Reading the evidence: fossils, shared bones and the DNA record
By the end of this lesson you will be able to
- Define evolution as a change in the inheritable characteristics of a population over time, and explain why it is populations, not individuals, that evolve.
- Describe how fossils form and are dated, and calculate the age of a sample from the fraction of a radioactive isotope remaining.
- Interpret the fossil record of the horse and of transitional forms as evidence of change over time.
- Distinguish homologous, analogous and vestigial structures, and explain what each tells us about ancestry.
- Analyse DNA and protein differences between species and construct and interpret a branching evolutionary diagram.
You met this before
- Every living thing is classified in a hierarchy — kingdom, phylum, class, order, family, genus, species — and named with a two-part (binomial) name in italics: Equus ferus caballus for the domestic horse, Homo sapiens for us (Year 3, Unit 4).
- Individuals of a species vary; some variation is inherited through genes, some is caused by the environment, and only inherited variation can be passed on (Year 3, Unit 4).
- Darwin’s natural selection: more offspring are produced than survive; they vary; those best suited to the environment survive and reproduce more; they pass on their inherited features; over many generations the population changes (Year 3, Unit 4).
- DNA is a double helix of nucleotides with the bases A, T, C and G; the order of bases in a gene codes for the order of amino acids in a protein (Unit 2).
- Mutations — changes in the base sequence — create new alleles, and meiosis and fertilisation shuffle alleles into new combinations (Unit 9).
A fossil hunter says: “Fossils are the remains of animals that died millions of years ago.” Give two ways in which this statement is incomplete.
Reveal
Fossils are not only animals: plants, fungi, bacteria (stromatolites) and pollen fossilise too. They are not only remains: trace fossils — footprints, burrows, dung, tooth marks — record behaviour. And not all are millions of years old: a fossil is any preserved evidence of past life, usually taken to be more than about 10 000 years old, and some (in amber, ice or tar) keep original tissue.
Revise it in full: Year 3 · Classification, variation and natural selection · Lesson 5 — Evidence and examples: fossils, breeders and resistant bacteria · Year 3 · Classification, variation and natural selection · Lesson 4 — Darwin and the idea that changed biology · Year 3 · Classification, variation and natural selection · Lesson 2 — Naming and ordering life: from kingdom to species
The puzzle
Deep inside the body of a sperm whale, buried in muscle and attached to nothing, lie two small bones about the length of a pencil. They are the remains of a pelvis — the hip girdle that in you anchors your legs.
A whale has no legs. Its tail is driven by the spine and swings up and down, not side to side like a fish’s. Its flipper, dissected, contains an upper-arm bone, two forearm bones, wrist bones and five sets of finger bones, the same set you have in your arm.
Why would an animal that has never walked be built with a hip and a hand? In 1859 Darwin had an answer, but no fossil to prove it. The fossils turned up between 1981 and 2001 in Pakistan and India — and then DNA pointed at the whale’s closest living relative. It was not a fish, or a seal. It was the hippopotamus.
Before you read on: the whale’s hip bones and hand bones are either the product of design for swimming, or leftovers from ancestors that lived differently. Predict what evidence you would need to find, in rocks and in DNA, to decide between these two explanations.
Compare your answer
If the bones are leftovers, three independent kinds of evidence should agree. The rocks should hold fossils of whale-like animals with working legs, in older layers, and forms with smaller and smaller legs in younger layers.
The bones should match, one for one, the bones of land mammals — not fish fins. And the whale’s DNA should be most similar to that of a particular group of land mammals, the same group the fossils point to.
All three were found. A designed swimming machine would need none of them: a fish’s fin works perfectly with no arm bones at all. When evidence from rocks, anatomy and molecules converges on one answer, that answer is a theory, not a guess.
The science — structured notes
1.1 What evolution is — and what it is not
Evolution is the change in the inheritable characteristics of a population over time. Because inheritable characteristics are carried by genes, the same idea can be stated genetically: evolution is happening whenever the frequencies of alleles in a population change from one generation to the next.
Three words in that definition matter. Inheritable: a gazelle that grows strong legs by running has not evolved, because the change is not in its genes and its young will not inherit it. Population: an individual lives and dies with the genes it was born with; only a population — a group of the same species living and breeding in one place — can change its gene pool.
Over time: evolution is measured across generations, which for bacteria is minutes and for elephants decades.
“A giraffe that stretches its neck to reach high leaves passes a longer neck to its calves, and this is how giraffes evolved.”
Reveal answer
False. This is Lamarck’s idea (1809) of the inheritance of acquired characteristics. Stretching does not change the DNA in the giraffe’s sperm or eggs, so the calf inherits nothing from the stretching.
