Fossil Record, Molecular Clocks, and Evolution in Action

The fossil record, molecular evidence and observations of evolution in action all show that populations change over time and that living things share common ancestors. In brief: fossils show the order in which groups appeared and include transitional forms, DNA and protein comparisons show how closely species are related, and antibiotic resistance in bacteria is evolution that can be seen within years. Humans and chimpanzees, for example, have DNA sequences that are about 98 to 99 percent identical in the regions that can be aligned.

These lines of evidence are independent of one another, and they agree, which is why scientists have great confidence in the theory of evolution. This guide explains how fossils form and are dated, gives examples of transitional fossils, describes molecular evidence and the molecular clock, looks at antibiotic resistance as a modern case, works through a half-life dating example and corrects common mistakes.

What is the fossil record?

Fossils are the preserved remains or traces of organisms that lived in the past. Most form when an organism dies and is quickly buried in sediment, for example in a river or sea. Hard parts such as bones, teeth and shells are most likely to fossilize. Minerals may replace the original material, or the organism may leave an imprint or a cast. Rarely, whole organisms are preserved in amber, ice or tar. Because the process is rare, the fossil record is incomplete, but thousands of species have been found.

Layers of sedimentary rock (strata) are laid down over time, so in an undisturbed sequence the deeper layers are older. Fossils in the layers show a pattern: simpler organisms in older strata, and more recent groups in younger strata. Mammals do not appear in layers as old as those with trilobites, and humans do not appear in layers as old as those with dinosaurs.

How are fossils dated?

There are two main approaches. Relative dating uses the order of strata and index fossils (fossils of species that lived for a short time and were widespread) to decide that one fossil is older than another. Absolute dating uses radioactive decay. Unstable isotopes decay at a constant rate, described by the half-life, the time for half of the atoms in a sample to decay.

• Carbon-14 (half-life 5 730 years) is used for organic remains up to about 50 000 years old.
• Potassium-40 (half-life about 1.25 billion years) and uranium-238 (about 4.5 billion years) are used for volcanic rocks and give ages for older layers, by dating volcanic ash layers above and below the fossils.

Using these methods, Earth’s age is estimated at about 4.54 billion years, and the oldest accepted fossils of microorganisms date to around 3.5 billion years.

What are transitional fossils?

Transitional fossils show features of two groups and illustrate how one group evolved from another. Examples include:

• Archaeopteryx (about 150 million years old): had feathers and wings like a bird, but also teeth, a long bony tail and clawed fingers like small theropod dinosaurs.
• Tiktaalik (about 375 million years old): a fish with a flat head, a neck and limb-like fins with wrist bones, found in Arctic Canada after scientists predicted where to look for rocks of the right age.
• Whale ancestors, such as Pakicetus, Ambulocetus and Rodhocetus, which show the changes from land mammals to fully aquatic whales over about 10 to 15 million years: the nostrils moved back, the hind limbs got smaller and the ear bones changed.
• Hominin fossils such as Australopithecus afarensis (“Lucy”, about 3.2 million years old) and Homo erectus show the evolution of upright walking and larger brains.

What does molecular evidence show?

All living things use DNA as genetic material and the same genetic code, with nearly the same 20 amino acids. This universality is evidence of common ancestry. Closely related species have more similar DNA and protein sequences. For example, human and chimpanzee hemoglobin chains are identical, the beta chains of humans and gorillas differ by a single amino acid, and human and frog hemoglobins differ by many more. Cytochrome c, a protein that is needed for respiration, differs by one amino acid between humans and rhesus monkeys, and by about 10 between humans and dogs, and by more than 20 between humans and yeast.

Scientists use DNA sequences to build phylogenetic trees. The trees obtained from DNA usually agree with those drawn from anatomy and fossils, which is strong support for the theory. Shared “mistakes” in DNA also provide evidence: humans and other primates share many of the same broken genes, such as the gene for vitamin C synthesis (GULO), which is non-functional in all of them.

What is a molecular clock?

Mutations accumulate in DNA at a fairly steady rate over time, particularly those with no effect on fitness. The number of differences between the sequences of two species is therefore proportional to the time since they shared a common ancestor. If the rate of change is known (calibrated using a fossil date), the number of differences can be used to estimate the time of divergence. The clock is not perfectly regular, as rates vary between genes and lineages, so estimates are given with a range of uncertainty.

What is antibiotic resistance?

Evolution can be observed directly in organisms that reproduce quickly. When an antibiotic is used, it kills sensitive bacteria, and any bacteria with a mutation or a gene for resistance survive and multiply. Within a few generations, the population is mostly resistant. Resistant bacteria such as MRSA (methicillin-resistant Staphylococcus aureus) are examples. Other examples are insecticide resistance in mosquitoes and the evolution of herbicide resistance in weeds. Misuse of antibiotics, such as incomplete courses or use for viral infections, increases selection for resistance.

Fossil examples and what they show

Worked example: radiometric dating and a molecular clock

Carbon-14 dating

A bone fragment has 25 percent of the carbon-14 that a living organism would have. The half-life is 5 730 years. How old is it?

1. After one half-life, 50 percent remains. After two half-lives, 25 percent remains.
2. The number of half-lives is therefore 2.
3. Age = 2 × 5 730 = 11 460 years.

If 12.5 percent remained, three half-lives would have passed: 3 × 5 730 = 17 190 years. For non-whole numbers, use the formula age = half-life × log₂(initial ÷ remaining). For 40 percent remaining: log₂(100 ÷ 40) = log₂(2.5) ≈ 1.32, so the age is 1.32 × 5 730 ≈ 7 570 years.

Molecular clock

Two species differ at 12 positions in a gene of 1 000 bases. Fossils show that their lineages split 30 million years ago, based on a calibration with another pair, in which 20 differences corresponded to 50 million years.

1. Rate from the calibration pair: 20 differences ÷ 50 million years = 0.4 differences per million years, counted between the two sequences (both lineages together).
2. Time for the new pair: 12 differences ÷ 0.4 differences per million years = 30 million years.

The calculation gives 30 million years, consistent with the fossil estimate. This agreement between independent methods is the type of consistency that gives confidence in the dating. The example is simplified, and real calibrations use many genes and statistical methods.

How has the evidence developed?

Mary Anning found important marine reptile fossils in England in the early nineteenth century, and Darwin discovered fossil mammals in South America. Archaeopteryx was discovered in 1861, soon after On the Origin of Species. Willard Libby developed radiocarbon dating in the late 1940s and received the Nobel Prize in Chemistry in 1960. Emile Zuckerkandl and Linus Pauling proposed the molecular clock in the early 1960s. Tiktaalik was found in 2004.

Which mistakes are common?

Mistake 1: Saying that there is a “missing link” that disproves evolution

Many transitional fossils have been found. The record is incomplete, since fossilization is rare, but this does not undermine the evidence.

Mistake 2: Using carbon dating on very old rocks

Carbon-14 decays too fast for samples older than about 50 000 years. Other isotopes are used for older materials.

Mistake 3: Treating a molecular clock as perfectly accurate

Mutation rates vary, so estimates have a margin of error and need calibration.

Mistake 4: Confusing resistance that develops in one person with evolution

Resistance evolves in the bacterial population by selection. A person’s body does not become “resistant to antibiotics”.