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Updated: Jul 15, 2026

Following the Dynamics of Structural Variants in Experimentally Evolved Populations
Published on: February 3, 2023
Stepping-stone spatial structure causes slow decay of linkage disequilibrium and shifts the site frequency spectrum
1Department of Statistics, Cornell University, Ithaca, New York 14853, USA.
Abstract:
The symmetric island model with D demes and equal migration rates is often chosen for the investigation of the consequences of population subdivision. Here we show that a stepping-stone model has a more pronounced effect on the genealogy of a sample. For samples from a small geographical region commonly used in genetic studies of humans and Drosophila, there is a shift of the frequency spectrum that decreases the number of low-frequency-derived alleles and skews the distribution of statistics of Tajima, Fu and Li, and Fay and Wu. Stepping-stone spatial structure also changes the two-locus sampling distribution and increases both linkage disequilibrium and the probability that two sites are perfectly correlated. This may cause a false prediction of cold spots of recombination and may confuse haplotype tests that compute probabilities on the basis of a homogeneously mixing population.
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