IB DP Biology: Classification and cladistics: clades, cladograms and the three domains (HL) (DP Biology)

This study guide follows the IB Biology guide, first assessment 2025, and covers section A3.2 (Classification and cladistics) in Theme A, Unity and diversity. All of A3.2 is additional higher level content, so it is HL only: there is no SL content in this section. It applies to you if you sit the Diploma Programme Biology examinations from the first assessment in 2025.

Related pages: revision notes, practice questions, the IB Biology hub, the printable checklist and the Theme A overview. To find your weak spots first, try the free 10-minute diagnostics.

What this unit covers

Section	What you must be able to do	Tier
A3.2.1	Explain why organisms need to be classified	HL only
A3.2.2	Explain why the traditional ranked hierarchy is hard to apply	HL only
A3.2.3	Explain the advantages of classifying by evolutionary relationship	HL only
A3.2.4	Define a clade and say what evidence best places organisms in one	HL only
A3.2.5	Use the molecular clock to estimate divergence times	HL only
A3.2.6	Build cladograms from sequence data using parsimony	HL only
A3.2.7	Analyse cladograms: root, node, terminal branch	HL only
A3.2.8	Use cladistics to test whether a classification is correct	HL only
A3.2.9	Explain the three-domain system and its rRNA evidence	HL only

A3.2.1 The need for classification

Millions of species are thought to exist, and new ones are still being described. Classification sorts them into groups, and that gives you several things.

• A shared system of names and groups, so biologists in different countries know which organism is meant.
• A way to identify an unknown specimen by working through the groups it could belong to.
• Order that makes comparison possible: what a group has in common, and how it differs from others.
• A base for further work, such as choosing which species to compare in physiology, medicine or conservation.

The guide states that a broad range of further study becomes possible once classification is done.

A3.2.2 Problems with the traditional hierarchy

The traditional hierarchy runs kingdom, phylum, class, order, family, genus, species. Each rank holds the rank below it. The problem is that evolution does not produce neat, equal layers.

• Ranks are arbitrary. Nothing fixes how different two groups must be to deserve separate families rather than separate orders. Variation is graded, but a ranked scheme forces sharp cut-offs.
• Ranks are not comparable. A family of beetles and a family of mammals need not represent the same amount of evolutionary time or divergence.
• Groups may not match branching history. A group built on visible similarity can leave out some descendants of its own ancestor, or can unite lineages that arose separately.

Cladistics offers an alternative: it uses unranked clades, with no fixed number of levels. The guide treats the shift from rank-based to clade-based thinking as an example of a paradigm shift, where a scientific field changes its framework rather than adding a fact.

A3.2.3 Why classify by evolutionary relationships

The ideal classification reflects ancestry. Every member of a group has evolved from a common ancestor, so the group is a true branch of the tree of life.

Two advantages follow.

1. Prediction. Members of a group share characteristics inherited from that ancestor. If a newly found species falls in a well-studied clade, you can predict features it is likely to have.
2. Meaning. A group defined by ancestry says something real about history.

Prediction is a probability, not a guarantee, because a member may have lost a trait.

A3.2.4 Clades and the evidence for them

A clade is a group of organisms that includes a common ancestor and all of its descendants. Members share characteristics because they inherited them. Test any proposed group with one question: if you cut a single branch of the tree, do you capture the ancestor and every descendant on it? If a descendant is left out, the group is not a clade.

Example: the animals traditionally called reptiles (lizards, snakes, turtles, crocodiles) exclude birds. Crocodiles share a more recent ancestor with birds than with lizards, so a group of “reptiles without birds” leaves out descendants and is not a clade.

Evidence. The guide states that the most objective evidence comes from the base sequences of genes or the amino acid sequences of proteins. Sequences can be compared site by site and counted. Morphological traits can still be used to assign organisms to clades, but they are open to judgement and can mislead. Similar structures may arise by convergent evolution, where unrelated lineages evolve alike because of similar selection pressures. The camera-type eye of an octopus and a human is one case.

A3.2.5 The molecular clock

Mutations arise in DNA over time. After two lineages split, each accumulates its own changes. The number of sequence differences between two species therefore grows with the time since they shared an ancestor. This is the molecular clock.

To turn differences into time you need a calibration: a pair of lineages whose split date is known, usually from fossils. Then use proportion.

Worked example. A gene of 600 base positions is compared. Two species whose lineages diverged 90 million years ago (from the fossil record) differ at 36 positions. Two other species differ at 27 positions. When did they diverge?

Calibration rate = 36 differences / 90 million years = 0.4 differences per million years (both lineages combined)
Time = 27 / 0.4 = 67.5 million years ago

Answer: about 67.5 million years ago.

The result is only an estimate. The guide names several factors that alter mutation rates: generation time (more generations per year gives more chances for copying errors), population size, the intensity of selective pressure, and others. Another reason is that a site can mutate twice, so the true number of changes is higher than the number of visible differences. A clock calibrated in one lineage may run at a different speed in another.

