Wahlund effect

In population genetics, the Wahlund effect refers to reduction of heterozygosity in a population caused by subpopulation structure. Namely, if two or more subpopulations have different allele frequencies then the overall heterozygosity is reduced, even if the subpopulations themselves are in a Hardy-Weinberg equilibrium. The underlying causes of this population subdivision could be geographic barriers to gene flow followed by genetic drift in the subpopulations.
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The finding of excess homozygosity in a large sample of population consisted of several subpopulations. It is due to differences in gene frequencies in the subpopulations and purely a mathematical complication. Link to lectures on Wahlund effect (1) and (2) and a simulation.