Strains Often Differ in Gene Frequency Only

Consider a trait such as chin whisker hairs in the fictional organism the New Jersey Rumbunny.  The chin whiskers were measured on 2000 rumbunnies from the Pine Barrens' strain of rumbunnies (collected near the town of Kallikak) and the average number of chin whiskers was 27.6.  The average number of chin whiskers in 1780 rumbunnies from the Carteret Salt Marsh strain of rumbunnies was 22.8

Samples of these strains were established in a laboratory and reared under tightly controlled conditions.  That is, the experimenters were conducting a strain experiment to answer Hall's Goal number 1.  The difference in the mean number of chin whiskers was maintained.  The experimenters concluded that the number of chin whiskers was genetic.

Goal two is to determine the number and nature of the genes.  Through a series of breeding investigations, the experimenters concluded that the inheritance of chin whiskers was the same in both strains of  rumbunnies.  In these two strains, chin whisker number was determined by  two genes, and each gene had two alleles.  The traits are strictly additive.  

Therefore the difference between the strains of Rumbunnies was a probably difference in gene frequency and not due to a difference in segregating genes or in the alleles of the genes segregating in the strains. (see examples of differences in alleles or differences in segregating genes).

Pine Barrens and Carteret Rumbunnies have at least 20 chin whiskers (due to genes which are not segregating in these strains). The number of additional whiskers is controlled by genotype according to the following rules.

A₁ allele adds 4 chin whiskers; A₂ allele adds 0 chin whiskers

B₁ allele add adds 2 chin whiskers; B₂ allele adds 0 chin whiskers.

Further investigation demonstrated that the two strains of rumbunnies approximated Hardy-Weinberg equilibrium for chin whiskers.

The gene frequencies in the two populations were as follows:

Thus the expected distribution of chin whiskers by genotype is:

 All phenotypes occur both strains; they only differ in gene frequencies.  For example, if you were randomly given a rumbunny of genotype A₁A₁B₂B₂ you would not be able to decide what population that it came from.  You might assign probabilities (e.g., a genotype A₁A₁B2B2 would be 3 times more likely to come from the Pine Barrens population, but the individuals within the Pine Barrens strain are identical to the individuals from the Carteret strain).

Strains may differ only in gene frequencies. However, they may also differ in the presence or absence of specific alleles.