Key Idea: Topic A3.2 is cladistics: classifying organisms by their evolutionary relationships — by shared ancestry — rather than by how alike they look. The core unit is the clade: an ancestor plus all of its descendants. We work out clades from shared derived characteristics (features inherited from a common ancestor) and show the result as a cladogram — a branching tree where each node is a common ancestor. Today the strongest evidence comes from molecules: comparing DNA base sequences and protein amino-acid sequences. The more differences between two species, the longer ago they shared an ancestor — the idea behind the molecular clock. When this molecular evidence disagrees with the old look-based grouping, organisms get reclassified. This topic is tested on Paper 1 (read-the-cladogram MCQs) and Paper 2 (the 'use the data to explain the relationship' questions).
🌳 Classifying by common ancestry — clades (1.7.1)
A clade is a complete branch of the tree of life: a common ancestor together with every one of its descendants. Cladistics accepts only clades (also called monophyletic groups) as valid groups, because only they reflect real evolutionary history. Clades are defined by shared derived characteristics — new features that first appeared in the common ancestor and were passed on (for example, hair defines the mammal clade). We must use homologous features (shared by ancestry), not analogous ones: a bird's wing and an insect's wing look similar but evolved independently (convergent evolution), so they do not show shared ancestry.
| Grouping | What it means | Accepted in cladistics? |
|---|---|---|
| Clade (monophyletic group) | An ancestor AND all of its descendants — a complete branch cut from the tree | Yes — this is the only valid kind of group |
| Paraphyletic group | An ancestor but only SOME of its descendants (one or more left out) | No — incomplete, so cladistics rejects it |
| Polyphyletic group | Members from different branches, grouped by a look-alike trait, not shared ancestry | No — based on convergence, not common descent |
Homologous = same underlying structure from a shared ancestor (the one-bone/two-bone limb plan in a human arm, bat wing and whale flipper). These build the tree. Analogous = similar job/appearance but different evolutionary origin (bird wing vs insect wing). These are convergence and must be excluded — grouping by them gives a false (polyphyletic) group. Cladistics groups by shared ancestry, never by 'looks the same'.
Clade = the whole branch, snapped off cleanly: the ancestor and all its descendants — leave one out and it is not a clade. Homologous = same origin (homo = same); analogous = a copy-cat look that evolved separately.
📊 Constructing & reading cladograms (1.7.2)
A cladogram is a branching diagram of relationships. Each branch tip is a species (or group), each node is a common ancestor, and the root is the deepest shared ancestor. The single rule for reading one: the two taxa that meet at the most RECENT node (the node nearest the tips) are the most closely related, because they share the youngest common ancestor. To build one, you score which species share which derived characteristics, then place the species sharing the most derived features closest together. A cladogram shows branching order, not how much time passed or how 'advanced' a species is.
A cladogram is a branching diagram of shared ancestry, NOT of similarity. Read it by the nodes: the closest relatives are the pair that join most recently. The lion and domestic cat share the most recent ancestor, so they are the closest pair; the dog and seal branch off earlier and are more distantly related.
🔒 Interactive diagram
Explore the labelled diagram, charts and maps for this topic in study mode.
How to read any cladogram in an exam
- Find the tips (the species) and the nodes (each node = a common ancestor).
- To find the closest pair, look for the two tips that join at the most recent node (nearest the tips).
- The deeper (closer to the root) a node, the older the split and the more distantly related those branches are.
- Groups are valid only if they form a clade — a node plus everything above it; you cannot pick and choose tips.
- Don't read left-to-right order as 'more evolved' — rotating a branch at a node changes nothing.
Recent node = related. Closest relatives are the pair that meet last before the tips. Deeper node = an older split = more distant cousins.
