Genetic Diversity and Allele Frequencies

Spec Mapping — OCR H420 Module 4.2.1 — Biodiversity, content statements covering the measurement of genetic diversity within a population, the calculation of allele frequencies, and factors (selection, drift, bottleneck, founder effect) that change them (refer to the official OCR H420 specification document for exact wording). This lesson is the genetic foundation for everything in Module 4.2.2 — without allele-frequency change there is no evolution.

Genetic diversity is the raw material of evolution. Without variation in alleles, natural selection has nothing to act on and populations cannot adapt to environmental change. This lesson examines how genetic diversity is measured, why it matters, and how human activities (both destructive and constructive) alter allele frequencies over time. OCR A-Level Biology A Module 4.2.1 requires you to calculate genetic diversity within a population and to explain the factors that affect it.

The mathematical framework of population genetics was built in the early twentieth century by Godfrey Hardy (Cambridge mathematician) and Wilhelm Weinberg (Stuttgart physician), each in 1908 independently deriving the equation that bears both their names. Gregor Mendel's 1866 work on inheritance — overlooked for nearly forty years — provided the particulate-inheritance foundation on which Hardy-Weinberg rests. The synthesis of Mendelian genetics with natural selection in the 1930s and 1940s (Fisher, Haldane, Wright) produced the modern synthesis that defines evolution as a change in allele frequencies over generations. Theodosius Dobzhansky's famous observation that nothing in biology makes sense except in the light of evolution applies with particular force here: allele frequencies are the operational currency of evolution.

Key Definitions:

• Gene — a sequence of DNA that codes for a protein (or functional RNA).
• Allele — a variant form of a gene.
• Locus — the position of a gene on a chromosome.
• Polymorphic locus — a locus where more than one allele exists in the population at a frequency above 1%.
• Genetic diversity — the variety of alleles and genotypes within a population.
• Gene pool — the complete set of alleles in a population.

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Measuring Genetic Diversity

One common measure is the proportion of polymorphic gene loci:

$\text{Proportion of polymorphic loci} = \frac{\text{Number of polymorphic loci}}{\text{Total number of loci}}$Proportion of polymorphic loci=Total number of lociNumber of polymorphic loci​

A locus is considered polymorphic if two or more alleles are each present at frequencies of at least 1% (i.e. a second allele is not just a rare mutation).

Worked example: A study of a population of snails examines 50 gene loci and finds that 18 of them have two or more alleles at frequencies ≥ 1%. The proportion of polymorphic loci is:

18 / 50 = 0.36 \text{ (or 36%)}

Other measures include:

• Mean number of alleles per locus — averaged across all loci studied.
• Heterozygosity — the proportion of individuals that are heterozygous at a given locus.
• Allele frequency — the proportion of one allele relative to all alleles at a locus.

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Allele Frequency Calculations

For a gene with two alleles (A and a), the allele frequencies are conventionally called p (frequency of A) and q (frequency of a), with p + q = 1.

Example: In a population of 100 butterflies, the genotypes are:

• AA: 36
• Aa: 48
• aa: 16

Each individual has two alleles, so the total number of alleles = 200.

Number of A alleles = (2 × 36) + 48 = 72 + 48 = 120 Number of a alleles = (2 × 16) + 48 = 32 + 48 = 80

$p = 120/200 = 0.60, \quad q = 80/200 = 0.40$p=120/200=0.60,q=80/200=0.40

Check: p + q = 1.00 ✓

Exam Tip: Allele frequency calculations reward careful bookkeeping. Count all alleles (each individual contributes two), then divide. Mistakes come from forgetting that heterozygotes contribute one of each allele.

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Why Genetic Diversity Matters

flowchart LR
    A[Genetic Diversity] --> B[More alleles]
    B --> C[More phenotypic variation]
    C --> D[Natural selection has more to choose from]
    D --> E[Population adapts to change]
    A --> F[Reduced inbreeding]
    F --> G[Fewer recessive diseases expressed]

• Adaptability. Populations with more alleles are more likely to contain individuals with resistance to new diseases, pollutants or climates.
• Long-term survival. Small, inbred populations accumulate deleterious recessive alleles — a phenomenon called inbreeding depression.
• Ecosystem function. Genetically diverse plant populations are more productive and resilient.
• Conservation value. Species with low genetic diversity (cheetah, Hawaiian honeycreeper) need special management.

