Evidence map›Paper›PMID 40667000›Full record

ArticlebioRxiv : the preprint server for biology2025

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 and 6 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

16 authors.

PingHsun HsiehDepartment of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN, USA.ORCID 0000-0001-8294-6227
Natthapon SoisangwanBioinformatics and Computational Biology Graduate Program, University of Minnesota, Twin Cities, MN, USA.ORCID 0000-0003-0425-2232
David S GordonDepartment of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN, USA.
Athef JavidhBioinformatics and Computational Biology Graduate Program, University of Minnesota, Twin Cities, MN, USA.
William T HarveyDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
David PorubskyDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Kendra HoekzemaDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Carl BakerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Katherine M MunsonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Christopher KinipiStrand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, University 134, National Capital District, Papua New Guinea.
Matthew LeavesleyStrand of Anthropology, Sociology and Archaeology, School of Humanities and Social Sciences, University of Papua New Guinea, University 134, National Capital District, Papua New Guinea.
Nicolas BrucatoCentre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, France.
Murray P CoxCollege of Sciences, Massey University, Palmerston North, New Zealand.
François-X RicautCentre 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 RomeroHuman Genomics and Evolution, St Vincent's Institute of Medical Research, Fitzroy, Australia.ORCID 0000-0003-1613-8998
Evan E EichlerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID 0000-0002-8246-4014

Funding

Sequence and Assembly of Segmental DuplicationsR01HG002385 · NHGRI · UNIVERSITY OF WASHINGTON · PI Evan Eichler · 2001 to 2026
$13.3M
The fitness effects of de novo structural variantsR00HG011041 · NHGRI · UNIVERSITY OF MINNESOTA · PI HSIEH, PINGHSUN · 2023 to 2025
$729k
NHGRI NIH HHS R00 HG011041NHGRI NIH HHS R01 HG002385
6 · The paper itself

Abstract

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.

Indexed as

adaptive introgressionHuman evolutionstructural variation

Identifiers

PMID40667000
PMCPMC12262424

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.