This PDF file includes:

• Supplementary Materials and Methods
• Fig. S1. Heterozygosity as a function of FL value for genome SS6004468 of the SGDP (14).
• Fig. S2. Observed site pattern frequencies excluding the Vindija genome.
• Fig. S3. Associations between estimates of several pairs of parameters after second stage in analysis of model αβγδ.
• Table S1. Model-averaged parameter estimates.
• Table S2. Estimates under model α.
• Table S3. Estimates under model αβγδ with a data set that excludes the Vindija Neanderthal genome.
• References (36–39)

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