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A3.2.5 (HL)—Molecular clock

Molecular clocks estimate divergence time from accumulated DNA or amino acid substitutions, assuming calibrated rates of sequence change over lineages.

Syllabus
First assessment 2025
Objective
A3.2.5
Level
HL

Exam analysis

Chance of appearing1%of analysed past papers
Latest appearanceNovember 2023
Most common paperPaper3
Typical marks1

Common command terms

  • Outline
  • State

Scoring notes

Common mistake
Saying only that the relationship is linear without stating that substitutions increase with divergence time.

Recent exam appearances

November 2023Paper3 ["HL"] · TZ211(a)[ 1 ]A3.2.5 (HL)—Molecular clock
Practice this objective

Coverage 2023–2023 · Updated 15 Jul 2026

A Molecular Clock Estimates Divergence Time

HL only

A molecular clock estimates when clades diverged by relating differences in homologous DNA or amino-acid sequences to an independently calibrated rate of change.

After two lineages split, sequence differences can accumulate in both. A calibration from fossils or another dated event connects genetic distance to time, allowing an estimated divergence date.

The estimate is uncertain because mutation rates can differ with generation time, population size, selective pressure, gene and lineage. A suitable sequence, evolutionary model, calibration and uncertainty range must all be stated.

If two candidate clades show fewer differences in the same calibrated gene than another pair, the clock model supports a more recent divergence for the first pair, assuming comparable rates.

A molecular clock gives an estimate, not a direct timestamp. Genetic distance cannot be converted to time reliably without calibration and rate assumptions.

Molecular clock

HL only

Assessment in practice

1 marks
How it is assessed

This objective is assessed through structured response, commonly using Outline / State.

Command terms

Outline / State

What earns marks

Build the answer around this relationship: Sequence differences can be counted to estimate time since divergence.

Watch for

Saying only that the relationship is linear without stating that substitutions increase with divergence time.

Representative question

Question 1

[Maximum number: 1]

State the relationship between divergence time and number of substitutions.

Read And Defend A Cladogram

HL only

A3.2 exam answers are strongest when they sound like evidence arguments. Classification organizes diversity, but fixed ranks and morphology can mislead. Evolutionary classification should match phylogeny using monophyletic clades supported by synapomorphies. Molecular clocks estimate divergence time from calibrated sequence differences. Cladograms are built from aligned sequence data and interpreted by nodes, not tip positions. Cladistics can reclassify old taxa, and rRNA evidence supports the three-domain system.

  • Classification should reveal relationships, not just names.
  • Fixed ranks and convergence can mislead.
  • Monophyletic clades include an ancestor and all descendants and are supported by synapomorphies.
  • Molecular clocks need calibration and can vary in rate.
  • Cladograms are built from aligned sequences using computer analysis and parsimony.
  • Read relatedness from most recent common ancestors, not tip positions.
  • Figwort and three-domain examples show molecular evidence changing classification.

Concept essentials

  • Sequence differences can be counted to estimate time since divergence.
  • More substitutions usually indicate a longer divergence time.
  • Molecular clocks require calibration because rates can vary.
  • DNA and amino acid sequence data can both be used in molecular-clock reasoning.