A global map for introgressed structural variation and selection in humans
Abstract
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.
Related
- Stabilizing selection generates selection against introgressed DNA
- Genomic structural variations distinguishing archaic and modern humans are associated with neurodevelopment
- Denisovan introgression left differential selection regimes in Humans and Neanderthals on the SLC30A9 gene
- Natural Selection of the Common STING Allele HAQ in Anatomically Modern Humans
- Triangulating evidence to detect signatures of stabilizing selection acting on protein levels in humans
BibTeX
@article{hsieh2026global,
title = {{A global map for introgressed structural variation and selection in humans}},
author = {Pinghsun Hsieh and Natthapon Soisangwan and David S Gordon and Athef Javidh and William T Harvey and David Porubsky and Kendra Hoekzema and Carl Baker and Katherine M Munson and Christopher Kinipi and Matthew Leavesley and Nicolas Brucato and Murray P Cox and Francois-Xavier Ricaut and Irene Gallego Romero and Evan E Eichler},
journal = {Science},
year = {2026},
month = jun,
doi = {10.1126/science.adz7518},
url = {https://hal.science/hal-05769504v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - A global map for introgressed structural variation and selection in humans
AU - Pinghsun Hsieh
AU - Natthapon Soisangwan
AU - David S Gordon
AU - Athef Javidh
AU - William T Harvey
AU - David Porubsky
AU - Kendra Hoekzema
AU - Carl Baker
AU - Katherine M Munson
AU - Christopher Kinipi
AU - Matthew Leavesley
AU - Nicolas Brucato
AU - Murray P Cox
AU - Francois-Xavier Ricaut
AU - Irene Gallego Romero
AU - Evan E Eichler
PY - 2026
DA - 2026/06/11
JO - Science
DO - 10.1126/science.adz7518
UR - https://hal.science/hal-05769504v1
AB - 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.
SN - 0036-8075
SN - 1095-9203
ER -