Evidence map›Paper›PMID 40695280›Full record

ArticleCell2025

Human-specific gene expansions contribute to brain evolution.

Daniela C Soto, José M Uribe-Salazar, Gulhan Kaya, Ricardo Valdarrago, Aarthi Sekar, Nicholas K Haghani, Keiko Hino, Gabriana La, Natasha Ann F Mariano, Cole Ingamells and 8 more

Abstract read
In one paragraph

Article in Cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.

0numbers the graph read from it
0cells of the map it votes in
16citing 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

16 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Germline hypomethylation shapes dynamic CpG reservoirs in ape genomes.bioRxiv : the preprint server for biology · 2026
    Article
  5. Article
  6. Influence ofGenome research · 2026
    Article
  7. Article
  8. Review
  9. Article
  10. Review
  11. Article
  12. Article
  13. Influence ofbioRxiv : the preprint server for biology · 2025
    Article
  14. A complete diploid human genome benchmark for personalized genomics.bioRxiv : the preprint server for biology · 2025
    Article
  15. Article
  16. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

18 authors.

Daniela C SotoDepartment of Biochemistry & Molecular Medicine, MIND Institute, University of California, Davis, Davis, CA 95616, USA; Genome Center, University of California, Davis, Davis, CA 95616, USA.
José M Uribe-SalazarDepartment of Biochemistry & Molecular Medicine, MIND Institute, University of California, Davis, Davis, CA 95616, USA; Genome Center, University of California, Davis, Davis, CA 95616, USA.
Gulhan KayaDepartment of Biochemistry & Molecular Medicine, MIND Institute, University of California, Davis, Davis, CA 95616, USA; Genome Center, University of California, Davis, Davis, CA 95616, USA.
Ricardo ValdarragoDepartment of Molecular & Cellular Biology, University of California, Davis, Davis, CA 95616, USA.
Aarthi SekarDepartment of Biochemistry & Molecular Medicine, MIND Institute, University of California, Davis, Davis, CA 95616, USA; Genome Center, University of California, Davis, Davis, CA 95616, USA.
Nicholas K HaghaniDepartment of Biochemistry & Molecular Medicine, MIND Institute, University of California, Davis, Davis, CA 95616, USA; Genome Center, University of California, Davis, Davis, CA 95616, USA.
Keiko HinoDepartment of Cell Biology & Human Anatomy, University of California, Davis, Davis, CA 95616, USA.
Gabriana LaDepartment of Biochemistry & Molecular Medicine, MIND Institute, University of California, Davis, Davis, CA 95616, USA; Genome Center, University of California, Davis, Davis, CA 95616, USA.
Natasha Ann F MarianoDepartment of Biochemistry & Molecular Medicine, MIND Institute, University of California, Davis, Davis, CA 95616, USA; Genome Center, University of California, Davis, Davis, CA 95616, USA; Postbaccalaureate Research Education Program, University of California, Davis, Davis, CA 95616, USA.
Cole IngamellsDepartment of Biochemistry & Molecular Medicine, MIND Institute, University of California, Davis, Davis, CA 95616, USA; Genome Center, University of California, Davis, Davis, CA 95616, USA.
Aidan BarabanDepartment of Biochemistry & Molecular Medicine, MIND Institute, University of California, Davis, Davis, CA 95616, USA; Genome Center, University of California, Davis, Davis, CA 95616, USA.
Zoeb JamalDepartment of Biochemistry & Molecular Medicine, MIND Institute, University of California, Davis, Davis, CA 95616, USA; Genome Center, University of California, Davis, Davis, CA 95616, USA.
Tychele N TurnerDepartment of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.
Eric D GreenNational Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Sergi SimóDepartment of Cell Biology & Human Anatomy, University of California, Davis, Davis, CA 95616, USA.
Gerald QuonGenome Center, University of California, Davis, Davis, CA 95616, USA; Department of Molecular & Cellular Biology, University of California, Davis, Davis, CA 95616, USA.
Aida M AndrésUCL Genetics Institute, Department of Genetics, Evolution and Environment, University College, London, Cambridge WC1E 6BT, UK.
Megan Y DennisDepartment of Biochemistry & Molecular Medicine, MIND Institute, University of California, Davis, Davis, CA 95616, USA; Genome Center, University of California, Davis, Davis, CA 95616, USA. Electronic address: mydennis@ucdavis.edu.

