Population Genetics: Study Guide (Biology 7.4)

What “evolution” means in a population

In Topics 7.2 and 7.3 you saw selection change traits over generations. Population genetics looks at the same change through the genes. A population is a group of individuals of one species living in one area that can interbreed. Together their alleles form the gene pool.

The key measure is allele frequency: the fraction of all copies of a gene in the population that are one particular allele.

allele frequency = copies of that allele ÷ total copies of the gene

In a diploid population, each individual carries two copies of each gene, so the total is 2 × the number of individuals. A homozygote (AA) carries two copies of A; a heterozygote (Aa) carries one.

A population evolves when its allele frequencies change across generations. So a measured change in allele frequency is direct evidence that evolution has happened. Natural selection is one cause. This topic adds the causes that do not depend on whether an allele is useful: mutation, genetic drift and gene flow.

Mutation: the source of new alleles

A mutation is a change in the DNA sequence (Topic 6.7). Mutations arise at random: a cell does not produce the mutation it “needs”. Most have no effect or are harmful; a few are useful in a particular environment.

• Mutation is the only process that creates brand-new alleles. All variation that selection acts on traces back to mutation.
• For any one gene, mutation is rare, so mutation alone shifts allele frequencies very slowly.
• What happens to a new allele next depends on selection and on chance.

Genetic drift: change by chance

Genetic drift is a change in allele frequencies caused by chance events, not by the alleles’ effects. Each generation, only some individuals happen to breed, and each parent passes on one of its two alleles at random. The next generation is a sample of the alleles in the parents, and samples rarely match exactly.

Think of tossing a coin. Ten tosses can easily give 7 heads (70%); a thousand tosses will almost never give 700. In the same way, drift is strong in small populations and weak in large ones.

Reading Figure 1. All six populations start at 0.5 and experience no selection at all. Within 15 generations, two of the three small populations reached 1.0 (the allele is fixed: every copy is that allele) or 0 (the allele is lost). Once that happens, drift cannot bring the allele back; only mutation or gene flow can. The large populations stayed between 0.44 and 0.69. The direction of drift is random; which allele wins is a matter of chance.

Consequences of drift:

• It reduces genetic variation within a population, as alleles are lost or fixed.
• It can make a harmful allele common or remove a useful one, because chance, not effect, is in control.
• It makes separate small populations of one species diverge from each other, even in identical environments.

The bottleneck effect

A bottleneck happens when a population is cut to a small number of individuals for at least one generation, for example by a flood, a fire, disease or hunting. The survivors’ alleles are a chance sample of the original gene pool. Alleles that happened not to be among them are gone, even if the population later grows large again.

A real example. Hunting in the 1800s cut the northern elephant seal to a tiny remnant, perhaps a few tens of animals. Protected, the population has since grown to well over 100,000, but genetic studies show a sharp loss of variation and high homozygosity. Size recovered; lost alleles did not.

The founder effect

The founder effect happens when a few individuals leave a population and start a new, separate one, for example by colonising an island. The new gene pool contains only the founders’ alleles, at the founders’ frequencies. A rare allele can become common in the new population simply because one founder happened to carry it.

Human examples exist: some genetic conditions are much more common in small, long-isolated communities descended from few founders. For instance, Ellis–van Creveld syndrome, a rare inherited condition that includes extra fingers (polydactyly), is far more common among the Old Order Amish of Lancaster County, Pennsylvania, than in most other populations.

Bottleneck or founder effect? In a bottleneck, the original population itself shrinks. In a founder event, a small group splits off and the original population may continue unchanged. Both are drift: the new gene pool is a chance sample.

Gene flow: alleles on the move

Gene flow is the movement of alleles between populations, when individuals migrate and breed (or when pollen or seeds are carried). It can add alleles to a population, including new ones, and it removes alleles from the population that the migrants leave.

Gene flow makes connected populations more similar. Each exchange pulls their allele frequencies toward each other. This is why continued gene flow stops two populations from splitting into separate species. Cut off gene flow (a new dam, road or rising sea) and drift, mutation and selection can act on each population separately, so they drift apart.

Gene flow can also help a population that has lost variation. Bringing in individuals from a larger population restores alleles, a process conservation biologists call genetic rescue.

Process	Random?	Effect on variation within a population	Effect on differences between populations
Mutation	yes	adds new alleles (slowly)	can increase
Genetic drift (incl. bottleneck, founder)	yes	decreases (alleles lost or fixed)	increases
Gene flow	not selective	usually increases	decreases
Natural selection	no	often decreases	can increase (different environments)

Worked example 1: a bottleneck in numbers

Question. A fictional island population of 500 ground beetles has these genotypes for a wing-colour gene: 180 AA, 240 Aa, 80 aa. A storm leaves 12 survivors: 2 AA, 4 Aa, 6 aa. (a) Calculate the frequency of A before and after the storm. (b) Has the population evolved? (c) State a null hypothesis for whether the storm acted as selection, and say what you would need to test it.