The Darwinian explanation is that giraffes varied in neck length because of different alleles; in dry seasons those with longer necks reached more food, survived and bred more, so the alleles for longer necks became more frequent in the population over many generations.
1.2 The fossil record: how a body becomes stone, and how we date it
A fossil is any preserved evidence of past life. Most form when a dead organism is buried quickly in sediment — mud, sand or volcanic ash — before scavengers and decomposers destroy it. Soft tissue usually decays; hard parts (bones, teeth, shells, wood) remain.
Over thousands to millions of years, water seeping through the sediment deposits minerals in the spaces of the bone and then replaces it, while the sediment above compresses the layers below into rock. Other fossils are moulds and casts (the shape left in rock), trace fossils (footprints, burrows) and rare whole bodies in amber, tar or frozen ground.
The record is therefore incomplete. Animals without hard parts rarely fossilise; those living where there is no sediment (mountains, dry forest) are rarely buried; most fossils are later eroded, crushed or never found. Palaeontologists estimate that only a tiny fraction of all the species that ever lived are known as fossils — which is why each transitional form matters.
Relative dating puts fossils in order. In undisturbed sedimentary rock, lower layers were laid down first and are older — the principle of superposition, stated by Nicolas Steno in 1669 — so a fossil in a lower layer is older than one above it.
Absolute (radiometric) dating gives an age in years. Some atoms are radioactive isotopes that decay at a fixed rate; the half-life is the time for half of the atoms in a sample to decay. Measuring the fraction of the original isotope left tells us how many half-lives have passed.
| Isotope (decays to) | Half-life | What it dates | Useful range |
|---|---|---|---|
| Carbon-14 (nitrogen-14) | 5 730 years | Once-living material: bone, wood, charcoal, shell | Up to about 50 000 years |
| Potassium-40 (argon-40) | 1.25 × 10⁹ years | Volcanic rock and ash layers above and below fossils | From about 100 000 years to billions of years |
| Uranium series (uranium-234 to thorium-230) | about 245 000 years (uranium-234) | Cave deposits such as flowstone, and teeth | Up to about 500 000 years |
Carbon-14 works on the organism itself: a living body keeps taking in carbon, so its carbon-14 fraction matches the air, and at death the clock starts. Fossils older than about 50 000 years have too little carbon-14 left to measure, so they are dated by bracketing: the volcanic ash layers above and below are dated by potassium–argon, as in the diagram.
A mammoth bone contains 12.5 % of the carbon-14 that a living animal contains. Calculate its age.
Fraction remaining = 12.5 % = 0.125
Each half-life halves the fraction: 1 → 0.5 → 0.25 → 0.125
Number of half-lives = 3
Age = number of half-lives × half-life
Age = 3 × 5 730 years
Age = 17 190 years, about 17 000 years (2 significant figures, as the half-life count comes from a measurement)
Check the answer is in range: 17 000 years is well inside carbon-14’s 50 000-year limit. A mammoth bone at 3 % would be about 5 half-lives, roughly 29 000 years; at 0.1 % it would be about 10 half-lives, some 57 000 years — beyond the limit, so the date would be unreliable.
A piece of charcoal from an ancient hearth contains 25 % of the carbon-14 found in living wood. A second sample, from a layer below it, contains 6.25 %. Calculate both ages and the time between the two fires.
Reveal answer
25 % = 0.25 = two half-lives
Age 1 = 2 × 5 730 years = 11 460 years
6.25 % = 0.0625 = four half-lives (0.5 → 0.25 → 0.125 → 0.0625)
Age 2 = 4 × 5 730 years = 22 920 years
Time between = 22 920 − 11 460 = 11 460 years
The lower sample is older, as superposition predicts: relative and absolute dating agree, which is itself a check on both.
1.3 A story in stone: the horse
The IB’s example is the modern horse, Equus ferus caballus, because its fossil record in North America and Eurasia is unusually rich. Arranged by the age of the rocks, the fossils show a lineage changing over about 55 million years as forests gave way to open grassland.
| Genus (approximate age) | Height at the shoulder | Toes on the front foot | Teeth | Habitat |
|---|---|---|---|---|
| Hyracotherium, often called Eohippus (about 55 million years ago) | about 30–40 cm, the size of a small dog | 4, spread, with pads | low-crowned, for browsing soft leaves | forest |
| Mesohippus (about 37–32 million years ago) | about 60 cm | 3, all reaching the ground | low-crowned | forest and woodland |
| Merychippus (about 17–11 million years ago) | about 1 m | 3, weight on the large middle toe; side toes off the ground | high-crowned, ridged, for grinding grass | spreading grassland |
| Pliohippus (about 12–6 million years ago) | about 1.2 m | 1 (side toes reduced to splints) | high-crowned | open grassland |
| Equus (from about 4 million years ago) | about 1.5–1.7 m | 1, with a hoof; two splint bones remain | very high-crowned | grassland; includes zebras and donkeys |
The trends make sense as adaptations. Grass contains hard silica and wears teeth down, so taller, ridged crowns lasted longer. On open plains, where predators could be seen but not hidden from, longer legs and a single strong toe gave a longer stride and faster running.
