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

These are original questions written for Marlbridge, for revision and practice on this content. They are not reproduced past-paper questions, and they do not replicate the exam’s exact structure, question count or mark tariffs – the IB holds copyright in its own papers. Use these alongside the official past papers available through your school or the IB store.

These questions follow the IB Biology guide, first assessment 2025, section A3.2 (Classification and cladistics). All of A3.2 is additional higher level, so every question is HL only. Use the study guide and revision notes for explanations. Course pages: IB Biology hub and printable checklist.

Questions

1. (HL only) State two reasons why organisms are classified. [2]

2. (HL only) Explain why the traditional ranked scheme running from kingdom down to species is not always a good match for evolutionary history. [3]

3. (HL only) Gorillas, chimpanzees and orangutans are sometimes grouped together as “non-human great apes”. Humans share a more recent common ancestor with chimpanzees than chimpanzees do with orangutans.

(a) Define the term clade. [1] (b) Explain why “non-human great apes” is not a clade. [2]

4. (HL only) A protein of 250 amino acids is compared in several species. Two species whose lineages split 50 million years ago, according to fossils, differ at 20 amino acid positions. A third pair of species differs at 14 positions.

(a) Calculate the rate of change, in differences per million years. [1] (b) Estimate when the third pair diverged. [2] (c) State one reason why the estimate is uncertain. [1]

5. (HL only) Two lineages split from a common ancestor at the same time. One consists of small insects with a very short generation time. The other consists of large mammals with a long generation time. Explain why the sequences of a gene may differ more between the insect species than between the mammal species. [3]

6. (HL only) Nine base positions of a gene were sequenced. O is an outgroup.

Species	Sequence
O	CATGGCATA
F	GCAGGCGTA
G	CATATCAGC
H	GCAGGCAGA
J	CATATAATA

(a) Identify the sites at which a derived base is shared by some, but not all, of F, G, H and J. [2] (b) The cladogram that pairs F with H and G with J requires 10 changes. Show how this total is reached. [3] (c) The pairing of F with J and G with H needs 14 changes. State which cladogram is preferred and why. [1]

7. (HL only) The cladogram shows five groups of plants.

root
 |-- green alga
 `-- node 1
      |-- moss
      `-- node 2
           |-- fern
           `-- node 3
                |-- pine
                `-- lily

(a) State what node 3 represents. [1] (b) Identify the closest relative of the pine on this cladogram. [1] (c) Name the members of the clade that begins at node 2 and explain why they form a clade. [2] (d) A student claims that the fern is more closely related to the green alga than to the lily because it is drawn nearer the top. Evaluate this claim. [2]

8. (HL only) A herb genus was placed in family M because its flowers are tubular with two lips. Sequence data from several genes show that the genus is nested within family N, whose other members have flat, open flowers.

(a) Suggest an explanation for the similar flowers of the genus and family M. [1] (b) State what should be done with the classification of the genus. [1] (c) Explain how this case illustrates that scientific knowledge claims may be falsified. [2]

9. (HL only) The table shows the percentage of identical bases in a stretch of ribosomal RNA gene sequence between four organisms (illustrative figures).

Pair	Identical bases (%)
Bacterium and archaeon	49
Bacterium and yeast	48
Bacterium and maize	47
Archaeon and yeast	62
Archaeon and maize	61
Yeast and maize	77

(a) Identify the two organisms with the most similar rRNA and state what this suggests. [2] (b) Explain what the data suggest about the placing of the archaeon relative to the bacterium and the eukaryotes. [2] (c) Explain why rRNA is suitable evidence for comparing all organisms. [2]

10. (HL only) A newly discovered species of shrub is sequenced. The sequence places it inside a clade in which all five known members make a particular bitter compound.

(a) Predict whether the new shrub makes the compound and justify your prediction. [2] (b) Explain why the prediction might be wrong. [2]

11. (HL only) Differences in a gene are counted between four species. Species D is known to branch earliest.

Pair	Sequence differences
A and B	10
A and C	40
B and C	40
A and D	55
B and D	55
C and D	55

Fossils show that C diverged from the lineage leading to A and B 60 million years ago.

(a) Deduce the branching order and describe the cladogram. [3] (b) Calculate the number of differences per million years. [1] (c) Estimate when A and B diverged. [2] (d) Estimate when D diverged from the other three. [2] (e) State one reason why these dates are estimates. [1]

Answers

1. Two from: there are very many species, so a system is needed to handle them [1]; it allows identification [1]; it allows comparison and further study; groups based on ancestry allow predictions. [2] Examiner insight: Two distinct reasons are needed for two marks; restating “to sort organisms” twice in different words is usually one point at best.

2. Ranks are arbitrary because variation between organisms is gradual, and a fixed cut-off decides where one rank ends [1]; ranks are not equivalent in different groups, for example one family may be much older or more diverse than another [1]; groups built on similarity may not match the branching pattern produced by evolution, for example by excluding descendants of an ancestor [1]. [3] Examiner insight: A strong answer links the criticism to evolution, not to inconvenience.

