Fig. 1

Neandertal introgresssed haplotypes in the OAS region. a Neighbor-joining tree of 5008 phased haplotypes spanning chr12: 113344739–113449528 (hg19) from phase 3 of the 1000 Genomes Project. Haplotypes were condensed into 10 core haplotypes based on the majority allele after clustering into groups of haplotypes with pairwise differences of 60 or less. The figure illustrates that the Altai haplotype is very similar to “cluster 2” haplotypes found in several human populations, while the Denisovan haplotype is not more closely related to any of the remaining (non-cluster 2) sequences in this dataset. Bootstrap values (1000 replicates) are provided in blue boxes at each node. b Frequencies of the 10 core haplotypes within each 1000 Genomes Project population sample. The most common Neandertal-like haplotype, cluster 2, is found only outside of sub-Saharan African samples, with the exception of recently admixed populations. Population codes can be found in Additional file 2: Table S7