Two cautions. First, this is a branching bush, not a ladder: dozens of horse genera lived, many side by side, and most branches died out; the table picks one path through the bush to the only survivor. Second, the plains zebras of Botswana’s Makgadikgadi migration are Equus too — cousins of the domestic horse on the same surviving branch.
The side toes of Merychippus did not touch the ground, and modern Equus keeps two thin “splint bones” beside its cannon bone. Explain why the splint bones are evidence that Equus evolved from three-toed ancestors, rather than evidence of a fault in the horse.
Reveal answer
The splint bones are the reduced remains of the second and fourth metacarpals — the bones of the side toes that three-toed horses such as Merychippus still had.
They carry no weight and have no toe on them, so they make sense only as structures inherited from ancestors in which they were useful. As running on open ground favoured a single strong toe, individuals whose side toes were smaller were not disadvantaged, and the side toes shrank over generations; they have not yet been lost completely. Structures reduced in this way are called vestigial.
1.4 Transitional fossils: the forms in between
A transitional fossil shows a mixture of features of an older group and a younger group, in the layer of rock where evolution predicts it. Three famous examples:
- Tiktaalik roseae (about 375 million years ago, found on Ellesmere Island, Canada, in 2004): a fish with gills and scales, but also a flat head, a neck, lungs and fins containing wrist-like bones — between fish and the first four-legged animals. The team searched rocks of that age because the record predicted the transition there.
- Archaeopteryx (about 150 million years ago, first skeleton found in Germany in 1861): feathers and wings like a bird; teeth, clawed fingers and a long bony tail like a small dinosaur.
- Early whales: Pakicetus (about 50 million years ago) had four walking legs and a whale-type ear; Ambulocetus (about 49 million years ago) paddled with large feet; Basilosaurus (about 40 million years ago) was fully aquatic with tiny hind legs that could not have supported it.
Suppose a fully modern rabbit fossil were found in rock dated 500 million years old, below the first fish. What would this do to the theory of evolution, and why do scientists treat this as a real test?
Reveal answer
It would be a serious problem: evolution predicts mammals appear only after fish, amphibians and reptile-like ancestors, so a mammal before any vertebrates would contradict the order the theory requires. The biologist J. B. S. Haldane is reported to have named “fossil rabbits in the Precambrian” as the kind of find that would disprove evolution.
The point is that the theory makes risky predictions — it forbids certain fossils in certain layers — so it could be shown wrong. In more than a century and a half of collecting, no such out-of-order fossil has been confirmed, while predicted transitional forms such as Tiktaalik have turned up where expected.
1.5 Comparative anatomy: homologous, analogous and vestigial structures
Homologous structures have the same basic structure because they were inherited from a common ancestor, even if they now do different jobs.
The IB’s example is the pentadactyl limb (“five-fingered”) of mammals: the same sequence of bones — one upper-arm bone (humerus), two forearm bones (radius and ulna), a group of wrist bones (carpals), palm bones (metacarpals) and finger bones (phalanges) — in the human arm, the bat wing, the whale flipper and the horse leg.
Modification of one ancestral structure for different functions in different environments is called divergent evolution.
Analogous structures do the same job but have a different basic structure and different origins: the wing of a bird (bones of a pentadactyl limb) and the wing of a butterfly (a sheet of chitin with no bones). They arise by convergent evolution — unrelated organisms under similar selection pressures evolving similar solutions. The streamlined shapes of a shark (a fish) and a dolphin (a mammal) are another example.
Vestigial structures are reduced remnants with little or no function in the organism now, but homologous to functional structures in its relatives: the whale’s pelvis, the horse’s splint bones, the small hind-limb spurs of pythons and boas, the human tailbone (coccyx).
A student writes: “The wing of a bat and the wing of a moth are homologous because they are both used for flying. The flipper of a whale and the fin of a shark are also homologous. This is called divergent evolution.” Find three errors and correct them.
Reveal answer
(1) Bat and moth wings are analogous, not homologous: same function, different structure (bones against a chitin sheet) and no shared wing-bearing ancestor.