A3.2.6 Building cladograms with parsimony

A cladogram is a hypothesis about branching order. Sequence data are the raw material. The guide uses parsimony to select the most probable cladogram: choose the tree that explains the observed sequence variation with the smallest number of sequence changes. The guide also notes that choosing different judging criteria can produce different hypotheses, so a cladogram is a best-supported hypothesis, not a fact.

Method:

1. Include an outgroup, a species known to branch off before the others. Its bases show the likely ancestral state.
2. For each site, mark which species have a derived base, one that differs from the outgroup.
3. A derived base shared by two or more species but not all is evidence for grouping them.
4. Count the minimum number of changes each candidate tree needs. Choose the lowest.

Worked example. Eight base positions from a gene, with O as outgroup:

Species	Sequence
O	AGCTAGCT
W	TACTAGAG
X	TACTAGCT
Y	AGGCGGCG
Z	AGGCGTCT

Compare each with O.

• Sites 1 and 2: W and X share derived bases (T, A). That points to a W+X group.
• Sites 3, 4 and 5: Y and Z share derived bases (G, C, G). That points to a Y+Z group.
• Site 6: only Z has T. Site 7: only W has A. These single changes fit any tree, so they do not help choose.
• Site 8: W and Y both have G. This conflicts with the others.

Count changes for the three ways of pairing the four species.

Tree	Changes needed
(W,X) with (Y,Z)	9
(W,Y) with (X,Z)	13
(W,Z) with (X,Y)	14

For the first tree: one change each for sites 1 to 5 (5), one each for sites 6 and 7 (2), and two for site 8 because G must arise twice, once on the W branch and once on the Y branch (2). Total 9. The most parsimonious cladogram pairs W with X and Y with Z. Site 8 is then explained as a coincidence, which is how the method treats convergent changes.

A3.2.7 Analysing cladograms

Here is a cladogram of six groups, drawn as an indented tree. Each pair of lines under a node is a fork.

root
 |-- lamprey
 `-- node 1
      |-- shark
      `-- node 2
           |-- trout
           `-- node 3
                |-- frog
                `-- node 4
                     |-- lizard
                     `-- mouse

Key terms:

• Root: the base of the tree, representing the most ancient common ancestor of all the groups shown.
• Node: a branching point. It represents a hypothetical common ancestor, inferred from the data and not a known fossil.
• Terminal branch: a branch ending in a living (or sampled) group.

What you can deduce:

• Relationships. Closeness is read from the most recent node two groups share. Lizard and mouse share the most recent node on this tree, so they are each other’s closest relatives here.
• Clades. Any node plus everything above it is a clade. Frog, lizard and mouse form a clade. Shark, trout, frog, lizard and mouse form a larger one.
• Misleading groups. “Fish” would include lamprey, shark and trout but leave out the frog, lizard and mouse that descend from the same ancestor as trout. So “fish” is not a clade.
• Not deducible. The length of a branch does not show similarity unless the diagram says its lengths are scaled, and the order of the tips from top to bottom means nothing. A node can be rotated without changing the relationships.

A3.2.8 Testing classifications with cladistics

Cladistics lets you check whether an existing group corresponds to evolutionary relationships. If sequence-based cladograms show that a group’s members do not share a single common ancestor to the exclusion of others, the classification is wrong and species are moved.

The guide suggests the figwort family (Scrophulariaceae) as a case study. This family was built mainly on flower and plant form. Sequence-based work showed that it combined lineages that were not each other’s closest relatives. Many of its genera were moved to other families, including a large share to the snapdragon family (Plantaginaceae), and genera with parasitic habits were moved to the broomrape family (Orobanchaceae). A much smaller family remained. You do not need to memorise the case details.

The point about the nature of science is that knowledge claims can be falsified. Here, similarity of form that arose through convergent evolution, not through inheritance from a shared ancestor, had suggested a classification that cladistics showed to be false. Either the common or the scientific name of an organism is accepted in an examination.

A3.2.9 Three domains

In 1977, a reclassification introduced an extra level above kingdoms: the domain. The evidence was the base sequence of ribosomal RNA (rRNA). All organisms have ribosomes, so rRNA can be compared across all of life. It changes slowly in many regions, so old divergences can be traced.

The comparison showed that prokaryotes were not one group. Organisms were sorted into three domains:

Domain	Contains
Bacteria	Bacteria
Archaea	Archaea, formerly lumped with bacteria
Eukarya	Organisms with a nucleus, including protists, fungi, plants and animals

Archaea turned out to be distinct from bacteria at the level of rRNA, and the sequences also placed archaea closer to eukaryotes than to bacteria. A group formerly counted among the bacteria could not stay there, so a new top level was needed. This is a clear example of a paradigm shift.

Common errors

• Writing that a node is an actual ancestor species. It is hypothetical.
• Judging relatedness by how close two tips sit on the page.
• Calling a group a clade when it leaves out descendants.
• Claiming the molecular clock gives exact dates, or forgetting the outgroup in parsimony.
• Treating the three domains as a replacement for kingdoms rather than a level above them.

Official syllabus

This page is aligned to the Biology guide, first assessment 2025, published by the International Baccalaureate Organization. Section A3.2 is additional higher level only.