Funding

UC Davis MCB T32 Administrative Supplement to Recognize Excellence in Diversity, Equity, Inclusion, and Accessibility (DEIA) MentorshipT32GM007377 · NIGMS · UNIVERSITY OF CALIFORNIA DAVIS · PI CHEDIN, FREDERIC LOUIS · 1985 to 2023
$9.9M
Research Project: Pathologic Significance of Maternal AutoantibodiesP50HD103526 · NICHD · UNIVERSITY OF CALIFORNIA AT DAVIS · PI LEONARD J. ABBEDUTO, Melissa Dawn Bauman · 2020 to 2026
$9.7M
Postbaccalaureate Research Education Program at UC DavisR25GM116690 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI JOANNA Chungyen CHIU · 2017 to 2026
$3.7M
The function of duplicated genes in human brain evolution and diseaseDP2MH119424 · NIMH · UNIVERSITY OF CALIFORNIA AT DAVIS · PI DENNIS, MEGAN Y · 2018 to 2018
$2.4M
Linking genetics to cellular behavior and disease via multimodal data integrationDP2MH129987 · NIMH · UNIVERSITY OF CALIFORNIA AT DAVIS · PI QUON, GERALD · 2021 to 2024
$2.3M
The UC Davis enhanced Molecular, Cellular, and Developmental Biology Training ProgramT32GM153586 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI Frederic Louis Chedin, ELVA D DIAZ · 2024 to 2026
$2.3M
Human gene duplications in neurodevelopment and diseaseRF1MH132818 · NIMH · UNIVERSITY OF CALIFORNIA AT DAVIS · PI DENNIS, MEGAN Y · 2025 to 2025
$2.1M
Regulation of hippocampal morphogenesis and homeostasis by the E3 ubiquitin ligase CRL5R01NS109176 · NINDS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI SIMO, SERGI · 2019 to 2023
$1.7M
Human gene duplications in neurodevelopment and diseaseR01MH132818 · NIMH · UNIVERSITY OF CALIFORNIA AT DAVIS · PI DENNIS, MEGAN Y · 2023 to 2024
$1.4M
NICHD NIH HHS P50 HD103526NIGMS NIH HHS R25 GM116690NIGMS NIH HHS T32 GM007377NIGMS NIH HHS T32 GM153586NIMH NIH HHS DP2 MH119424NIMH NIH HHS DP2 MH129987NIMH NIH HHS R01 MH132818NIMH NIH HHS RF1 MH132818NINDS NIH HHS R01 NS109176Wellcome Trust
6 · The paper itself

Abstract

Duplicated genes expanded in the human lineage likely contributed to brain evolution, yet challenges exist in their discovery due to sequence-assembly errors. We used a complete telomere-to-telomere genome sequence to identify 213 human-specific gene families. From these, 362 paralogs were found in all modern human genomes tested and brain transcriptomes, making them top candidates contributing to human-universal brain features. Choosing a subset of paralogs, long-read DNA sequencing of hundreds of modern humans revealed previously hidden signatures of selection, including for T cell marker CD8B. To understand roles in brain development, we generated zebrafish CRISPR "knockout" models of nine orthologs and introduced mRNA-encoding paralogs, effectively "humanizing" larvae. Our findings implicate two genes in possibly contributing to hallmark features of the human brain: GPR89B in dosage-mediated brain expansion and FRMPD2B in altered synapse signaling. Our holistic approach provides insights and a comprehensive resource for studying gene expansion drivers of human brain evolution.

Indexed as

Biological EvolutionBrainGene DuplicationGenome, HumanAnimalsGene DosageGene Knockout TechniquesHumansMultigene FamilyOrgan SizeReceptors, G-Protein-CoupledTelomereTight Junction ProteinsTranscriptomeZebrafishFRMPD2 protein, humanReceptors, G-Protein-CoupledTight Junction Proteinsbraincopy-number variationgene duplicationsgene expressionhuman evolutionnatural selectionneurodevelopmentsegmental duplicationssequencingzebrafish

Identifiers

PMID40695280
PMCPMC12313184

What Socratic holds

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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 Socratic graph.