Wahlundeffect

The Wahlund effect is a reduction in the observed heterozygosity of a population caused by subpopulation structure. It occurs when a population is composed of two or more subpopulations that have different allele frequencies, and individuals mate at random in the total population rather than within each subpopulation. Even though mating may be random within subpopulations, the combined population exhibits genotype frequencies that deviate from Hardy-Weinberg expectations.

Mathematically, if subpopulations i have allele frequencies p_i and relative sizes w_i, the overall allele frequency is p = sum(w_i p_i). Under random mating in the total population, the expected heterozygosity is 2p(1−p). However, the observed heterozygosity equals sum(w_i 2 p_i (1−p_i)), which is typically lower than 2p(1−p) when p_i differ across subpopulations. This yields an apparent excess of homozygotes and a positive inbreeding coefficient F_IS in the subdivided sample.

The Wahlund effect has implications for population genetics and genetic epidemiology. It can bias estimates of genetic diversity, relatedness, and population structure (for example, F-statistics and association studies) if population subdivision is not accounted for. Recognizing the effect helps in designing sampling strategies and interpreting deviations from Hardy-Weinberg equilibrium.

The effect is named after Svante Wahlund, who described the phenomenon in the early 20th century.