3. (a) A group consisting of a common ancestor and all of its descendants [1]. [1] (b) The common ancestor of gorillas, chimpanzees and orangutans is also an ancestor of humans [1]; humans are descendants that have been left out, so not all descendants are included [1]. [2] Examiner insight: The definition needs “all descendants”. Describing a clade as “animals that look alike” does not answer the question asked.

4. (a) 20 / 50 [1] = 0.4 differences per million years. [1] (b) Time = 14 / 0.4 [1] = 35 million years ago [1]. [2] (c) Any one: mutation rates vary with generation time, population size or selection pressure; repeated changes at one site are hidden; the rate may differ between lineages [1]. [1] Examiner insight: Show the division, and give units, so the working shows which way round the ratio went.

5. Mutations arise during DNA replication, so they occur in each generation [1]; the insects pass through many more generations in the same time, so more mutations accumulate [1]; the clock therefore runs faster in the insect lineage, and the sequences differ more even though the split date is the same [1]. [3] Examiner insight: Mentioning the same time period turns “short generation time” into an explanation.

6. (a) Sites 1, 2 and 3 (F and H share derived bases) [1]; sites 4 and 5 (G and J share) and site 8 (G and H share) [1]. [2] (b) Sites 1, 2 and 3 each need one change on the branch leading to F and H together: 3 [1]; sites 4 and 5 each need one change on the branch to G and J: 2; sites 6, 7 and 9 each change in one species only: 3 [1]; site 8 is shared by G and H, which are on different branches in this tree, so it needs two changes: 2, giving 3 + 2 + 3 + 2 = 10 changes [1]. [3] (c) The cladogram pairing F with H and G with J is preferred, since 10 is fewer than 14 and parsimony selects the tree needing the smallest number of changes [1]. [1] Examiner insight: Show the count site by site rather than quoting a total.

7. (a) A hypothetical common ancestor of pine and lily [1]. [1] (b) The lily [1]. [1] (c) Fern, pine and lily [1]; they are all descended from the common ancestor at node 2 and include all of its descendants shown [1]. [2] (d) The claim is wrong [1]; relatedness is shown by the most recent shared node, and the fern and lily share node 2, whereas the fern and green alga share only the root, so the fern is more closely related to the lily; the position of tips on the page does not show relatedness [1]. [2] Examiner insight: When evaluating a claim, give a verdict plus the node-based reason.

8. (a) Convergent evolution, for example both groups evolved similar flowers because of similar selection pressures such as the same pollinators [1]. [1] (b) The genus should be moved to family N [1]. [1] (c) The classification based on flower shape had been accepted as correct [1]; sequence evidence showed it did not reflect common ancestry, so the earlier claim was shown to be false and was replaced [1]. [2] Examiner insight: Name the mechanism (convergent evolution), not just “coincidence”. In part (c), give both the old claim and the evidence that overturned it.

9. (a) Yeast and maize [1], at 77 percent identity; this suggests they share a more recent common ancestor than the other pairs do [1]. [2] (b) The archaeon is more similar to yeast and maize (61 to 62 percent) than to the bacterium (49 percent) [1], so it is more closely related to eukaryotes than to bacteria and should not be grouped with the bacterium even though both are prokaryotes [1]. [2] (c) All organisms have ribosomes, so rRNA can be compared across all life [1]; rRNA changes slowly enough in many regions to show old divergences [1]. [2] Examiner insight: Quote figures from the table when interpreting data.

10. (a) It is likely to make the compound [1]; members of a clade share characteristics inherited from the common ancestor [1]. [2] (b) The trait may have been lost in the new species by mutation or selection [1]; the compound may depend on a feature not shared by all members, or the clade placement may be wrong if the sequence data are limited [1]. [2] Examiner insight: A prediction is a probability. Answers that say the clade “proves” the trait exists risk losing the second mark.

11. (a) A and B have the fewest differences (10), so they share the most recent ancestor [1]; C is next, differing from both by 40 [1]; D differs most (55) and branches earliest, so it is the outgroup: the cladogram is D, then C, then A paired with B [1]. [3] (b) 40 / 60 [1] = 0.67 differences per million years (2 s.f.; exactly 2/3). [1] (c) Time = 10 / (40/60) [1] = 15 million years ago [1]. [2] (d) Time = 55 / (40/60) [1] = 82.5 million years ago [1]. [2] (e) Any one: mutation rates depend on generation time, population size or selection pressure; the clock was calibrated with one fossil date; rates may differ between lineages [1]. [1] Examiner insight: Keep the exact fraction 40/60 in the working; rounding the rate to 0.67 first gives about 14.9 and 82.1.

Where marks are usually lost

• Treating a node as a real species instead of a hypothetical ancestor.
• Judging relatedness from where tips are placed instead of from the nodes.
• Counting a change found in one species alone as evidence for a group.
• Explaining the similarity of unrelated organisms as common ancestry instead of convergent evolution.
• Saying domains replaced kingdoms; they are a level above them.

Next steps

• Revision notes for this unit
• Study guide for this unit
• IB Biology hub
• Printable checklist
• All free 10-minute diagnostics
• Book a free trial class

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.