(2) A whale flipper and a shark fin are also analogous: the flipper holds a humerus, radius, ulna, carpals and phalanges; the shark fin is supported by cartilage rods with no such pattern.
(3) Similar structures produced independently in unrelated groups arise by convergent evolution; divergent evolution is one ancestral structure modified for different functions, as in the pentadactyl limb.
1.6 The molecular record: DNA and proteins
All known organisms use DNA, the same four bases and — with minor exceptions — the same genetic code, in which the same triplet codes for the same amino acid in bacteria, trees and people. A shared code is exactly what common descent predicts; there is no functional reason why a bacterium and a human should use the same dictionary.
Because mutations accumulate in a lineage generation after generation, two species that shared an ancestor recently have had little time to diverge and have few differences in their DNA and proteins; species whose lineages split long ago have many. Counting differences therefore measures relatedness.
| Species compared with humans | Differences in cytochrome c (104 amino acids) |
|---|---|
| Chimpanzee | 0 |
| Rhesus monkey | 1 |
| Horse | 12 |
| Chicken | 13 |
| Tuna | 21 |
| Baker’s yeast | about 44 |
Cytochrome c is a protein of respiration found in the mitochondria of almost every eukaryote, which makes it a fair comparison across kingdoms. Whole genomes say the same: human and chimpanzee DNA differ at about 1.2 % of aligned base pairs, and the difference grows steadily as we compare humans with gorillas, orangutans, monkeys and then other mammals.
The molecular clock idea follows: if differences accumulate at a roughly steady rate, the number of differences estimates the time since two lineages split. Clocks must be calibrated with dated fossils and carry wide uncertainties, so their dates are always ranges.
Use the cytochrome c table. (1) Calculate the percentage of amino acids that are identical in humans and horses, and in humans and tuna. (2) State which of horse and chicken is more closely related to humans according to this protein, and evaluate how strong that conclusion is.
(1) Identical amino acids, horse = 104 − 12 = 92
Percentage identical = 92 ÷ 104 × 100
Percentage identical = 88.5 %
Identical amino acids, tuna = 104 − 21 = 83
Percentage identical = 83 ÷ 104 × 100
Percentage identical = 79.8 %
(2) Horse (12 differences) is slightly closer to humans than chicken (13).
Evaluate: a difference of one amino acid out of 104 is weak evidence on its own — a single mutation could account for it.
The conclusion that mammals (horse) are closer to us than birds (chicken) is supported much more strongly by the whole genome and by anatomy (hair, milk, three middle-ear bones), so the protein agrees with other evidence rather than proving the point alone. Examiners want this kind of comparison: numbers from both, a statement, and a judgement of how far the data go.
The fossil record and anatomy placed whales among the even-toed hoofed mammals (pigs, cattle, camels, hippos). In the 1990s, DNA comparisons found that whales share more DNA sequence features with hippos than with any other living group. Explain why this agreement matters more than either line of evidence alone.
Reveal answer
The two lines of evidence are independent: fossil bones say nothing about DNA sequences, and DNA sequences were measured with no reference to bones. If whales had not evolved from land mammals, there would be no reason for both to point at the same group.
The agreement was sharpened in 2001, when ankle bones of early whales such as Pakicetus and Rodhocetus turned out to have the “double-pulley” shape found only in even-toed hoofed mammals — the DNA had predicted what the fossils would show. Convergence of independent evidence is what makes a scientific explanation robust.
1.7 Branching evolutionary diagrams
Evolutionary relationships are shown as branching diagrams (also called phylogenetic trees or cladograms). The tips are living (or fossil) species. Each branch point (node) represents the last common ancestor of everything above it. Time runs from the root, at the bottom, towards the tips.
Read relatedness from the branch points, not from the order of the tips: two species are more closely related if they share a more recent common ancestor — a branch point nearer the tips. Branches can rotate at any node like a mobile without changing the relationships.
Use the diagram. Is the gorilla more closely related to the orangutan or to the human? Justify your answer using branch points.
Reveal answer
To the human. The gorilla and the human share branch point 3, about 8–10 million years ago; the gorilla and the orangutan share only branch point 4, further back, about 12–16 million years ago. The more recent the shared ancestor, the closer the relationship — even though the gorilla is drawn next to the orangutan at the tips.
Four species, P, Q, R and S, are compared by the number of differences in a 300-base section of one gene: P–Q 6; P–R 24; P–S 45; Q–R 25; Q–S 44; R–S 43. Construct the branching diagram, and use a molecular clock of 1 difference per 2.0 million years (between two species) to estimate the time since P and Q last shared an ancestor.
Reveal answer
Smallest difference first: P and Q (6) are each other’s closest relatives, so they join at the most recent branch point.
