PingHsun Hsieh, Natthapon Soisangwan, David Gordon, Athef Javidh, William T. Harvey, David Porubskỳ, Kendra Hoekzema, Carl Baker, Katherine M. Munson, Christopher Kinipi, Matthew Leavesley, Nicolas Brucato, Murray P. Cox, François‐Xavier Ricaut, Irene Gallego Romero, Evan E. Eichler
Genetic introgression from Neanderthals and Denisovan has shaped modern human genomes; however, introgressed structural variants (SVs ≥50 base pairs) remain challenging to discover. We integrated high-quality phased assemblies from four new Papua New Guinea (PNG) genomes with 94 published assemblies of diverse ancestry to infer an archaic introgressed SV map. Introgressed SVs are overall enriched in genes (44%, n=1,592), including critical genomic disorder regions, and most abundant in PNG. We identify 11 centromeres likely derived from archaic hominins, adding unexplored diversity to centromere genomics. Pangenome genotyping across 1,363 samples reveals 16 candidate adaptive SVs, many associated with immune-related genes and their expression, in the PNG. We hypothesize that archaic SV introgression contributed to reproductive success, underscoring introgression as a significant force in human adaptive evolution.