Evidence map›Paper›PMID 39990470›Full record

ArticlebioRxiv : the preprint server for biology2025

Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants.

Scott V Edwards, Bohao Fang, Danielle Khost, George E Kolyfetis, Rebecca G Cheek, Devon A DeRaad, Nancy Chen, John W Fitzpatrick, John E McCormack, W Chris Funk and 5 more

Abstract readPreprint
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

15 authors.

Scott V EdwardsDepartment of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 2138, USA.ORCID 0000-0003-2535-6217
Bohao FangDepartment of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 2138, USA.ORCID 0000-0001-5283-067X
Danielle KhostInformatics Group, Harvard University, 52 Oxford St, Cambridge, MA, 2138, USA.
George E KolyfetisDepartment of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 2138, USA.ORCID 0000-0002-9601-1526
Rebecca G CheekDepartment of Biology, Graduate Degree Program in Ecology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO, 80523, USA.ORCID 0000-0002-7935-3153
Devon A DeRaadMoore Laboratory of Zoology, Occidental College, 1600 Campus Rd, Los Angeles, CA, 90041, USA.
Nancy ChenDepartment of Biology, University of Rochester, 477 Hutchison Hall, Box 270211, Rochester, NY, 14627, USA.ORCID 0000-0001-8966-3449
John W FitzpatrickCornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Rd, Ithaca, NY, 14850, USA.
John E McCormackMoore Laboratory of Zoology, Occidental College, 1600 Campus Rd, Los Angeles, CA, 90041, USA.ORCID 0000-0002-0912-1461
W Chris FunkDepartment of Biology, Graduate Degree Program in Ecology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO, 80523, USA.ORCID 0000-0002-6466-3618
Cameron K GhalamborDepartment of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, Realfagbygget D1-137, Trondheim, 7491, Norway.ORCID 0000-0003-2515-4981
Erik GarrisonDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, 71 S. Manassas Street, Memphis, TN, 38163, USA.
Andrea GuarracinoDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, 71 S. Manassas Street, Memphis, TN, 38163, USA.ORCID 0000-0001-9744-131X
Heng LiDepartment of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Mailstop: CLSB 11007, Boston, MA, 2215.ORCID 0000-0003-4874-2874
Timothy B SacktonInformatics Group, Harvard University, 52 Oxford St, Cambridge, MA, 2138, USA.ORCID 0000-0003-1673-9216

Funding

A Unified High Performance Web Service for Systems Genetics and Precision MedicineR01GM123489 · NIGMS · UNIVERSITY OF TENNESSEE HEALTH SCI CTR · PI PRINS, PJOTR, SEN, SAUNAK · 2017 to 2024
$3.7M
System genetics of menthol and nicotine addictionU01DA047638 · NIDA · UNIVERSITY OF TENNESSEE HEALTH SCI CTR · PI CHEN, HAO, WILLIAMS, ROBERT W. · 2019 to 2023
$3.1M
Statistical and high-throughput models of enhancer function and evolutionR01HG011485 · NHGRI · HARVARD UNIVERSITY · PI EDWARDS, SCOTT V., FARLEY, EMMA KIRSTEN · 2021 to 2024
$2.5M
Population genomics with pedigrees: new approaches for studying contemporary evolutionR35GM133412 · NIGMS · UNIVERSITY OF ROCHESTER · PI CHEN, NANCY · 2019 to 2023
$1.9M
NHGRI NIH HHS R01 HG011485NIDA NIH HHS U01 DA047638NIGMS NIH HHS R01 GM123489NIGMS NIH HHS R35 GM133412
6 · The paper itself

Abstract

Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (

Identifiers

PMID39990470
PMCPMC11844517

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.