A global map for introgressed structural variation and selection in humans
Hsieh PPapers in this archive, Soisangwan NPapers in this archive, Gordon DSPapers in this archive, Javidh APapers in this archive, Harvey WTPapers in this archive, Porubsky DPapers in this archive, Hoekzema KPapers in this archive, Baker CPapers in this archive, Munson KMPapers in this archive, Kinipi CPapers in this archive, Leavesley MPapers in this archive, Brucato NPapers in this archive, Cox MPPapers in this archive, Ricaut FXPapers in this archive, Romero IGPapers in this archive, Eichler EEPapers in this archive
Abstract
Author Manuscript Genetic introgression from Neanderthals and Denisovan 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 most abundant in PNG. We identify 11 centromeres likely derived from archaic hominins, adding unexplored diversity to centromere genomics. Pangenome genotyping of these 98 assemblies across 1,363 samples reveals 16 adaptive SVs, many associated with immune-related genes and expression, in the PNG. We hypothesize that archaic SVs contributed to reproductive success, underscoring introgression as a significant force in human adaptive evolution. Author Manuscript Keywords Human evolution; adaptive introgression; structural variation
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