Coalescent simulations using scrm (32) were used to compute the expected distribution of times to TMRCAs for the mitochondrial genomes, given different population split times (from 100 to 200 ka ago, with a step of 10 ka). To be able to compare these to the estimated date for the common mitochondrial ancestor of HST and Vindija, the simulations followed the Vindija demographic history estimated from the Pairwise Sequentially Markovian Coalescent model (PSMC) (33) [that assumed a mutation rate of 1.45 × 10−8 per base pair per generation and a generation time of 29 years (20)]. The scaling for the mitochondrial effective population size was calculated according to the females-to-males ratio, previously estimated to be 1.54 for the Altai Neandertal population (note S11) (8).

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