Evidence map›Paper›PMID 42777703›Full record

ArticleCell genomics2026

Intraspecific sequence variation and complete genomes refine the identification of rapidly evolved regions in humans.

Yanting Luo, Riley J Mangan, Seth Weaver, Sarah A Zhao, Federica Mosti, Michael C Thomas, Ravi Karra, Debra L Silver, Manolis Kellis, Craig B Lowe

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Yanting LuoDepartment of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA; Department of Cell Biology, Duke University, Durham, NC 27710, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA.
Riley J ManganComputer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, MA 02139, USA; The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Genetics Training Program, Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA.
Seth WeaverDepartment of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA; Department of Cell Biology, Duke University, Durham, NC 27710, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA.
Sarah A ZhaoComputer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, MA 02139, USA; The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
Federica MostiDepartment of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA; Department of Cell Biology, Duke University, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
Michael C ThomasDivision of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
Ravi KarraDivision of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA.
Debra L SilverDepartment of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA; Department of Cell Biology, Duke University, Durham, NC 27710, USA; Duke Institute for Brain Sciences and Duke Regeneration Center, Duke University Medical Center, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
Manolis KellisComputer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, MA 02139, USA; The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
Craig B LoweDepartment of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA; Department of Cell Biology, Duke University, Durham, NC 27710, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA. Electronic address: craig.lowe@duke.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Humans exhibit significant phenotypic differences from other great apes, yet pinpointing the underlying genetic changes has been limited by incomplete reference genomes and a reliance on single assemblies to represent a species. We aligned 20 telomere-to-telomere (T2T) assemblies spanning great ape divergence and variation to define 1,596 Consensus HAQERs (consensus human ancestor quickly evolved regions), regions that diverged rapidly between the human-chimpanzee ancestor and an ancestral node of modern humans. Unlike prior HAQER sets, Consensus HAQERs incorporate population variation, thereby reducing the likelihood of intraspecies variation appearing as interspecies divergence. Consensus HAQERs exhibit signatures of elevated mutation rates, ancient positive selection, and bivalent regulatory function; are enriched in disease-linked loci; and often emerged in previously inaccessible repetitive DNA. Through multiplex, single-cell enhancer assays, we identify HAQERs as active enhancers in the developing brain and cardiomyocytes, and we highlight their potential contributions to human-specific gene regulation across multiple tissues.

Indexed as

Evolution, MolecularGenetic VariationGenome, HumanAnimalsEnhancer Elements, GeneticHumansPan troglodytesSpecies SpecificityTelomerecardiac developmentcomparative genomicsgene regulationHAQERhuman evolutionneurodevelopmentSTARR-seqT2Ttelomere-to-telomere

Identifiers

PMID42777703
PMCPMC13689511

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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.