Fig. 1
Archaic linkage blocks. a Timeline for the formation of archaic haplotypes. As a rough estimate, the chimpanzee line separated from the h. sapiens line about 5 million years ago, while the Denisova h. split off around 500,000 years ago. This provides a time window of 0.5–5 million years, at which point mutations accumulated in the genome of the common ancestor of Denisova h. and H. sapien. The derived “archaic” haplotypes formed by these mutations were preserved in Denisova and serve as a reference for the recombination events rearranging these haplotypes in the human during a period of at least 500,000 years after separation. b Formation of archaic linkage blocks. NCO recombination between the derived archaic haplotype (blue), consisting of the derived alleles of these SNPs (solid circles), and the corresponding ancestral haplotype (green) created a set of haplotype variants that are still present in modern humans. In the given example the archaic linkage block consists of 6 SNPs of which SNPs 1, 3, and 6 are still in perfect linkage (block SNPs). The derived alleles of these SNPs form the core haplotype (hap), which represents the remaining fragment of the derived archaic haplotype. SNPs 2, 4, and 5 are singletons whose alleles had been shifted between haplotypes by NCO recombination. Their association to the derived haplotype is indicated by the linkage disequilibrium (D’a,hap) between their derived alleles (a) and the core haplotype (hap). c Example of an archaic linkage block. The panel shows the location of the SNPs of an archaic linkage block in reference to the intron/exon structure of the ESYT2 gene. In this visualization, the association of the derived alleles to the core haplotype (r2 = 1) is indicated by the respective r2a,hap value. The horizontal line connecting the block SNPs indicates the location of the core haplotype; single vertical lines indicate the NCO rate and location of the singleton SNPs. d Haplotype composition of the linkage block. The panel displays the haplotype composition of the ESYT2 linkage block defined for the 99 individuals of the LWK cohort. The presence of derived alleles (red circles) and ancestral alleles (white circles) for each haplotype variant is indicated. Numbers indicate the absolute frequency of the haplotype in the cohort; downward and upward arrows on top of the plot respectively indicate retracting and expanding derived alleles, a double arrow indicates a neutral allele that switched the position in several haplotypes without affecting its allele frequency; horizontal lines refer to block SNPs