R differs from P and Q by 24–25, so R joins the P–Q pair at the next branch point. S differs from all three by 43–45, so S joins at the root. Tree: ((P, Q), R), S.
Time since P–Q split = 6 differences × 2.0 million years per difference
Time since P–Q split = 12 million years
This is an estimate: the clock rate must be calibrated with a dated fossil, and a short 300-base section gives few differences, so one extra mutation changes the answer by 2 million years. Longer sequences and several genes narrow the range.
Try it — the clock inside a fossil: half-life with dice
Radiometric dating relies on a strange fact: no one can say when a particular radioactive atom will decay, yet a large number of them decay at a perfectly predictable rate.
This lab models that with dice. Each throw is one unit of time; every die showing a six “decays” and is removed. You will measure the half-life of your dice — and then use it exactly as a geologist uses the half-life of potassium-40 to date the ash layers above and below a fossil.
Mean dice remaining from 100: throw 0 → 100; 1 → 83; 2 → 69; 3 → 58; 4 → 48; 5 → 40; 6 → 33; 8 → 23; 10 → 16. Determine the half-life, show that it is constant, and use it to say how many dice would remain after 3 half-lives.
Reveal answer
100 falls to 50 between throws 3 (58) and 4 (48), at about 3.8 throws. 50 falls to 25 between throws 7 and 8 (23 at 8), at about 7.6 throws — a second interval of about 3.8 throws. The half-life is constant: the time to halve does not depend on how many dice are left.
After 3 half-lives the fraction remaining = 0.5 × 0.5 × 0.5 = 0.125
Dice remaining = 100 × 0.125 = 12.5, about 12 or 13 dice (after about 11.4 throws)
This is the logic of the mammoth-bone EXAMPLE: the fraction remaining tells you the number of half-lives, whatever the starting amount.
Common mistakes to avoid
- “The animal evolved to survive” — individuals do not evolve; populations change as allele frequencies change across generations.
- “Fossils are always bones” — footprints, burrows, moulds, casts, amber and pollen are fossils too; trace fossils record behaviour.
- Treating the fossil record as complete — gaps are expected, because fossilisation needs quick burial and hard parts.
- Halving the age instead of the amount — each half-life halves the amount of isotope left, and adds one half-life to the age.
- Homologous = same function — homologous means same basic structure from a common ancestor; same function with different structure is analogous.
- “Humans evolved from chimpanzees” or “monkeys” — we share a common ancestor; the chimpanzee is a cousin.
- Reading tips instead of branch points on an evolutionary tree.
- “The sequences are similar” — a comparison needs numbers from both species and a statement of which pair differs least.
Study smart: how this is examined
Study routine. Today: draw the pentadactyl limb four times from memory — human, bat, whale, horse — colouring the same bones the same colour; then write the three definitions (homologous, analogous, vestigial) with one example each.
In two days: do three half-life calculations (25 %, 12.5 %, 3.125 %) and build a tree from a table of differences. In a week: run the dice lab, take the quiz, and explain to someone at home why the whale’s pelvis is evidence for evolution in four linked sentences.
How we found out — reading the rocks, then the molecules
In 1669 the Danish anatomist Nicolas Steno argued that “tongue stones” found in rocks were the teeth of ancient sharks and that rock layers are laid down one on top of another — the principle of superposition. In 1796 the French naturalist Georges Cuvier showed that mammoth bones differed from those of living elephants and concluded that whole species had become extinct, an idea many then resisted.
On the English south coast, Mary Anning (1799–1847), with little formal education and no access to the scientific societies of her day, uncovered one of the first ichthyosaur skeletons to be recognised by scientists (with her brother, around 1811–1812) and the first near-complete plesiosaur (1823). Her finds proved that strange, vanished animals had lived in the seas.
When Darwin published On the Origin of Species in 1859, he devoted a chapter to “the imperfection of the geological record”, expecting critics to ask where the intermediate forms were. Two years later, in 1861, the first skeleton of Archaeopteryx was found in Germany: a feathered animal with teeth and a bony tail.
In 1876 Thomas Henry Huxley used the American fossil horses collected by Othniel Marsh in lectures in New York as a demonstration of gradual change over time. But the ages were only relative until 1911, when Arthur Holmes used radioactive decay to date rocks, and until 1949, when Willard Libby developed radiocarbon dating (Nobel Prize in Chemistry, 1960).
The molecular record arrived in the 1960s. Emile Zuckerkandl and Linus Pauling compared haemoglobin sequences and proposed in 1962–1965 that protein differences accumulate at a roughly steady rate — a “molecular clock”. In the 1990s DNA studies placed whales next to hippos, which many palaeontologists doubted.
