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Counting Genes in a Crowd: Allele & Genotype Frequencies

Population genetics starts by counting. Meet the gene pool, and learn to turn a tally of genotypes into allele frequencies you can track over time.

From one family to a whole population

Classical Mendelian genetics follows alleles through one family — parents to offspring. Population genetics zooms all the way out: it treats a whole interbreeding population as a single unit and asks how common each allele is, and whether that commonness changes over the generations.

The key abstraction is the gene pool: imagine pooling every allele carried by every individual at one locus into a single bag. A diploid population of 100 individuals carries 200 alleles at each locus. The frequency of an allele is simply its share of that bag — a number between 0 and 1.

Genotype frequency vs. allele frequency

There are two things you can count. The genotype frequency is the fraction of individuals with each genotype (AA, Aa, aa). The allele frequency is the fraction of allele copies in the pool (A vs. a). They are related but not the same — and converting between them is the single most useful move in this whole track.

  1. Count individuals of each genotype: nAA, nAa, naa. The total is N.
  2. Each AA contributes two A alleles; each Aa contributes one A and one a; each aa contributes two a.
  3. Frequency of A (call it p) = (2·nAA + nAa) ÷ (2·N). Frequency of a (call it q) = (2·naa + nAa) ÷ (2·N).
  4. Check: p + q should equal 1, because every copy is either A or a.
Sampled population, one locus, two alleles A and a

Genotype counts:
  AA = 36 individuals
  Aa = 48 individuals
  aa = 16 individuals
  N  = 100 individuals   →   2N = 200 allele copies

Genotype frequencies:
  AA = 36/100 = 0.36
  Aa = 48/100 = 0.48
  aa = 16/100 = 0.16

Allele frequencies:
  count of A = (2*36) + 48 = 72 + 48 = 120
  count of a = (2*16) + 48 = 32 + 48 =  80
  p = freq(A) = 120/200 = 0.60
  q = freq(a) =  80/200 = 0.40
  check: p + q = 0.60 + 0.40 = 1.00  OK
Turning a genotype tally into allele frequencies p and q.

Why frequencies, not counts

Frequencies let you compare populations of different sizes and track change over time on a fixed 0-to-1 scale. When a polymorphism exists — two or more common alleles at a locus — the interesting question is always how those frequencies move. The rest of this track is a tour of the forces that move them.