Figure S6.

Putatively Introgressed Variants, Related to Figure 2E and Table 1

Top: fiber-FISH of chr16 Oceanian-specific expansion shared with Denisovan genome at ∼82% frequency in all three Oceanian populations. Cartoon illustration of location of original (16p12.2) and inserted site 7Mb away (16p11.2) into clone RP11-368N21 (green). Bottom: MS4A1 deletion: IGV screenshot of a deletion in an exon of MS4A1, which encodes the B cell differentiation antigen CD20. The deletion is shared by both Neanderthals (Altai top, Vindija middle track) and American populations (reaches ∼26% in Surui and Pima). The deletion is not present in the Denisovan genome (lower track). Bottom track shows Loupe screenshot of the region in HGDP01043 showing the two haplotypes resolved using 10x linked-reads, with one carrying the deletion.