A global map for introgressed structural variation and selection in humans
- PingHsun Hsieh
- Natthapon Soisangwan
- David S. Gordon
- Athef Javidh
- William T. Harvey
- David Porubsky
- Kendra Hoekzema
- Carl Baker
- Katherine M. Munson
- Christopher Kinipi
- Matthew Leavesley
- Nicolas Brucato
- Murray P. Cox
- François‐X Ricaut
- Irene Gallego Romero
- Evan E. Eichler
2026-06-11
Genetic introgression from Neanderthals and Denisovans 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) haploid genomes with 94 published assemblies of diverse ancestry to infer an introgressed SV map. Introgressed SVs are enriched in genes (47%), including critical genomic disorder regions, and are most abundant in PNG genomes. We identified 11 centromeres likely derived from archaic hominins, adding unexplored diversity to centromere genomics. Pangenome genotyping of these 98 assemblies across 1363 samples revealed 16 adaptive SVs, many associated with immune-related genes and expression, in the PNG genomes. We hypothesize that archaic SVs contributed to reproductive success, underscoring introgression as a major force in human adaptive evolution.