Case Study: The Cheetah Bottleneck

Around 10,000 years ago, cheetah populations crashed — possibly to fewer than 100 individuals — during the end of the Pleistocene. Every modern cheetah is descended from those few survivors. As a result, cheetahs are so genetically similar that skin grafts between unrelated individuals are not rejected — a level of homogeneity normally seen only in inbred laboratory mice. Cheetahs show high juvenile mortality, low sperm count and susceptibility to disease, all linked to genetic poverty.

Case Study: Florida Panthers

By the 1990s, the Florida panther population had fallen to fewer than 30 individuals, with kinked tails, heart defects and low fertility — all signs of inbreeding depression. Conservationists introduced eight female Texas cougars in 1995 to add genetic variation. Within a decade, the population had tripled and health problems declined.

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Sources of Genetic Variation

Where does genetic diversity come from? From several sources:

1. Mutation. Random changes in DNA sequence generate new alleles. Point mutations, indels, duplications and chromosomal rearrangements all contribute.
2. Meiosis. Independent assortment of chromosomes and crossing over shuffle existing alleles into new combinations.
3. Random fertilisation. Any sperm can fertilise any egg, multiplying the possible combinations.
4. Gene flow. Immigration of individuals from other populations introduces new alleles.
5. Sexual reproduction in general, because it combines alleles from two parents.

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Factors that Reduce Genetic Diversity

Factor	Mechanism
Small population size	Random drift eliminates alleles by chance
Population bottlenecks	Disasters (fires, hunting, disease) kill most individuals and alleles
Founder effect	A small group colonises a new area; only a subset of alleles goes with them
Inbreeding	Mating between relatives increases homozygosity
Artificial selection	Breeders select for a few traits, discarding the rest
Habitat fragmentation	Isolates populations and prevents gene flow

Population Bottleneck Example

The northern elephant seal was hunted to near-extinction in the 19th century; by 1890 fewer than 30 individuals remained. Today's population has rebounded to around 175,000 but shows almost no variation at many loci — a direct legacy of the bottleneck.

Founder Effect Example

When a small group of Europeans settled the South African Cape in the 17th century, they carried a relatively high frequency of the allele causing variegate porphyria. The disease is now unusually common among their Afrikaner descendants — a classic founder effect.

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Selective Breeding and Loss of Diversity

Modern agriculture depends on highly selected breeds and varieties that have dramatically reduced genetic diversity. Commercial bananas, for example, are almost all a single clonal variety (Cavendish), making them vulnerable to any disease that can overcome their defences. The original Gros Michel banana was wiped out by Panama disease in the 1950s; the Cavendish now faces the same threat from a new strain (TR4).

Similar concerns apply to:

• Wheat and rice — industrial cultivars dominate, while land races (traditional varieties) are lost.
• Pedigree dog breeds — closed studbooks inbreed founding stock; hip dysplasia in German Shepherds and respiratory problems in pugs result.
• Dairy cattle — Holsteins dominate dairy farming and show accumulating inherited defects.

Seed banks and living collections (see Lesson 6) preserve this lost diversity for future use.

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Hardy-Weinberg Principle (Brief)

Though more detailed in Module 6, Hardy-Weinberg is relevant here. Under idealised conditions (no mutation, no selection, no migration, random mating, large population), allele frequencies remain constant from generation to generation:

$p^2 + 2pq + q^2 = 1$p2+2pq+q2=1

Where:

• p² = frequency of homozygous dominant (AA)
• 2pq = frequency of heterozygous (Aa)
• q² = frequency of homozygous recessive (aa)

If observed frequencies differ from Hardy-Weinberg expectations, evolution is occurring. OCR may ask you to use this principle to estimate carrier frequencies for recessive genetic disorders.

