Fig. 5

Worldwide frequencies of alleles shared with the Denisovan genome. Worldwide frequencies of alleles shared with the Denisovan genome in the region flanking NUMT 3_1384 in (a) Oceanian sample UV925, and (b) the same region in the sub-Saharan African sample NA19309. The alleles are within 20 kbp before or after the insertion site (vertical dashed line) and on the same phase. Frequencies were calculated in the 1000 Genomes Project (1000 GP) (black) and Simons Genome Diversity Project (SGDP) (grey) datasets. X-axis intervals are not linear, but indicate positions of shared alleles. High-frequency shared alleles reflect either homoplasy or incomplete lineage sorting; the greater abundance of low-frequency alleles shared with the Denisovan genome close to the insertion point (grey area) in the Oceanian sample vs. the sub-Saharan African sample suggests a Denisovan-introgressed haplotype in the Oceanian