Effect of uncertainty in ancestral population size

To investigate whether changing the ancestral population size (N_A) in the MSMC trajectories would result in SFSs that better fit the observed SFS, we adjusted the CEU MSMC 2-haplotype model to have a variety of N_A values. We also trimmed the model to remove ancient events (older than 225.5 KYA) to better match the time period (in years) encompassed by the Gutenkunst et al.’s (2009) model. These adjusted stepwise models were then used to calculate the expected SFS in ∂a∂i, as above. Supplementary Note 7 in File S1 describes the values of N_A used when testing the trimmed and untrimmed models (Figures S10–S13 in File S1).