Evidence map›Paper›PMID 39875578›Full record

ReviewNature genetics2025

Functional innovation through new genes as a general evolutionary process.

Shengqian Xia, Jianhai Chen, Deanna Arsala, J J Emerson, Manyuan Long

Erratum issuedAbstract readReview
In one paragraph

Review in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 32 papers.

0numbers the graph read from it
0cells of the map it votes in
32citing 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

32 citing papers in PubMed.

  1. Article
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  5. Review
  6. Article
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  10. Review
  11. Article
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  14. Descent from a common ancestor restricts exploration of protein sequence space.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  15. Article
  16. Article
  17. Review
  18. Integrative analysis ofFrontiers in plant science · 2026
    Article
  19. Review
  20. Sex-biased duplicates are rapidly generated duringbioRxiv : the preprint server for biology · 2025
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Shengqian XiaDepartment of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.
Jianhai ChenDepartment of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.ORCID 0000-0003-0093-2003
Deanna ArsalaDepartment of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.
J J EmersonDepartment of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA.ORCID 0000-0001-9474-0891
Manyuan LongDepartment of Ecology and Evolution, The University of Chicago, Chicago, IL, USA. mlong@uchicago.edu.ORCID 0000-0002-6755-197X

Funding

Reference-quality Drosophila genome assemblies for evolutionary analysis of previously inaccessible genomic regionsR01GM116113 · NIGMS · UNIVERSITY OF ARIZONA · PI CLARK, ANDREW G, LONG, MANYUAN · 2016 to 2019
$2.3M
Structural variation population size and the evolution of genome complexityR01GM123303 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI EMERSON, JAMES JORDAN · 2017 to 2021
$1.5M
The origin, maintenance, and adaptive consequences of variation in genome structureR35GM153327 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI James Jordan Emerson · 2024 to 2026
$1.1M
Assessing the generality of sexual conflict in new gene evolution in DrosophilaF32GM146423 · NIGMS · UNIVERSITY OF CHICAGO · PI ARSALA, DEANNA · 2022 to 2024
$213k
National Science Foundation (NSF) MCB2020667NIGMS NIH HHS F32 GM146423NIGMS NIH HHS R01 GM116113NIGMS NIH HHS R01 GM123303NIGMS NIH HHS R35 GM153327U.S. Department of Health & Human Services | National Institutes of Health (NIH) 1R01GM116113-01A1U.S. Department of Health & Human Services | National Institutes of Health (NIH) F32GM146423U.S. Department of Health & Human Services | National Institutes of Health (NIH) R01GM123303
6 · The paper itself

Abstract

In the past decade, our understanding of how new genes originate in diverse organisms has advanced substantially, and more than a dozen molecular mechanisms for generating initial gene structures were identified, in addition to gene duplication. These new genes have been found to integrate into and modify pre-existing gene networks primarily through mutation and selection, revealing new patterns and rules with stable origination rates across various organisms. This progress has challenged the prevailing belief that new proteins evolve from pre-existing genes, as new genes may arise de novo from noncoding DNA sequences in many organisms, with high rates observed in flowering plants. New genes have important roles in phenotypic and functional evolution across diverse biological processes and structures, with detectable fitness effects of sexual conflict genes that can shape species divergence. Such knowledge of new genes can be of translational value in agriculture and medicine.

Indexed as

Evolution, MolecularAnimalsGene DuplicationGene Regulatory NetworksHumansMutationPhenotypePlantsSelection, Genetic

Identifiers

PMID39875578
PMCPMC12844861

What OpenQuestion holds

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Registered trials

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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.