Then in 2001 two teams, led by Philip Gingerich and Hans Thewissen, described ankle bones of early whales from Pakistan with the double-pulley shape found only in even-toed hoofed mammals. Bones and DNA, gathered by different people with different methods, told the same story — and minds changed.
Darwin had no dated rocks, no transitional whales and no DNA. Explain why his theory nevertheless predicted what later scientists found, and name the finding that tested it most directly.
Reveal answer
Common descent with modification makes predictions about the order and form of things not yet discovered: intermediate forms should exist in layers of intermediate age; homologous structures should reflect ancestry; and any other inherited material in organisms should show the same pattern of relatedness.
Each later method was an independent test: radiometric dating confirmed the order and the great age of the layers; Archaeopteryx and Tiktaalik appeared where predicted; and DNA — unknown to Darwin — ranked species in the same order as anatomy. The most direct test is the molecular one, because the theory was built without any knowledge of DNA, yet the DNA pattern matches the tree drawn from bones.
Where it is used now
- The Karoo, South Africa. The rocks of the Karoo Basin preserve a long record of therapsids, the “mammal-like reptiles” whose jaws and ears change, layer by layer, towards the mammal pattern — one of the richest transitional sequences on Earth, studied at the University of the Witwatersrand in Johannesburg and elsewhere.
- Wildlife forensics. The same DNA comparison that places whales next to hippos identifies the species in seized ivory, rhino horn or pangolin scales, and can often trace a sample to the population it came from — evidence used in courts across Africa and Asia.
- Medicine. Because humans share genes with other species through common descent, drugs are tested in mice, and the yeast version of a human gene can often be studied in its place. Knowing how closely two species are related tells researchers how far a result may transfer.
- Tracking disease. Branching diagrams built from virus genomes trace outbreaks: during COVID-19, laboratories including in Botswana and South Africa sequenced samples and drew trees that revealed new variants within days of their appearance.
- Museums and teaching. Horse, whale and hominin fossil casts in museums from Nairobi to Johannesburg to London let anyone check the evidence with their own eyes.
Science now — and the scientist you need to be
What is happening in 2026
The evidence for evolution is being read at a speed Darwin could not imagine. DNA sequencing has become so cheap that projects such as the Earth BioGenome Project aim to sequence the genomes of all known eukaryotic species, and by the mid-2020s its affiliated projects had released reference genomes for a few thousand species. Every new genome adds a tip to the tree of life and a test of relationships drawn from anatomy.
Fossils themselves now yield molecules. Proteins survive far longer than DNA in tooth enamel, and in 2025 researchers reported protein sequences from the enamel of roughly two-million-year-old Paranthropus robustus fossils from Swartkrans cave in South Africa — a new line of evidence where ancient DNA cannot survive.
Fossils are increasingly studied without being touched: CT and synchrotron scans let researchers “dissect” a skull inside its rock, share 3D files with anyone, and print copies for classrooms.
Machine-learning tools that compare sequences and shapes help build trees with millions of branches. The questions for the next decade are about precision: how fast molecular clocks tick in different lineages, and how often genes cross between species (in bacteria, often).
Careers that grow from this lesson include palaeontologist, geochronologist (who dates rocks), bioinformatician, museum scientist and wildlife forensic analyst; all begin with reading a table of differences correctly.
The mindshift
What you need to be able to do
Define evolution in terms of a population; explain a homologous and a vestigial structure in a linked chain; calculate an age from a half-life; turn a table of differences into percentages and a tree; and judge how strong each piece of evidence is. The exam asks for comparisons with numbers — never “they are similar”.
See an example
In one trial the assistant drew the correct tree, ((P, Q), R), S, but divided instead of multiplying for the clock (“6 ÷ 2.0 = 3 million years”). The rate was given as 1 difference per 2.0 million years, so 6 differences take 6 × 2.0 = 12 million years.
A second request produced the right answer but no warning that the estimate needs a calibrated clock. The lesson: check units in every rate, and always state the uncertainty of a molecular-clock date.
