text: **Neanderthal admixture and deep structure simulation.**Our simula- 
  tion in Extended Data Fig. 5d emulates Neanderthal admixture, in which 
  Neanderthals and ancestors of modern humans split 25,000 genera- 
  tions ago and admixture occurs 2,000 generations ago. The resulting 
  admixed non-African-like population coexists with the non-admixed 
  African-like population until the present day. Furthermore, two 
  Neanderthal populations split from each other 7,000 generations ago, 
  which can be interpreted as emulating the Altai and Vindija Neanderthal 
  populations, with Vindija being closer to the admixing source. 
  
  We filter any site for which more than 2% of sites have an imputation 
  posterior of less than 0.8 and retain all remaining sites so as not to have 
  any missing genotypes at individual SNPs. 
  
  **Relate-inferred genealogies.**We merge imputed ancient genomes 
  with a subset of the 1000GP dataset, including all European popula- 
  tions (CEU, Utah residents with northern and western European ances- 
  try; CHB, Han Chinese in Bejing, China; FIN, Finnish in Finland; GBR, 
  British in England and Scotland; BS, Iberian populations in Spain; TSI, 
  Toscani in Italy, YRI, Yoruba in Ibadan, Nigeria). We create a second 
  dataset in which we merge imputed genomes with the Simons Genome 
  Diversity Project75 (SGDP) downloaded from https://sharehost.hms. 
  harvard.edu/genetics/reich_lab/sgdp/phased_data2021/. These two 
  datasets contain, respectively, a total of 2,270 and 1,834 modern and 
  ancient individuals. 