Table 2. Comparison of r² values in population with bottlenecks producing similar average pairwise differences (π).

Model	N0/Nb	ta	π	App MLE r2/bp	Direct Est. r2/bp
Thornton & Andolfatto [31]	0.047	0.021	0.0029	0.011±0.078	0.0125±0.082
Severe Bottleneck	0.0235	0.042	0.0028	0.005±0.035	0.0056±0.036
Mild Bottleneck	0.094	0.0105	0.0028	0.026±0.123	0.0266±0.122

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 4N_e. All models had the same number of post bottleneck generations as the Thornton & Andolfatto model.