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Dating genomic variants and shared ancestry in population-scale sequencing data

https://doi.org/10.1371/journal.pbio.3000586

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What this work says

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inferred← citeshttps://doi.org/10.1093/molbev/msac121openalex-snapshot

Genetic Variation in Reproductive Investment Across an Ephemerality Gradient inDaphnia pulex

inferred← citeshttps://doi.org/10.1093/molbev/msac201openalex-snapshot

Evolutionary Responses of a Reef-building Coral to Climate Change at the End of the Last Glacial Maximum

inferred← citeshttps://doi.org/10.1093/molbev/msad160openalex-snapshot

Multiple Sources of Uncertainty Confound Inference of Historical Human Generation Times

inferred← citeshttps://doi.org/10.1093/molbev/msad211openalex-snapshot

Inference of Coalescence Times and Variant Ages Using Convolutional Neural Networks

inferred← citeshttps://doi.org/10.1093/molbev/msad273openalex-snapshot

Mapping and Functional Dissection of the Rumpless Trait in Piao Chicken Identifies a Causal Loss of Function Mutation in the Novel Gene Rum

inferred← citeshttps://doi.org/10.1093/molbev/msaf292openalex-snapshot

Coexisting With Humans: Genomic and Behavioral Consequences in a Small and Isolated Bear Population

inferred← citeshttps://doi.org/10.1093/nar/gkab925openalex-snapshot

PopHumanVar: an interactive application for the functional characterization and prioritization of adaptive genomic variants in humans

inferred← citeshttps://doi.org/10.1093/nar/gkaf971openalex-snapshot

Conserved facultative heterochromatin across cell types identify regulatory sequences underpinning cell identity and disease

inferred← citeshttps://doi.org/10.1093/plcell/koad296openalex-snapshot

Forces driving transposable element load variation during Arabidopsis range expansion

inferred← citeshttps://doi.org/10.1101/2020.05.26.117358openalex-snapshot

Identifying non-identical-by-descent rare variants in population-scale whole genome sequencing data

inferred← citeshttps://doi.org/10.1101/2020.06.01.127555openalex-snapshot

Ancient Admixture into Africa from the ancestors of non-Africans

inferred← citeshttps://doi.org/10.1101/2020.12.16.20248300openalex-snapshot

Systematic review reveals multiple sexually antagonistic polymorphisms affecting human disease and complex traits

inferred← citeshttps://doi.org/10.1101/2021.01.22.427608openalex-snapshot

Fine-grained temporal mapping of derived high-frequency variants supports the mosaic nature of the evolution of Homo sapiens

inferred← citeshttps://doi.org/10.1101/2021.06.23.449662openalex-snapshot

Polygenic variation in sexual investment across an ephemerality gradient in Daphnia pulex

inferred← citeshttps://doi.org/10.1101/2021.09.03.21262975openalex-snapshot

Insights from complex trait fine-mapping across diverse populations

inferred← citeshttps://doi.org/10.1101/2021.09.20.461171openalex-snapshot

Polygenic signals of sexually antagonistic selection in contemporary human genomes

inferred← citeshttps://doi.org/10.1101/2022.11.28.518185openalex-snapshot

Selection-driven trait loss in independently evolved cavefish populations

inferred← citeshttps://doi.org/10.1101/2023.01.06.522935openalex-snapshot

Ultra-fast genome-wide inference of pairwise coalescence times

inferred← citeshttps://doi.org/10.1101/2023.02.05.525539openalex-snapshot

Mapping the genetic evolutionary timeline of human neural and cognitive traits

inferred← citeshttps://doi.org/10.1101/2023.02.10.23285704openalex-snapshot

The genetic architecture of human cerebellar morphology supports a key role for the cerebellum in human evolution and psychopathology

inferred← citeshttps://doi.org/10.1101/2023.03.10.23287070openalex-snapshot

Diversity of CFTR variants across ancestries characterized using 454,727 UK biobank whole exome sequences

inferred← citeshttps://doi.org/10.1101/2023.03.17.533108openalex-snapshot

Genetically diverse populations hold the keys to climatic adaptation: a lesson from a cosmopolitan raptor

inferred← citeshttps://doi.org/10.1101/2023.04.02.535252openalex-snapshot

Improved inference of population histories by integrating genomic and epigenomic data