Key terms
| Evolution | The change in the inheritable characteristics of a population over time; a change in allele frequencies. |
| Population | A group of organisms of one species living and interbreeding in the same area at the same time. |
| Fossil | Preserved remains or traces of an organism that lived in the past. |
| Superposition | In undisturbed sedimentary rock, lower layers are older than the layers above them. |
| Half-life | The time taken for half of the radioactive atoms in a sample to decay. |
| Transitional fossil | A fossil with features of both an ancestral group and a descendant group. |
| Homologous structures | Structures with the same basic plan, inherited from a common ancestor, which may have different functions. |
| Analogous structures | Structures with the same function but different structure and separate evolutionary origins. |
| Vestigial structure | A reduced structure with little or no function, homologous to a functional structure in related species. |
| Divergent / convergent evolution | One ancestral structure modified for different functions / unrelated organisms evolving similar features. |
| Molecular clock | Using the number of DNA or protein differences, calibrated with dated fossils, to estimate when two lineages split. |
| Branching evolutionary diagram | A tree showing relationships; each branch point is the last common ancestor of the species above it. |
Think like a scientist
Criterion A A museum is preparing a display called “Three lines of evidence”. It has three exhibits.
Exhibit 1: a fossil jaw with three-toed foot bones from a mudstone layer lying between two volcanic ash layers. Potassium–argon dating gives the lower ash an age of 14 million years and the upper ash an age of 4.0 million years.
Exhibit 2: skeletons of the forelimbs of a mole (digging), a seal (swimming) and a human. Exhibit 3: a table of differences in the 146 amino acids of the β-chain of haemoglobin compared with humans (textbook values): gorilla 1; rhesus monkey 8; dog 15; horse 25; chicken 45; frog 67.
(a) State what is meant by evolution, and explain why a single fossil jaw cannot show evolution on its own. [2]
(b) State the age range of the fossil in Exhibit 1 and explain how you know. [2]
(c) Explain how Exhibit 2 provides evidence for evolution, using the terms homologous and divergent evolution. [3]
(d) Calculate the percentage of β-chain amino acids that are identical between humans and dogs, and between humans and chickens. [2]
(e) Draw (or describe) a branching diagram for human, gorilla, dog and chicken consistent with Exhibit 3, and identify which branch point represents the most recent common ancestor of humans and dogs. [3]
(f) A visitor says: “The frog is at the bottom of the table, so it is the most primitive animal.” Evaluate this statement. [2]
Model answer
(a) Evolution is the change in the inheritable characteristics of a population over time — a change in allele frequencies across generations [1]. A single fossil is one individual at one moment; evolution is change, which can only be shown by comparing forms from different times — a sequence of fossils from layers of different ages [1].
(b) Between about 14 and 4.0 million years old [1]: by superposition the mudstone was laid down after the lower ash (so it is younger than 14 million years) and before the upper ash (so it is older than 4.0 million years) [1].
(c) The mole, seal and human forelimbs contain the same bones in the same arrangement — humerus, radius and ulna, carpals, metacarpals and phalanges — so they are homologous structures [1]. This shared plan is best explained by inheritance from a common ancestor with a pentadactyl limb [1]. In different environments natural selection modified the same plan for digging, swimming and grasping — divergent evolution [1].
(d) Dog:
Identical = 146 − 15 = 131
Percentage = 131 ÷ 146 × 100
Percentage = 89.7 % [1]
Chicken:
Identical = 146 − 45 = 101
Percentage = 101 ÷ 146 × 100
Percentage = 69.2 % [1]
(e) Human and gorilla join at the most recent branch point (1 difference); dog joins that pair at the next branch point (15 differences); chicken joins at the root (45 differences): ((human, gorilla), dog), chicken [2]. The most recent common ancestor of humans and dogs is the second branch point, the one where the dog joins the human–gorilla pair [1].
(f) The statement is not valid. The table lists differences from humans, so the frog is simply the most distantly related to humans of those listed — its lineage split from ours earliest [1].
It has evolved for exactly as long as humans since that split and is well adapted to its own environment; “primitive” would only describe particular ancestral features, not the whole animal, and the order in a table says nothing about which species is more advanced [1].
Probe deeper — exam-style questions
Attempt every question before opening the answer. Marks in brackets show what a full answer is worth.
Outline two conditions that make it more likely that a dead organism will become a fossil.
Reveal answer
Any two: rapid burial in sediment such as mud, sand or volcanic ash [1], which keeps out scavengers and oxygen and slows decay [1]; hard parts such as bones, teeth or shells [1]; conditions without oxygen (lake or sea floor) [1]; mineral-rich water seeping through the sediment to replace the tissue [1]. (Maximum 2.)
A piece of wood contains 3.125 % of the carbon-14 found in living wood. Calculate its age (half-life 5 730 years).
Reveal answer
100 → 50 → 25 → 12.5 → 6.25 → 3.125 %: five half-lives [1]
Age = 5 × 5 730 years
Age = 28 650 years, about 29 000 years [1]
Describe three changes seen in the fossil record of the horse from Hyracotherium to Equus, and suggest an environmental reason for one of them.
