Fig. 6
Signatures of selection and archaic introgression from Neandertals (NDL) and Denisovans (DNS) for the deletion of 335 base pairs at 1p36.32. A Absolute integer copy numbers for a sliding window of 100 base pairs (bp) and a step size of 50 bp around the deletion. Each row represents the copy numbers of a sample over the region. B Genotyping results for the deletion among different populations. Pie charts along the x-axis indicate the population distribution for different structural variation (SV) genotypes (colors are the same as populations), and pie charts along the y-axis illustrate the frequency distribution for a given population (colors are the same as copy number of 2/1/0). C Distributions of single nucleotide variants (SNVs) with significant fd-statistic (purple dots) and cross-population Extended Haplotype Homozygosity (XP-EHH, blue dots). D Hierarchical clustering for the region around the deletion. Rows illustrate the individual haplotypes. The column indicates the genotypes of 90 variants with selection signals (XP-EHH > 2). The color of gray and black represents the ancestral and derived alleles, respectively. E TCS haplotype network for 20 linkage disequilibrium (LD)-linked SNVs to the deletion with selection signals (XP-EHH > 2). All haplotypes with the deletion in Tibetans and Hans, and the haplotypes with or without the deletion in the ancient genomes are clustered together within the dotted box