# Genetic Variation in Populations

> Single nucleotide polymorphisms, DNA sequencing and profiling, gene pools, allele frequencies and how population genetics is used in conservation and health.

From HSC Biology on WhizzNotes, free study notes for NSW students: https://whizznotes.com/biology/genetic-variation-in-populations/. Updated 3 November 2026.
Year 11 and Year 12 boxes go deeper than the Year 10 text around them.

### Story time: The Tasmanian devil detectives
Since the 1990s, a contagious cancer called devil facial tumour disease has killed most of the wild Tasmanian devils. To save them, scientists keep an "insurance population" of healthy devils in sanctuaries and zoos.

But which devils should breed? Scientists take a small DNA sample from each one and compare thousands of points in their genomes. Then they pair devils that are the **least** related, to keep as much genetic variety as possible in the population. Without DNA tools, they would be guessing.

**In short:** Genetic variation is the differences in DNA between individuals, caused by mutation, meiosis, random fertilisation and gene flow. All the alleles in a population form its gene pool, and selection, gene flow and genetic drift change how common each allele is.

## Starting point: what you already know

- Alleles are versions of a gene. Meiosis and fertilisation create variation (see DNA, Chromosomes and Cell Division).
- DNA bases pair A with T and C with G.
- A population is all the members of one species in an area.

## Where genetic variation comes from

- **Mutations** make new alleles.
- **Meiosis** (crossing over and independent assortment) shuffles alleles.
- **Random fertilisation** joins any sperm with any egg.
- **Gene flow**: alleles move between populations when individuals migrate and breed.

## Single nucleotide polymorphisms (SNPs)

Any two people's DNA is about 99.9% the same. Most of the 0.1% difference is made of **SNPs** (said "snips"): places where people differ by a **single base**. One person may have an A where another has a G.

There are millions of SNPs in the human genome. Most have no effect, but some affect disease risk or how a person responds to a medicine. Scanning SNPs lets scientists link genes to traits and work out family relationships.

## Reading and comparing DNA

**DNA sequencing** reads the exact order of bases. The Human Genome Project took 13 years and about 3 billion dollars to read one human genome (finished in 2003). Today a genome can be read in a day for a few hundred dollars.

**DNA profiling** (DNA fingerprinting) compares sections of DNA that vary a lot between people, called **short tandem repeats (STRs)**: short sequences repeated a different number of times in different people.

1. DNA is taken from cells (blood, cheek swab, hair root).
2. **PCR** makes millions of copies of the STR regions.
3. **Gel electrophoresis** separates the copies by size: an electric current pulls DNA (which is negative) through a gel, and smaller pieces travel further.
4. The pattern of bands is compared.

### Worked example: Who is the father?
A child's DNA bands each come from either the mother or the father. Any band in the child that is **not** in the mother must come from the biological father. If a man has none of those bands, he cannot be the father.

DNA profiling is used in crime scenes, paternity tests, identifying disaster victims and tracing family history.

## Population genetics

A **gene pool** is all the alleles in a population. **Allele frequency** is how common an allele is in the gene pool.

### Worked example: Calculating an allele frequency
In a population of 100 frogs: 36 are BB, 48 are Bb, 16 are bb. There are 200 alleles in total.

Number of b alleles: $48 + (2 \times 16) = 80$

$$\text{frequency of b} = \frac{80}{200} = 0.4$$

So the frequency of B is $1 - 0.4 = 0.6$.

Allele frequencies change through **natural selection**, **mutation**, **gene flow** and **genetic drift** (random change, strongest in small populations).