Reveal answer
Increase in size, from about 30–40 cm to about 1.6 m at the shoulder [1]; reduction in the number of toes touching the ground, from four on the front foot to one hoof, with side toes left as splint bones [1]; teeth becoming higher-crowned and ridged [1].
Reason: grasslands spread and grass contains hard silica that wears teeth, so high-crowned teeth lasted longer (or open plains favoured fast running on long legs with one strong toe) [1]. (Maximum 3.)
Distinguish between homologous and analogous structures, giving an example of each.
Reveal answer
Homologous structures have the same basic structure because they were inherited from a common ancestor, though they may have different functions — for example the forelimbs of a human, bat and whale [1]. Analogous structures have the same function but different structures and separate origins — for example the wings of a bird and a butterfly [1].
The table gives the number of differences in a protein between four species: A–B 2; A–C 18; A–D 30; B–C 17; B–D 31; C–D 29. Identify the two most closely related species, and construct a branching diagram for all four.
Reveal answer
A and B are most closely related — only 2 differences [1]. C joins the A–B pair next (17–18 differences) [1]; D joins at the root (29–31 differences): ((A, B), C), D [1].
Explain why the pelvic bones of a whale are described as vestigial and why they are evidence for evolution.
Reveal answer
They are small, not attached to the spine and do not support legs, so they have little or no function for locomotion [1]. They are homologous to the pelvis that anchors the hind legs of land mammals [1]. Their presence is explained by descent from four-legged land ancestors (as shown by fossils such as Pakicetus and Ambulocetus), with the hind limbs reduced over many generations as the animals became aquatic [1].
7. A volcanic ash layer lies directly on top of a fossil. Its potassium-40 has gone through exactly 0.0024 of a half-life since the ash cooled (half-life 1.25 × 10⁹ years). A bone fragment in the same layer contains too little carbon-14 to measure. Calculate the age of the ash, and explain why carbon-14 cannot date the fossil and what the ash date tells you about it.
Reveal answer
Age = fraction of a half-life × half-life
Age = 0.0024 × 1.25 × 10⁹ years
Age = 3.0 × 10⁶ years (3.0 million years) [1]
Carbon-14’s half-life is 5 730 years; after 3 million years — over 500 half-lives — essentially none remains, and above about 50 000 years too little is left to measure [1].
The ash lies directly above the fossil, so by superposition the fossil is older than the ash: at least 3.0 million years [1]. To narrow the age, a second ash layer below the fossil would be dated; the fossil lies between the two dates [1].
8. Bird wings and bat wings are both built on the pentadactyl limb, but in birds the wing surface is made of feathers on a hand with fused, reduced fingers, while in bats it is skin stretched between four very long fingers. Pterosaurs (extinct flying reptiles) stretched skin from one enormously long fourth finger. Discuss whether these wings are homologous or analogous, and what this example shows about the limits of those two terms.
Reveal answer
As forelimbs they are homologous: all three contain a humerus, radius, ulna, carpals, metacarpals and phalanges inherited from the common four-limbed ancestor of reptiles, birds and mammals [1].
As wings they are analogous: the common ancestor did not fly, and each group turned the forelimb into a wing independently — feathers in birds, four fingers in bats, one finger in pterosaurs — so the flight surface evolved separately three times (convergent evolution) [1].
The different solutions (different fingers, different surfaces) are themselves evidence that the wings were not inherited as wings [1]. So “homologous” and “analogous” apply to a structure at a stated level — the same organ can be homologous as a limb and analogous as a wing; an answer must say which level it means [1].
Summary
- Evolution is the change in the inheritable characteristics of a population over time — a change in allele frequencies. Individuals do not evolve; populations do.
- Fossils form mainly by rapid burial and mineral replacement of hard parts; the record is incomplete. Superposition orders fossils; radiometric dating gives ages (carbon-14, half-life 5 730 years, to about 50 000 years; potassium-40 for volcanic ash above and below older fossils).
- The horse record (Hyracotherium to Equus, about 55 million years) shows increasing size, fewer toes and higher-crowned teeth as grasslands spread — one path through a branching bush. Transitional fossils (Tiktaalik, Archaeopteryx, early whales) appear where predicted.
- Homologous structures (the pentadactyl limb) show common ancestry and divergent evolution; analogous structures show convergent evolution; vestigial structures (whale pelvis, horse splint bones) are inherited remnants.
- The universal genetic code and counts of DNA and protein differences rank species by relatedness; branching diagrams show it, and relatedness is read from the most recent shared branch point.
Next time → Natural selection in depth: why variation, overproduction and competition make allele frequencies change, how to calculate an allele frequency, the three shapes of selection — and why a crocodile has hardly changed in tens of millions of years.