inferred← citeshttps://doi.org/10.1101/2023.04.19.23288831openalex-snapshot

Detection of distant familial relatedness in biobanks for identification of undiagnosed carriers of a Mendelian disease variant: application to Long QT syndrome

inferred← citeshttps://doi.org/10.1101/2023.07.20.549788openalex-snapshot

Robust inference of historical human generation times

inferred← citeshttps://doi.org/10.1101/2023.08.08.552553openalex-snapshot

Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates

inferred← citeshttps://doi.org/10.1101/2023.10.09.561569openalex-snapshot

Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls

inferred← citeshttps://doi.org/10.1101/2024.03.15.585102openalex-snapshot

High-resolution genomic ancestry reveals mobility in early medieval Europe

inferred← citeshttps://doi.org/10.1101/2024.08.14.605938openalex-snapshot

alpha-Actinin-3 deficiency protects from the effects of acute cold exposure through altered skeletal muscle Ca2+ and OXPHOS signaling.

inferred← citeshttps://doi.org/10.1101/2024.10.28.620690openalex-snapshot

Epigenetic constraint of cellular genomes evolutionarily links genetic variation to function

inferred← citeshttps://doi.org/10.1101/2025.04.02.25325097openalex-snapshot

Common variation in meiosis genes shapes human recombination phenotypes and aneuploidy risk

inferred← citeshttps://doi.org/10.1101/2025.05.19.654975openalex-snapshot

A catalog of ancient proxies for modern genetic variants

inferred← citeshttps://doi.org/10.1101/gr.277665.123openalex-snapshot

Ultrafast genome-wide inference of pairwise coalescence times

inferred← citeshttps://doi.org/10.1101/gr.278569.123openalex-snapshot

Large-scale genomic analysis of the domestic dog informs biological discovery

inferred← citeshttps://doi.org/10.1111/1755-0998.70105openalex-snapshot

Polarising SNPs Without Outgroup

inferred← citeshttps://doi.org/10.1111/2041-210x.13991openalex-snapshot

Identifying rare variants inconsistent with identity‐by‐descent in population‐scale whole‐genome sequencing data

inferred← citeshttps://doi.org/10.1111/ahg.70052openalex-snapshot

Population‐Level Nucleotide Diversity and Genetic Differentiation at SOD1 Across Global Human Populations

inferred← citeshttps://doi.org/10.1111/evo.14394openalex-snapshot

Systematic review reveals multiple sexually antagonistic polymorphisms affecting human disease and complex traits

inferred← citeshttps://doi.org/10.1111/gbb.12899openalex-snapshot

Human‐specific insights into candidate genes and boosted discoveries of novel loci illuminate roles of neuroglia in reading disorders

inferred← citeshttps://doi.org/10.1111/mec.15499openalex-snapshot

Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish

inferred← citeshttps://doi.org/10.1111/mec.17536openalex-snapshot

Evolution of gene networks underlying adaptation to drought stress in the wild tomato Solanum chilense

inferred← citeshttps://doi.org/10.1123/kr.2021-0057openalex-snapshot

The Human Genome, Physical Activity, Fitness, and Health

inferred← citeshttps://doi.org/10.1126/sciadv.abm5982openalex-snapshot

Rapid adaptive radiation of Darwin’s finches depends on ancestral genetic modules

inferred← citeshttps://doi.org/10.1126/sciadv.abm7047openalex-snapshot

Human generation times across the past 250,000 years

inferred← citeshttps://doi.org/10.1126/sciadv.adj5661openalex-snapshot

Functional EPAS1 / HIF2A missense variant is associated with hematocrit in Andean highlanders

inferred← citeshttps://doi.org/10.1126/sciadv.adw7768openalex-snapshot

Genome-wide association study reveals genetic architecture and evolution of human retinal pigmentation

inferred← citeshttps://doi.org/10.1126/sciadv.ady6667openalex-snapshot

Ancient Yellow River ancestry and divergent admixture histories in the Qiang people

