occurring at particular times (often estimated using fossils or molecular clocks, though the method is not the focus here).
If all tips (present-day taxa) line up at the same point in time, the tree is often time-calibrated and visually “level” at the ends.
What you can and cannot infer
When a time scale is present, you can compare:
Relative timing of divergences (which split happened earlier vs later)
Approximate duration between splits along a lineage
You still cannot assume anything about the rate of evolutionary change unless the diagram also indicates change per unit time.
Reading “amount of change” on a tree
Trees scaled to change (phylograms)
Other phylogenetic trees scale branch lengths to the amount of evolutionary change, often inferred from molecular data (e.g., DNA differences).
Branch-length representations on a phylogeny where lengths are drawn to scale and interpreted using a scale bar (commonly in substitutions per site). This illustrates how evolutionary change is read from a phylogram: longer branches indicate more inferred sequence divergence, not necessarily more time. Source
In these trees:
Longer branches indicate more change along that lineage, not necessarily more time.
Tips may not align, because different lineages can accumulate changes at different rates.
Branch length: The length of a branch in a tree that may be scaled to represent elapsed time or the amount of evolutionary change, depending on the diagram’s legend or axis.
Avoiding a common mistake
Do not interpret a long branch on a change-scaled tree as “older.” It may instead reflect:
Faster rates of molecular change
Different selective constraints on the sequences used
Unequal sampling or model effects (the key point is that change ≠ time unless explicitly calibrated)
How to tell which diagram you are looking at
Use the diagram’s visual cues:
Cladogram: no scale bar; branch lengths are arbitrary; spacing is for clarity.
Time tree: labelled time axis or dated nodes; branch lengths correspond to time.
Change tree: scale bar indicating substitutions or “distance”; branch lengths correspond to amount of change.
When no scale is shown, treat branch lengths as uninformative and focus only on branching order.
FAQ
Look for an axis or scale bar.
If there is no numeric scale and branches appear evenly spaced for neatness, treat it as a cladogram and ignore branch length.
Yes, on a change-scaled tree.
Different evolutionary rates can produce different amounts of molecular change over the same time interval, giving unequal branch lengths despite the same split time.
It often indicates the tips represent taxa sampled at the same time (typically the present).
If a time axis is shown, it is usually a time-calibrated presentation; without an axis, alignment alone is not proof of time scaling.
It standardises molecular difference by sequence length.
This makes branch lengths comparable across taxa when the underlying data are DNA/protein sequences, where raw counts of differences depend on how long the sequence is.
No.
A cladogram does not encode “degree of evolution,” and even on scaled trees, longer branches reflect time or change, not overall biological “advancement.”
Practice Questions
State one difference between a cladogram and a phylogenetic tree that is scaled to time. (2 marks)
Cladogram shows branching order only; branch lengths have no meaning / no time scale. (1)
Time-scaled phylogenetic tree has branch lengths proportional to time / includes a time axis or calibrated node ages. (1)
A student compares two diagrams with identical branching patterns. Diagram A includes a scale bar labelled “0.1 substitutions/site”. Diagram B has no scale. Explain what information about evolution can be inferred from each diagram, focusing on time and amount of change. (5 marks)
Identical branching pattern means both diagrams support the same relationships in terms of common ancestry (topology). (1)
In Diagram A, branch lengths represent amount of evolutionary change (e.g., substitutions per site), so longer branches indicate more change. (1)
Diagram A does not necessarily show time unless explicitly calibrated; change can accumulate at different rates. (1)
Diagram B is a cladogram-style diagram where branch lengths are not scaled, so you cannot compare time or amount of change from branch lengths. (1)
From Diagram B, only branching order/relative relatedness can be inferred, not divergence times or rates. (1)