(a) Before the storm.

1. Total alleles = 2 × 500 = 1000.
2. Copies of A = (2 × 180) + 240 = 360 + 240 = 600.
3. Frequency of A = 600 ÷ 1000 = 0.60; frequency of a = 1 − 0.60 = 0.40.

After the storm.

1. Total alleles = 2 × 12 = 24.
2. Copies of A = (2 × 2) + 4 = 8.
3. Frequency of A = 8 ÷ 24 = 0.333; frequency of a = 0.667.

Check. The two frequencies add to 1 in each case.

(b) The frequency of A fell by 0.267 (from 0.60 to 0.333). If the descendants keep these frequencies, the population has evolved: its allele frequencies have changed between generations. Strictly, you confirm evolution by measuring the next generation.

(c) Null hypothesis: “Survival in the storm was independent of genotype at this gene.” If survival were random, 12 survivors drawn from the original proportions would include about 4.3 AA, 5.8 Aa and 1.9 aa on average. The observed 2, 4 and 6 differ, most clearly the 6 aa beetles against about 1.9 expected. A difference this large would arise by chance only rarely (roughly 2 times in 100), so it hints at selection, but one storm and 12 beetles is a single small sample. To test the null hypothesis you would need more evidence: for example, repeat observations from several storms or islands, or a mechanism by which wing colour could affect survival. If aa beetles did better every time, selection is likely; if the direction varies, drift is the better explanation.

A second gene shows drift’s other effect. Allele B2 had a frequency of 0.02 before the storm (20 of 1000 copies). The chance that none of the 24 surviving alleles is B2 is 0.98²⁴ ≈ 0.62, so B2 is more likely than not to be lost, regardless of what it does.

Worked example 2: founders and gene flow

Question. On a fictional mainland, the frequency of a stripe allele S in a lizard population is 0.20. Eight lizards raft to an empty island: 1 SS, 3 Ss and 4 ss. (a) Calculate the frequency of S among the founders. (b) Many generations later the island holds 60 lizards with S at 0.40. Fifteen mainland lizards then arrive and breed. Calculate the new frequency of S. (c) Explain what continued migration would do.

(a) Total alleles = 2 × 8 = 16. Copies of S = (2 × 1) + 3 = 5. Frequency = 5 ÷ 16 = 0.3125 ≈ 0.31, already higher than the mainland’s 0.20 by chance alone: a founder effect.

(b) Count alleles in each group, then combine.

1. Island: 2 × 60 = 120 alleles; S = 0.40 × 120 = 48.
2. Migrants: 2 × 15 = 30 alleles; S = 0.20 × 30 = 6.
3. Combined: S = 48 + 6 = 54, out of 120 + 30 = 150 alleles.
4. New frequency of S = 54 ÷ 150 = 0.36.

(c) Each wave of migrants pulls the island frequency toward the mainland value (0.40 → 0.36). If the same proportion of migrants arrived every generation, and nothing else acted, the frequency would continue falling toward 0.20 (about 0.27 after five such generations). Gene flow is keeping the two populations alike, working against the divergence that the founder effect and drift started.

Common misconceptions

• “Organisms mutate because they need to adapt.” Mutations are random with respect to need. Selection then acts on whatever arises.
• “Genetic drift only happens in small populations.” It happens in all populations; it is just much stronger in small ones.
• “Drift favours the better allele.” Drift ignores an allele’s effect. Only selection favours alleles by their effects.
• “Once a bottlenecked population grows back, its variation returns.” Lost alleles stay lost unless mutation or gene flow restores them.
• “The founder effect and the bottleneck effect are the same.” In a founder event a small group separates; in a bottleneck the whole population shrinks.
• “Evolution means individuals change.” Individuals do not evolve. Populations evolve, as their allele frequencies change across generations.
• “Allele frequency = fraction of individuals showing the trait.” Count alleles, not phenotypes; heterozygotes carry one copy of each allele.

Where this leads

Next, Topic 7.5, Hardy–Weinberg Equilibrium, describes what allele and genotype frequencies look like when none of these processes is acting, and uses that as a null model to detect evolution. Test yourself with the practice questions, then use the revision notes and the checklist to consolidate. For how human choice changes allele frequencies, look back at Topic 7.3, Artificial Selection.