🧬 Molecular evidence & the molecular clock (1.7.3)
The most powerful modern evidence for clades is molecular: comparing the DNA base sequence of the same gene, or the amino-acid sequence of the same protein (such as cytochrome c or haemoglobin), across species. The logic is simple: the more differences between two sequences, the longer ago the two species shared a common ancestor — because mutations accumulate over time. The molecular clock takes this further: if neutral mutations build up at a roughly steady rate, then counting the differences lets us estimate the time since two lineages split. Molecular data often confirm trees built from anatomy — and sometimes overturn them.
| Molecular comparison | How it is read | What more differences mean |
|---|---|---|
| DNA base sequences | Line up the same gene in two species and count base differences | More differences → diverged longer ago → place further apart on the tree |
| Amino acid sequences | Compare the same protein (e.g. cytochrome c, haemoglobin) | More amino-acid differences → a more ancient common ancestor |
| Molecular clock | Treats neutral mutations as accumulating at a roughly steady rate | The number of differences estimates the TIME since two lineages split |
Key Idea: Two species can look alike through convergence yet be only distantly related; molecules sit in the DNA itself, so they track ancestry directly. More sequence differences → older common ancestor → branches further apart. Fewer differences → recently diverged → branches close together. This single rule turns a table of differences into a tree.
The clock assumes a constant mutation rate, but rates can vary between genes and lineages, and it must be calibrated against a known event (often a dated fossil). So molecular dates are estimates, not exact. A safe exam point: 'the molecular clock assumes a constant rate of neutral mutation, which is only approximately true, so the dates are estimates.'
🔄 Reclassification based on cladistics (1.7.4)
When cladistic and molecular evidence shows that the traditional, look-based grouping was wrong, organisms are reclassified so that every named group is a true clade. Classic outcomes: the figwort plant family was broken up and rearranged after DNA work; many reptile groupings changed once it was clear that birds are nested inside the dinosaur/reptile lineage (so a 'reptile' group that excludes birds is paraphyletic and not a valid clade). Reclassification is evidence-driven and provisional — as new molecular data arrive, the tree is revised again. That self-correcting nature is a strength of the method, not a weakness.
Why a group gets reclassified
- New molecular data (DNA or protein sequences) reveal the real branching order.
- The old group turns out not to be a clade — it left out descendants (paraphyletic) or mixed unrelated branches (polyphyletic).
- The group is redrawn so it contains an ancestor and all its descendants — a valid clade.
- Names and ranks may change, and the tree is updated; later evidence can revise it again (it is provisional).
When DNA and a cladogram place a species on a long branch of its own, it is evolutionarily distinct — a survivor of an old lineage. This is the kind of result that drives RECLASSIFICATION: the molecular tree, not surface looks, decides where the organism belongs.
🔒 Interactive diagram
Explore the labelled diagram, charts and maps for this topic in study mode.
Looks can lie; molecules don't. If the DNA tree disagrees with the old picture, the DNA wins and the group is redrawn into a proper clade. Birds are dinosaurs once you read the tree.
✍️ Worked examples
IB-style question — reading a cladogram
A cladogram shows four mammals. The branches of the lion and the domestic cat meet at the most recent node; the dog branches off earlier, and the seal branches off at the root. Identify which two species are the most closely related, and explain how the cladogram shows this. [3]
Model answer:
State the closest pair. The lion and the domestic cat are the most closely related species.
Give the reason from the diagram. Their branches meet at the most recent node — the node nearest the tips — so they share the youngest / most recent common ancestor.
Contrast with the others. The dog and seal join the tree at deeper (older) nodes, meaning they share only an older common ancestor with the cats, so they are more distantly related. (1 mark: lion + cat; 1 mark: most recent node / common ancestor; 1 mark: deeper node = more distant.)
The lion and the domestic cat are the most closely related, because their branches meet at the most recent node and so share the youngest common ancestor; the dog and seal join at deeper, older nodes and are therefore more distantly related.
IB-style question — using sequence data
Cytochrome c from a frog differs from the human protein at 18 amino acids, while the chimpanzee protein differs from the human at 0. Explain what these data show about evolutionary relationships, and state one assumption of using them as a molecular clock. [4]
Model answer:
Interpret the small difference. The chimpanzee sequence is identical (0 differences) to the human, so the two share a very recent common ancestor — they are closely related.
Interpret the large difference. The frog differs at 18 amino acids, so it shared a common ancestor with humans much longer ago — it is distantly related.
Give the general rule. More sequence differences → an older common ancestor → branches placed further apart on the cladogram.