Example: Cystic fibrosis affects about 1 in 2,500 UK births. So q² = 1/2500 = 0.0004, giving q = 0.02. Then p = 0.98, and the heterozygote (carrier) frequency is 2pq = 2 × 0.98 × 0.02 = 0.0392, or about 1 in 25 — a large fraction of the population.

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Preserving Genetic Diversity

Conservation strategies targeting genetic diversity include:

1. Maintaining large populations in nature reserves.
2. Connecting fragmented populations with wildlife corridors.
3. Gene banks and seed banks (e.g. Millennium Seed Bank at Kew).
4. Captive breeding with outbreeding protocols to maximise heterozygosity.
5. Protecting crop wild relatives — wild species closely related to cultivated crops, carrying genetic variation that has been lost from cultivars.

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Common Exam Mistakes

• Confusing genes and alleles. All members of a species share the same genes; they differ in alleles.
• Forgetting that heterozygotes contribute one of each allele. When counting alleles in a population, heterozygotes count as 1 A and 1 a, not 2 of either.
• Assuming mutation always decreases diversity. Mutation generates diversity; selection and drift remove it.
• Ignoring population size. Small populations lose diversity regardless of the selection pressure.
• Confusing bottleneck with founder effect. A bottleneck is a population reduction in place; the founder effect is a small group leaving to colonise elsewhere.

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Quick Recap

• Genetic diversity is the variety of alleles within a population, measured by polymorphic loci, heterozygosity or allele frequencies.
• Higher genetic diversity → greater adaptability, resilience and long-term survival.
• Sources of variation: mutation, meiosis, random fertilisation, gene flow.
• Diversity is reduced by bottlenecks, founder effects, inbreeding, artificial selection and habitat fragmentation.
• Hardy-Weinberg ($p^2 + 2pq + q^2 = 1$p2+2pq+q2=1) lets us estimate carrier frequencies from observed disease rates.

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Extended Hardy-Weinberg Worked Examples

Example: Sickle-Cell Anaemia

Sickle-cell anaemia is a recessive disorder caused by a single base substitution in the β-globin gene. In a hypothetical West African population, the homozygous-recessive incidence is roughly q² ≈ 0.04 (4 in 100 newborns affected — note this is a deliberately rounded illustrative figure, not a literal demographic claim). Then:

• $q = \sqrt{0.04} = 0.2$q=0.04​=0.2
• $p = 1 - q = 0.8$p=1−q=0.8
• Heterozygote (carrier) frequency = $2pq = 2 \times 0.8 \times 0.2 = 0.32$2pq=2×0.8×0.2=0.32, i.e. 32% are carriers
• Homozygous dominant = $p^2 = 0.64$p2=0.64, i.e. 64% are unaffected non-carriers

Check: $p^2 + 2pq + q^2 = 0.64 + 0.32 + 0.04 = 1.00$p2+2pq+q2=0.64+0.32+0.04=1.00 ✓.

Example: Phenylketonuria (PKU)

PKU has an incidence in the UK of roughly 1 in 10,000 births, so $q^2 \approx 1 \times 10^{-4}$q2≈1×10−4 and $q \approx 0.01$q≈0.01. Heterozygote frequency is then $2pq \approx 2 \times 0.99 \times 0.01 \approx 0.0198$2pq≈2×0.99×0.01≈0.0198, or about 1 in 50 — much higher than the affected-individual frequency, which is why genetic-counselling screens identify so many heterozygous carriers among reproductive-age adults.

KaTeX summary of HW assumptions

$p + q = 1 \quad \Longrightarrow \quad p^2 + 2pq + q^2 = 1$p+q=1⟹p2+2pq+q2=1

Equilibrium holds only when all five assumptions are simultaneously met:

Assumption	What it requires	Real-world violation
No mutation	No new alleles arising	Always violated, but at low rate
Random mating	No assortative mating	Many species mate assortatively (sexual selection)
No migration	Closed population	Gene flow is common
No selection	All genotypes equally fit	Almost always violated to some degree
Large population	No drift	Small populations drift heavily

If observed genotype frequencies differ from HW expectations, the population is not in equilibrium — meaning one or more of the assumptions fails, and evolution is taking place.

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