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.
Article Details
Journal Info
Science
American Association for the Advancement of Science
Authors (16)
PingHsun Hsieh
Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN, USA.
Natthapon Soisangwan
Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Twin Cities, MN, USA.
David S. Gordon
Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN, USA.
Athef Javidh
Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Twin Cities, MN, USA.
William T. Harvey
David Porubsky
Kendra Hoekzema
Carl Baker
Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Katherine M. Munson
Christopher Kinipi
The University Clinic, University of Papua New Guinea, Port Moresby, Papua New Guinea.
Matthew Leavesley
Strand of Anthropology, Sociology and Archaeology in the School of Humanities and Social Sciences, University of Papua New Guinea, National Capital District, Papua New Guinea.
Nicolas Brucato
Murray P. Cox
College of Sciences, Massey University, Palmerston North, New Zealand.
François‐X Ricaut
Centre de Recherche sur la Biodiversité et l’Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 – Paul Sabatier (UT3), Toulouse, France.
Irene Gallego Romero
Human Genomics and Evolution, St Vincent’s Institute of Medical Research, Fitzroy, Australia.
Evan E. Eichler