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

These revision notes condense section A3.2 of the IB Biology guide, first assessment 2025. Everything here is HL only. For full explanations and longer worked examples, read the study guide. When you are ready to test yourself, use the practice questions, the IB Biology hub, the printable checklist and the free 10-minute diagnostics. The wider Theme A revision notes put this section in context.

Key ideas at a glance

Section	One-line summary
A3.2.1	Classification is needed because species are so diverse; it makes further study possible
A3.2.2	Ranked taxa do not always match branching history; ranks are arbitrary
A3.2.3	Best classification follows ancestry, so group members share features and can be predicted
A3.2.4	A clade is an ancestor plus all its descendants; sequences are the most objective evidence
A3.2.5	Molecular clock: sequence differences build up over time, giving divergence estimates
A3.2.6	Cladograms from sequences; parsimony picks the tree needing fewest changes
A3.2.7	Root, node (hypothetical ancestor), terminal branch; deduce relationships and clades
A3.2.8	Cladistics tests old groupings; the figwort family was reorganised
A3.2.9	Three domains from rRNA: Bacteria, Archaea, Eukarya

Definitions to know

Term	Meaning
Taxon (plural taxa)	A group of organisms at any level of classification
Hierarchy of taxa	Kingdom, phylum, class, order, family, genus, species
Clade	A common ancestor and all of its descendants
Cladogram	A branching diagram showing a hypothesis of evolutionary relationships
Cladistics	Classification by clades, using shared ancestry
Root	Base of the tree, the oldest common ancestor shown
Node	A fork; stands for a hypothetical common ancestor
Terminal branch	A branch ending at a sampled organism or group
Outgroup	A species that branched off earlier, used to show the ancestral state
Parsimony	Choosing the explanation needing the smallest number of changes
Molecular clock	Using the build-up of sequence differences to estimate time since divergence
Convergent evolution	Unrelated lineages evolving similar features
Domain	Taxonomic level above kingdom

Why classify, and why ranks cause problems (A3.2.1 to A3.2.3)

Reasons to classify:

• Species are numerous, so they need a common system to be managed.
• Groups help in identification and in comparing organisms.
• Groups that follow ancestry let you predict traits of a new member.

Problems with the ranked hierarchy:

• Ranks are arbitrary: variation is a gradient, ranks are cut-offs.
• Ranks are not equivalent across groups.
• A rank-based group may not match the real pattern of divergence.
• Cladistics replaces ranks with unranked clades. This is a paradigm shift.

Clades and the evidence (A3.2.4)

Test for a clade: does the group contain the ancestor and every descendant?

• If any descendant is excluded, the group is not a clade.
• Strongest evidence: gene base sequences, or protein amino acid sequences.
• Morphology can be used, but convergent evolution can give similar structures in unrelated lineages.

Must-know distinction: shared because inherited (homologous, from a common ancestor) versus shared because of similar selection (convergent). Only the first supports grouping.

Molecular clock method (A3.2.5)

1. Find a calibration pair with a known split date, usually from fossils.
2. Rate = differences / time (both lineages combined).
3. Unknown time = differences / rate.

Worked reminder: a protein of 200 amino acids. Two species with a fossil-dated split of 40 million years ago differ at 16 positions. A second pair differs at 12 positions.

Rate = 16 / 40 = 0.4 differences per million years
Time = 12 / 0.4 = 30 million years

Answer: about 30 million years ago. Equivalent by proportion: 12/16 x 40 = 30.

Why it gives only estimates: mutation rate changes with generation time, population size and selective pressure, and rates can differ between lineages. Repeated changes at one site are hidden.

Parsimony in steps (A3.2.6)

1. List the sequences, including an outgroup.
2. Mark derived bases (different from the outgroup) at each site.
3. Find sites where two or more, but not all, species share a derived base. These suggest groupings.
4. Count the changes each candidate cladogram needs.
5. Choose the tree with the fewest.

