IB Biology HLNatural SelectionPaper 1 & 2~11 min read
Allele Frequencies: Skills
This page is mostly counting. Once you accept that every diploid individual carries exactly two alleles at a locus, working out an allele frequency stops being genetics and becomes arithmetic you can do in your head.
📚 What you need to know
Allele frequency is the relative frequency of one allele at a particular gene locus.
Alleles can differ from each other by as little as one nucleotide.
All the allele frequencies for one gene must add up to 1.
Every individual carries two alleles per locus, so a population has twice as many alleles as individuals.
A homozygous individual contributes two copies of one allele; a heterozygous individual contributes one of each.
Alleles are also called polymorphisms; the commonest type is a single nucleotide polymorphism (SNP).
Geographic separation allows allele frequencies to differ between populations.
Allele frequency data is used to study disease associations, drug resistance and human history.
What an allele frequency is
Definition
Allele frequency is the proportion of all the alleles at one gene locus in a population that are of a particular form
Notice what is being counted. Not organisms — allele copies. Two different alleles of the same gene can be almost identical, sometimes differing by just one nucleotide, but they are still counted as two different forms.
Because you are dealing with proportions, the frequencies of all the alleles of one gene must add up to 1. If there are two alleles and one has a frequency of 0.7, the other must be 0.3. That single fact answers a surprising number of exam questions on its own.
The counting rules
For any polymorphism, each individual carries two alleles per locus — one from each parent.
The exception is alleles on the X or Y chromosome, where males carry only one copy.
So in a population there are twice as many alleles as there are individuals.
A homozygous individual contributes two copies of that allele to the count.
A heterozygous individual contributes one copy of each allele.
Five individuals, ten alleles. Double the number of organisms first, every single time, and the rest is division.
🧩 Finding an allele frequency from genotype numbers
Find the total number of individuals and double it. That is your total number of alleles — the denominator.
Count copies of the allele you want: 2 for each homozygote, 1 for each heterozygote.
Divide the count by the total. That is the frequency.
Check by working out the other allele’s frequency the same way. They must add to 1.
Isolated populations
When a degree of geographic separation exists between two populations, differences in allele frequency emerge. Each population faces its own selection pressures, experiences its own genetic drift, and cannot exchange alleles with the other.
Human allele frequencies vary by geography and ethnicity, but clear-cut differences are rare. The reason is simple: humans travel and interbreed constantly, so truly isolated human populations are scarce. Frequencies blur across boundaries rather than dividing sharply.
The founder effect
The most dramatic frequency shifts happen when a small number of individuals start a brand new population. Whatever alleles those founders happen to carry become the entire gene pool of the new population — and whatever they do not carry is gone.
Nothing here is an adaptation. The new island’s gene pool is the result of an accident, which is genetic drift at its most extreme.
Polymorphisms and SNPs
Alleles are sometimes called polymorphisms, which just means many (poly-) different forms (-morphisms) of a gene. The most common type is a single nucleotide polymorphism, or SNP — a difference of exactly one base in the sequence.
Online databases list the frequencies of human alleles, and comparing those frequencies is genuinely useful.
Use of allele frequency data
What it tells us
Identifying genetic associations with diseases
Which alleles are found more often in people with a particular condition
Estimating disease susceptibility
How many individuals in a population are likely to be at risk
Estimating drug resistance
How common resistance alleles are in a bacterial or parasite population
Evolutionary and anthropological studies
How human populations have moved and mixed through history
Mathematical derivations of allele frequencies are not required for your exams. What is required is that you understand why the frequencies must total 1, and that you can count carefully under pressure. Most lost marks here are arithmetic slips, not biology.
Worked examples
WE 1
Calculate allele frequencies from genotypes
A population of 100 snails contains 30 individuals with genotype GG, 50 with Gg and 20 with gg. Calculate the frequency of each allele. (3 marks)
Step 1: total number of alleles
100 snails, each with 2 alleles, so 100 × 2 = 200 alleles in total.
Step 2: count the G alleles
GG gives 30 × 2 = 60, and Gg gives 50 × 1 = 50, so G total = 110.
Step 3: count the g alleles
gg gives 20 × 2 = 40, and Gg gives 50 × 1 = 50, so g total = 90.
Step 4: divide and check
frequency of G = 110 ÷ 200 = 0.55; frequency of g = 90 ÷ 200 = 0.45; 0.55 + 0.45 = 1
G = 0.55 and g = 0.45the heterozygotes are counted twice, once into each allele total — that is the step people forget
WE 2
A founder population
On the mainland the frequency of allele A is 0.50. Three beetles are blown onto an empty island: one is AA and two are Aa. Calculate the frequency of A in the new population and comment on your answer. (3 marks)
Step 1: total alleles
3 beetles × 2 = 6 alleles.
Step 2: count A
AA gives 2, and each Aa gives 1, so 2 + 1 + 1 = 4 copies of A.
Step 3: divide
frequency of A = 4 ÷ 6 = 0.67 (2 s.f.), so frequency of a = 0.33
Step 4: comment
The frequency has jumped from 0.50 to 0.67 by chance alone, because the founders were a tiny, unrepresentative sample. This is the founder effect, a form of genetic drift.
A = 0.67 — a large change caused by chance, not selection“comment on your answer” is asking for the biology behind the number, so always add a sentence
WE 3
Explain a difference between populations
Two populations of the same plant species live on separate mountain tops. One has a much higher frequency of a drought-tolerance allele. Suggest two reasons. (2 marks)
Reason 1: different selection pressures
If one mountain is drier, plants carrying the allele are more likely to survive and reproduce there, so its frequency rises.
Reason 2: no gene flow
The populations are geographically separated, so they have separate gene pools and cannot exchange alleles. Genetic drift can also push the two frequencies apart independently.
Different pressures acting on gene pools that cannot mix“suggest” means you are not expected to know the real answer — you are expected to give a biologically sensible one
💡 Exam tips
Double the number of individuals first. Writing the total allele number down before anything else prevents the commonest error.
Always finish with the check that the frequencies add to 1.
Give frequencies as decimals unless the question asks for percentages, and follow any instruction on significant figures.
Remember the X and Y exception if a question involves a sex-linked gene.
Know what a SNP is: one nucleotide of difference, the most common kind of polymorphism.
For “why are human allele frequency differences rarely clear-cut”, the answer is travel and interbreeding.
⚠ Common mistakes
Dividing by the number of individuals. Divide by the number of alleles, which is double.
Forgetting the heterozygotes. They contribute one copy to each allele total.
Confusing allele frequency with genotype frequency. One counts allele copies, the other counts individuals.
Assuming a frequency of 0 means the allele is harmful. Drift and the founder effect can remove a perfectly good allele.
Writing a frequency greater than 1. A proportion cannot exceed 1 — if yours does, recheck the denominator.
Treating human populations as neatly separate. Truly isolated human populations are scarce.
Up next: Types of Natural Selection. You can now measure a gene pool. Next we look at the three shapes that change takes — the population shifting one way, tightening around the middle, or splitting in two.
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