Table 1 Multinomial log-likelihoods comparing the fit of various models to the observed SFS derived from Sanger sequencing data and used by Gutenkunst et al. (2009) for their inference (SFSs in Figure 4)
ModelMultinomial LL∆LL (Model − Data)
CEU
 Data to data−21,5460
 Gutenkunst−21,555−9
 SMC++−21,599−53
 MSMC 2-haplotype−21,698−152
 MSMC 8-haplotype−21,816−270
 MSMC 4-haplotype−22,760−1214
CHB
 Data to data−20,1540
 Gutenkunst−20,202−48
 SMC++−20,277−123
 MSMC 8-haplotype−20,343−188
 MSMC 2-haplotype−20,370−216
 MSMC 4-haplotype−21,411−1257
YRI
 Data to data−29,6300
 Gutenkunst−29,647−17
 SMC++−29,779−150
 MSMC 2-haplotype−30,003−373
 MSMC 8-haplotype−31,282−1652
 MSMC 4-haplotype−32,976−3346
  • Data to data denotes the best log-likelihood possible when replacing the proportions predicted by the model with the observed proportions from the SFS used in Gutenkunst et al.’s (2009) study (see Supplementary Note 4 in File S1). Gutenkunst denotes the model inferred by Gutenkunst et al. (2009) fit to the observed SFS. SMC++ denotes the model inferred by Terhorst et al. (2017) using a combined whole genome and SFS approach. MSMC 2-, 4-, and 8-haplotype denote the demographic models inferred by Schiffels and Durbin (2014) using MSMC on two, four, and eight haplotypes, respectively.