State the molecular-clock assumption. It assumes mutations (neutral changes) accumulate at a roughly constant rate over time, so the number of differences can estimate the time since divergence. (1 mark each: chimp close / frog distant / more differences = older ancestor / constant-rate assumption.)
Zero differences means chimpanzee and human share a very recent common ancestor (closely related); 18 differences means the frog diverged much earlier (distantly related) — more differences means an older common ancestor. As a molecular clock this assumes neutral mutations build up at a roughly constant rate, so the differences estimate the time since divergence.
IB-style question — why reclassify?
Traditionally 'reptiles' was a group that excluded birds. Cladistic and molecular evidence shows birds evolved from within the reptile lineage. Explain why this means the traditional 'reptile' group must be reclassified. [3]
Model answer:
Define a valid group. Cladistics accepts only a clade — a common ancestor and all of its descendants.
Identify the problem. If birds arose from within the reptile lineage but are left out of 'reptiles', the group contains an ancestor but not all its descendants — it is paraphyletic, so it is not a valid clade.
Give the fix. The group must be redrawn to include birds (or the names revised) so that every recognised group is a true clade reflecting shared ancestry. (1 mark: clade = ancestor + all descendants; 1 mark: excluding birds = paraphyletic / not a clade; 1 mark: redraw to a valid clade.)
A valid group must be a clade — an ancestor and all its descendants. Excluding birds, which arose from within the reptile lineage, leaves out some descendants, making 'reptiles' paraphyletic and not a true clade, so it must be reclassified into a group that includes birds.
✅ Quick self-check
Tap each card to check yourself.
What exactly is a clade? A clade (monophyletic group) is a common ancestor together with ALL of its descendants — a complete branch of the tree. Groups that leave out some descendants (paraphyletic) or mix unrelated branches (polyphyletic) are not clades.
Homologous vs analogous — which builds the tree? Homologous structures (same underlying plan from a shared ancestor, e.g. the human arm, bat wing and whale flipper) show ancestry and build the tree. Analogous structures (similar look, separate origin, e.g. bird vs insect wings) are convergence and must be excluded.
How do you find the closest relatives on a cladogram? Find the two tips whose branches meet at the most recent node (nearest the tips) — they share the youngest common ancestor. Deeper nodes mean older splits and more distant relationships.
What does the molecular clock estimate, and how? It estimates the time since two species split. Neutral mutations accumulate at a roughly steady rate, so the number of DNA-base or amino-acid differences between the same gene/protein indicates how long ago they shared a common ancestor.
Why are organisms sometimes reclassified? New molecular/cladistic evidence shows the old group was not a true clade. The group is redrawn to contain an ancestor and all its descendants — e.g. birds nest within the reptile lineage, so excluding them makes 'reptiles' paraphyletic.
What is one limitation of the molecular clock? It assumes a constant mutation rate, but rates vary between genes and lineages and the clock must be calibrated (often against fossils), so molecular dates are estimates rather than exact.
Exam Tips
- The master idea: cladistics groups by SHARED ANCESTRY, not by appearance. A clade = an ancestor and ALL its descendants — leave any out and it is not a clade.
- Build trees from homologous (shared-ancestor) features only; exclude analogous features, which are convergence and would create a false group.
- Reading a cladogram: the closest relatives are the two tips that meet at the MOST RECENT node (nearest the tips); deeper nodes = older splits = more distant relatives.
- Branch ROTATION at a node changes nothing — left-to-right order is not 'more evolved'. Don't read direction as advancement.
- Molecular evidence rule: more DNA-base or amino-acid differences = an OLDER common ancestor = branches further apart. Fewer differences = recently diverged.
- Molecular clock: neutral mutations accumulate at a roughly constant rate, so counting differences estimates time since divergence — but it assumes a constant rate and needs calibration, so dates are estimates.
- Reclassification is evidence-driven: if molecular data show a group is paraphyletic (e.g. reptiles without birds) or polyphyletic, it is redrawn into a valid clade — and the tree stays provisional.
- On a Paper 2 data question, always quote the numbers: 'X has fewer base differences than Y, so X shares a more recent common ancestor.'