Fig. 2
Correlation of the NCO recombination rate with functional genomic parameters. a Function vs. fitness. The NCO rate 1 – D’2a,hap was used as a proxy for the NCO recombination rate. The correlation of this parameter of about 1.9 million archaic SNPs is shown for function-associated GWAVA scores (left panel) and fitness-associated fitCons scores. The plot displays the average scores for about 1.0 million block SNPs (red dot) and 900,000 singleton SNPs (blue dots). The singleton SNPs were binned according to the 1 – D’2a,hap value defined for the LWK population. Dashed horizontal lines indicate the average scores of the entire set of archaic SNPs. Asterisks indicate significant differences between data point pairs (p < 0.05; Mann-Whitney U test). b Meiotic CO recombination hotspots. The solid line represents the average NCO rate (1 – D’2a,hap) plotted in reference to the distance of the alleles to meiotic CO recombination hotspots (defined by DMC1 ChIP-Seq tracks of human testis [20]). The dashed line of the second peak represents the hypothetical NCO rate in reference to a second recombination hotspot located at the average distance of about 67 kb. c Gene boundaries. The average NCO rate (1 – D’2a,hap), is plotted in reference their distance to the boundary of the closest annotated gene. Peaks in NCO rate are evident at both 5′- and 3′-boundaries (indicated by dashed vertical lines). Gene regions are marked in red, intergenic regions in blue; dashed horizontal line represents the average NCO rate of the entire set of archaic alleles. (d) Genic sub-regions. Gene regions (red) were further delineated into their sub-regions (5′UTRs, introns, splice sites, exons and 3′UTRs); intergenic regions (blue) were divided according to their distance to the boundaries both upstream and downstream of the genic region (0–5 kb, 5–50 kb, >50kb). Bars represent the average NCO rate (1 – D’2a,hap) in the respective region. Asterisks indicate significant differences between the indicated bars (p < 0.05; Mann-Whitney U test). e Open chromatin. The line chart depicts the association of the NCO recombination rate with open chromatin. The average NCO rate (1 – D’2a,hap) is plotted in reference to the distance of the alleles to the boundary of open chromatin (defined by ENCODE tracks of DNase I sensitivity). Gray bars indicate the number of archaic SNPs in the respective distance-bin