Small reminder with an outgroup and four species, six sites:

Species	Sequence
Outgroup	ATGCAT
K	GCGCAC
L	GCGCAT
M	ATATAT
N	ATATGT

Sites 1 and 2: K and L share derived bases. Sites 3 and 4: M and N share derived bases. Site 5 changes only in N, and site 6 only in K, so these fit every tree. Changes needed: K with L and M with N needs 6; pairing K with M and L with N needs 10; pairing K with N and L with M needs 10. The most parsimonious cladogram groups K with L and M with N. Only sites where a derived base is shared by some but not all species help choose a tree.

Remember the guide’s nature-of-science point: using different judging criteria can produce different hypotheses, so a cladogram is a best-supported hypothesis.

Reading a cladogram (A3.2.7)

root
 |-- A
 `-- node 1
      |-- B
      `-- node 2
           |-- C
           `-- node 3
                |-- D
                `-- E

• Root: base of the tree.
• Nodes 1, 2 and 3: hypothetical common ancestors.
• Terminal branches: A, B, C, D and E.
• Closest relatives: D and E, which share node 3, the most recent node.
• Clade from node 2: C, D and E with their ancestor.
• C is more closely related to D than B is, because C and D share node 2, which B does not.
• Tip order and page position do not show closeness. Only the node structure does.

Testing a classification (A3.2.8)

• Compare the old group with a sequence-based cladogram.
• If the group is not a clade, move species.
• Case study: the figwort family (Scrophulariaceae) was divided after sequence evidence. Many genera went to the snapdragon family (Plantaginaceae); parasitic genera went to the broomrape family (Orobanchaceae). Details need not be memorised.
• Nature of science: similarity from convergent evolution led to a classification that cladistics showed to be false. Knowledge claims can be falsified.
• Common or scientific names are both accepted.

Three domains (A3.2.9)

Feature	Detail
Date	Proposed in 1977
Evidence	Base sequences of ribosomal RNA
Why rRNA	Found in all organisms, so comparable across life
Domains	Bacteria, Archaea, Eukarya
Key change	Archaea separated from bacteria; a level above kingdoms was added
Kingdoms	Fungi, plants and animals sit within Eukarya

Quick self-test

1. Give two reasons why organisms are classified.
2. Why is a fixed rank such as “family” described as arbitrary?
3. Define a clade.
4. Why are sequences more objective than morphology for placing organisms in a clade?
5. A gene of 500 bases differs at 20 positions between two species that split 80 million years ago. A second pair differs at 15 positions. Estimate their split.
6. Give two factors that make molecular clock dates uncertain.
7. What does a node on a cladogram represent?
8. In parsimony, which tree is preferred?
9. What is the point of an outgroup?
10. Name the three domains and the molecule used as evidence.
11. Why was the figwort family reorganised?

Answers

1. Huge diversity of species; it allows identification, comparison and further study (also prediction when classification follows ancestry).
2. Variation is graded, so where one rank ends and another begins is a human choice. Ranks are not equivalent in age or divergence across groups.
3. A group made of a common ancestor and all its descendants.
4. Sequences can be compared site by site and counted. Morphology needs judgement and can be misled by convergent evolution.
5. Rate = 20 / 80 = 0.25 differences per million years. Time = 15 / 0.25 = 60. About 60 million years ago.
6. Any two of: generation time, population size, selective pressure, differing rates between lineages, repeated mutation at one site.
7. A hypothetical common ancestor.
8. The one needing the smallest number of sequence changes.
9. It shows which base is ancestral, so derived bases can be identified.
10. Bacteria, Archaea, Eukarya; ribosomal RNA base sequences.
11. Sequence-based cladistics showed that groupings based on similar form combined lineages without a single shared ancestor, so genera were moved to other families.

Where marks are usually lost

• Calling a node a real species or a known fossil. It is hypothetical.
• Reading closeness from the position of tips on the page.
• Saying “evolved from” between living tips, such as one species evolving from another on the same tree.
• Writing “exact” for molecular clock dates instead of “estimate”.
• Giving only one factor (such as generation time) when two are asked for.
• Forgetting that the extra level of the domain sits above, and does not replace, kingdoms.
• In parsimony, counting sites where only one species differs as evidence for a grouping.
• Describing convergent evolution as inheritance from a common ancestor.
• Defining a clade without the words “all descendants”.

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.