text: We simulate an alternative model with two subgroups emulating 
  ancestral modern humans in Africa that have a non-zero symmetric 
  migration rate, ranging from 4 × 10−5 to 2 × 10−4 per generation, up until 
  3,000 generations before present. One of these subgroups gives rise 
  to a present-day African-like population, while the other gives rise to 
  a present-day non-African-like population. We further sample two 
  Neanderthal populations that split 7,000 generations ago and merge 
  25,000 generations ago with the same ancestral modern human sub- 
  group that will eventually give rise to a non-African-like population. 
  
  We then infer genealogies for the joint dataset of ancient and modern 
  genomes using Relate v. 1.2.1. We restrict our analysis to transversions 
  only and assume a mutation rate of 4 × 10−9 mutations per base per gen- 
  eration and input sample dates as shown in Supplementary Table 1. We 
  use coalescences rates pre-inferred for the 1000GP and SGDP datasets. 
  
  We simulate whole genomes with human-like recombination rates 
  and a mutation rate of 1.25 × 10−8 mutations per base per generation. 
  Diploid effective population sizes are set to 10,000 except on the 
  Neanderthal lineage, in which it is set to 3,000. We sample 2 haploid 
  sequences for each Neanderthal population and 20 haploid sequences 
  for the target admixed population and African non-admixed population. 