**Mind map**

```text
Genetic variation
  Sources
    Mutation
    Meiosis
    Fertilisation
    Gene flow
  SNPs
    One base differences
    Disease risk and medicines
  DNA tools
    Sequencing reads bases
    Profiling compares STRs
    PCR copies
    Gel electrophoresis sorts by size
  Populations
    Gene pool
    Allele frequency
    Selection, drift, flow
```

### Year 11: Using population genetics
- **Conservation**: low genetic diversity and inbreeding in small populations (devils, cheetahs, northern hairy-nosed wombats) lower fitness. DNA data guide breeding programs and moving animals between populations.
- **Health**: some alleles are more common in particular populations. Testing for them helps diagnose and treat disease.
- **Tracing ancestry**: mitochondrial DNA (from mothers) and Y chromosome DNA (from fathers) track human movement over tens of thousands of years. Studies of Aboriginal Australians' DNA, done in partnership with communities, support continuous occupation of Country for more than 50 000 years.
- **Ethics**: genetic data is private. Who owns it, who can see it, and could insurers use it? Research with Indigenous communities must follow agreed protocols and community consent.

**Founder effect and bottlenecks.** A few individuals starting a new population (birds blown to an island) carry only some of the alleles, so the new allele frequencies differ: the **founder effect**. A population crushed to a few survivors (northern elephant seals fell to about 20) goes through a **bottleneck** and keeps very low diversity even after it grows back.

**Fixed alleles.** If an allele's frequency reaches 1.00, every individual is homozygous for it and the other alleles are lost. It is **fixed**.

**Selection versus drift.** Natural selection changes frequencies because some alleles help survival. Drift changes them by chance, whatever the allele does.

**Heterozygote advantage.** People with one sickle cell allele resist malaria, so in malaria regions this allele stays common even though two copies cause disease.

**Why SNPs are common in non-coding DNA.** A change there usually has no effect, so it is not removed by selection. A change in coding DNA may harm the protein.

**Movement between zoos** acts as gene flow, bringing new alleles in and raising diversity.

### Year 12: The Hardy-Weinberg equation
If a population is large, mates randomly, and has no selection, mutation or migration, allele frequencies stay the same. Then, with $p$ = frequency of the dominant allele and $q$ = frequency of the recessive allele:

$$p + q = 1 \qquad p^2 + 2pq + q^2 = 1$$

$p^2$ is the frequency of homozygous dominant, $2pq$ of heterozygous, $q^2$ of homozygous recessive.

**Example.** 1 in 2500 babies has cystic fibrosis (recessive). So $q^2 = \frac{1}{2500}$, giving $q = \frac{1}{50} = 0.02$ and $p = 0.98$. Carriers: $2pq = 2 \times 0.98 \times 0.02 \approx 0.039$, about 1 in 25 people.

**Counting alleles.** 20 diploid animals carry 40 alleles. If 30 are R, the frequency of R is $\frac{30}{40} = 0.75$.

**Three alleles.** Frequencies still add to 1. If G1 is 0.6 and G2 is 0.25, G3 is 0.15. The expected frequency of G2G2 is $0.25^2 = 0.0625$.

**From the trait to carriers.** If 4% show a recessive trait, $q^2 = 0.04$, so $q = 0.2$, $p = 0.8$ and carriers are $2pq = 0.32$.

## Quick summary

- Variation comes from mutation, meiosis, random fertilisation and gene flow.
- SNPs are single-base differences between people.
- DNA profiling compares STRs using PCR and gel electrophoresis. Smaller pieces move further.
- A gene pool is all the alleles in a population. Allele frequency is how common one allele is.
- Selection, mutation, gene flow and genetic drift change allele frequencies.

## Quiz

Try these questions from the chapter quiz.

1. What is a SNP?
   - A. A whole extra chromosome
   - B. A difference of a single base between individuals
   - C. A type of protein
   - D. A missing gene
   - Answer: B. A difference of a single base between individuals. Single nucleotide polymorphism.

2. In gel electrophoresis, which DNA pieces travel furthest?
   - A. The smallest
   - B. The largest
   - C. The most negative
   - D. All travel the same distance
   - Answer: A. The smallest. Small pieces move through the gel more easily.

3. Which technique makes millions of copies of a piece of DNA?
   - A. Gel electrophoresis
   - B. PCR
   - C. Sequencing
   - D. Meiosis
   - Answer: B. PCR. The polymerase chain reaction copies DNA.

The whole chapter quiz is on the page, for signed-in students: https://whizznotes.com/biology/genetic-variation-in-populations/#quiz