(A) Pairwise differences between two high coverage Neandertal genomes (Chagyrskaya 8 and Altai Neandertal (Denisova 5)) in non-overlapping sliding windows of 276 kb (histogram) and in the KNL1 region (vertical cyan line; chr15:40,818,035–41,094,166, hg19). Windows with less than 10,000 genotype calls for both Neandertals were discarded. (B) The expected length distributions under a model of incomplete lineage sorting based on local recombination rate estimates from the African-American (AA) and deCODE recombination maps and the length of the modern human-like KNL1 haplotype in Neandertals (vertical cyan line). (C) Left panel: Time to the most recent common ancestor (TMRCA) between the Chagyrskaya 8 Neandertal (who carries the modern human-like haplotype) and KNL1 haplotypes in present-day humans with their 95% confidence intervals (bars) for chr15:40,885,107–40,963,160 (hg19). The size of the points corresponds to the number of chromosomes carrying this haplotype in the HGDP dataset. The black rectangles highlight subsets of haplotypes with TMRCAs more recent than the modern-archaic population split time (Prüfer et al., 2017) (shaded pink area). Right panel: Distribution of pairwise TMRCAs between the Neandertal and present-day humans from the HGDP dataset in the region of KNL1 and two other regions with archaic haplotypes in present-day humans (Controls, Zeberg and Pääbo, 2020; Dannemann et al., 2016; COVID risk region: chr3:45,859,651–45,909,024; TLR6, 1 & 10: chr4:38,760,338–38,846,385). We used the Vindija 33.19 genome for the COVID risk haplotype and the Chagyrskaya 8 genome otherwise.