Comparison of r2 values in population with bottlenecks producing similar average pairwise differences (π).

Different models of demography can result in very different linkage patterns while retaining similar π values making it difficult to differentiate the models using frequency spectrum based methods. LDx can distinguish between the models by estimating r2. The model with a mild, more prolonged bottleneck has lower r2 than the Thornton & Andolfatto reference model, while the model with a more severe, short bottleneck has higher r2. Estimation cells report mean r2 ± standard deviation.at is measured in generations scaled by 4Ne. All models had the same number of post bottleneck generations as the Thornton & Andolfatto model.