AP Syllabus focus:
‘Phylogenetic trees and cladograms show hypothetical evolutionary relationships among lineages that can be tested.’
Phylogenetic trees and cladograms are visual models used to propose how organisms are related through descent. In AP Biology, they are treated as scientific hypotheses: useful, evidence-based, and always open to testing and revision.
Phylogenies as testable hypotheses
A phylogeny is an explanation of evolutionary relationships, not a definitive historical record. Any diagram that proposes relationships among lineages is a hypothesis because:
it is inferred from available evidence (often incomplete)
multiple evolutionary histories can sometimes explain the same observations
new observations can support, weaken, or overturn it
Phylogenetic trees and cladograms
Both types of diagrams communicate a proposed pattern of descent among taxa.
Phylogenetic tree: A branching diagram that represents a hypothesis about evolutionary relationships among organisms or genes based on common ancestry.
A cladogram is a simplified branching diagram that emphasises branching order (the pattern of relationships) rather than implying extra information not encoded in the diagram itself. In practice, AP Biology often uses “phylogenetic tree” broadly, but you should always interpret what the figure actually shows.
Reading relationships on a branching diagram
Correct interpretation focuses on common ancestry and relative relatedness, not superficial similarity.
Core structural features
Labeled phylogenetic-tree anatomy (root, branch point, sister taxa, polytomy). This diagram highlights the standard parts of a rooted phylogenetic tree and shows how relatedness is read from shared branch points (common ancestors), not from how “close” tips look on the page. It also illustrates a polytomy, which represents uncertainty about branching order rather than a confirmed three-way split. Source
Branch (lineage): a line of descent through time (exact time may or may not be represented)
Node (branch point): where one lineage splits into two; represents a speciation event (or lineage divergence in a gene tree)
Taxon (plural taxa): a named group at a tip (species, population, or gene sequence)
Most recent common ancestor (MRCA): The most recent ancestral node shared by two taxa; taxa with a more recent MRCA are more closely related.
A key rule is that taxa are “more closely related” if they share a more recent MRCA, regardless of how close together they appear on the page.
Same topology, different-looking tree (node rotation). These two trees depict identical evolutionary relationships, but the order of the tips changes because a node has been rotated. The key takeaway is that relatedness is determined by the most recent common ancestor (the connecting node), not by the vertical order of taxa or the visual “distance” between tips. Source
What you can and cannot conclude
You can infer:
which taxa form a clade (a group consisting of an ancestor and all its descendants)
which taxa are sister taxa (each other’s closest relatives)
the sequence of branching events implied by the diagram’s topology
You should not infer (unless explicitly encoded by the figure):
that one living species “came from” another living species
that tips higher/lower on the page are “more evolved”
that branch lengths represent time or amount of change
Why different hypotheses can exist
A single dataset can be consistent with more than one branching pattern, especially when:
divergence events occurred close together in time
there is limited data (few traits or short sequences)
different traits suggest different groupings due to chance similarity
As a result, multiple alternative topologies (different branching arrangements) may compete, and scientists evaluate which hypothesis is best supported.
How phylogenetic hypotheses are tested
Because trees and cladograms are hypotheses, they must be testable using evidence that could potentially falsify them. Testing commonly involves checking whether the proposed relationships are consistent with additional observations.
Key approaches to testing (conceptual)
Independent lines of evidence: A proposed grouping gains credibility if different kinds of data support the same branching pattern.
Predictive power: If a tree is accurate, it can predict patterns you should observe (for example, which taxa should share particular inherited characteristics).
Comparison of competing hypotheses: Scientists can compare how well different tree hypotheses explain the same dataset and whether one requires fewer unsupported assumptions.
Testing does not “prove” a tree is true; it increases confidence that a particular hypothesis is the best current explanation of evolutionary relationships among lineages.
FAQ
A polytomy is a node that splits into more than two branches.
It usually indicates unresolved relationships: available evidence cannot confidently determine which divergence happened first.
Node support is a measure of confidence that a particular branching (a clade) is real.
Higher support means the same relationship is repeatedly recovered when the analysis is challenged (for example, by resampling the data).
A gene tree tracks the history of a particular gene, which may not match the history of species divergence.
Differences can arise when ancestral variation persists across speciation events, so gene lineages split earlier or later than species lineages.
With few characters, chance similarities can dominate the signal.
Random sampling error may group taxa incorrectly because the dataset is not large enough to distinguish true shared ancestry from coincidence.
If genes move between lineages, ancestry is not strictly branching for those genes.
This can make different parts of the genome support different relationships, so a single “tree” may not represent all evolutionary histories equally well.
Practice Questions
In a phylogenetic tree, taxa A and B share a node that is not shared with taxon C. State the relationship between A and B, and what this implies about their ancestry. (2 marks)
Identifies A and B as sister taxa / more closely related than either is to C (1)
States they share a more recent common ancestor with each other than with C (1)
Explain why phylogenetic trees and cladograms are considered hypotheses. Describe two distinct ways scientists can test a proposed evolutionary relationship shown by a tree. (6 marks)
States trees/cladograms are inferred models, not directly observed history (1)
Explains that different trees can fit the same limited/ambiguous evidence (1)
Links “hypothesis” to being testable/falsifiable with new evidence (1)
Describes testing via independent evidence (e.g., a separate dataset supporting/refuting the same branching pattern) (1)
Describes testing via predicted shared ancestry patterns (e.g., expected shared inherited features if the grouping is correct) (1)
Describes comparison of competing topologies for consistency with the data (1)