inferred← citeshttps://doi.org/10.1126/science.abi8264openalex-snapshot

A unified genealogy of modern and ancient genomes

inferred← citeshttps://doi.org/10.1126/science.abn8197openalex-snapshot

The landscape of tolerated genetic variation in humans and primates

inferred← citeshttps://doi.org/10.1126/science.adn0609openalex-snapshot

Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation

inferred← citeshttps://doi.org/10.1126/science.ads3888openalex-snapshot

A male Denisovan mandible from Pleistocene Taiwan

inferred← citeshttps://doi.org/10.1136/jmg-2025-111273openalex-snapshot

Expanded carrier screening in a Southwestern Chinese population indicates East Asian specific low-frequency pathogenic variants account for nearly half of the at-risk couple rate

inferred← citeshttps://doi.org/10.1177/13872877251396973openalex-snapshot

Identification of common human TMEM173 genotypes associated with Alzheimer's disease

inferred← citeshttps://doi.org/10.1186/s12711-021-00633-2openalex-snapshot

Variants at the ASIP locus contribute to coat color darkening in Nellore cattle

inferred← citeshttps://doi.org/10.1186/s12859-020-3508-8openalex-snapshot

Origins and characterization of variants shared between databases of somatic and germline human mutations

inferred← citeshttps://doi.org/10.1186/s12864-022-08354-6openalex-snapshot

Benchmarking phasing software with a whole-genome sequenced cattle pedigree

inferred← citeshttps://doi.org/10.1186/s13073-022-01035-9openalex-snapshot

A neurodegenerative disease landscape of rare mutations in Colombia due to founder effects

inferred← citeshttps://doi.org/10.1186/s13073-023-01244-wopenalex-snapshot

The role of admixture in the rare variant contribution to inflammatory bowel disease

inferred← citeshttps://doi.org/10.1186/s13073-024-01316-5openalex-snapshot

Diversity of CFTR variants across ancestries characterized using 454,727 UK biobank whole exome sequences

inferred← citeshttps://doi.org/10.1214/24-ba1418openalex-snapshot

A Bayesian Nonparametric Approach to Species Sampling Problems with Ordering

inferred← citeshttps://doi.org/10.1371/journal.pbio.3001768openalex-snapshot

Polygenic signals of sex differences in selection in humans from the UK Biobank

inferred← citeshttps://doi.org/10.1371/journal.pgen.1008384openalex-snapshot

An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data

inferred← citeshttps://doi.org/10.1371/journal.pgen.1008773openalex-snapshot

Scalable probabilistic PCA for large-scale genetic variation data

inferred← citeshttps://doi.org/10.1371/journal.pgen.1009564openalex-snapshot

From musk to body odor: Decoding olfaction through genetic variation

inferred← citeshttps://doi.org/10.1371/journal.pgen.1011537openalex-snapshot

Estimating evolutionary and demographic parameters via ARG-derived IBD

inferred← citeshttps://doi.org/10.1371/journal.pone.0259897openalex-snapshot

Lower promoter activity of the ST8SIA2 gene has been favored in evolving human collective brains

inferred← citeshttps://doi.org/10.1371/journal.pone.0269628openalex-snapshot

Spatio-temporal dynamics of pathogenic variants associated with monogenic disorders reconstructed with ancient DNA

inferred← citeshttps://doi.org/10.1371/journal.ppat.1013257openalex-snapshot

A comprehensive phylogeny of mammalian PRNP gene reveals no influence of prion misfolding propensity on the evolution of this gene

inferred← citeshttps://doi.org/10.21203/rs.3.rs-2062759/v1openalex-snapshot

Epi-Clock: A sensitive platform to help understand pathogenic disease outbreaks and facilitate the response to future outbreaks of concern.

inferred← citeshttps://doi.org/10.21203/rs.3.rs-2062759/v2openalex-snapshot

Epi-Clock: A sensitive platform to help understand pathogenic disease outbreaks and facilitate the response to future outbreaks of concern.

inferred← citeshttps://doi.org/10.21203/rs.3.rs-2062759/v3openalex-snapshot

Epi-Clock: A sensitive platform to help understand pathogenic disease outbreaks and facilitate the response to future outbreaks of concern.

inferred← citeshttps://doi.org/10.21203/rs.3.rs-2062759/v4openalex-snapshot

Epi-Clock: A sensitive platform to help understand pathogenic disease outbreaks and facilitate the response to future outbreaks of concern.

inferred← citeshttps://doi.org/10.21203/rs.3.rs-2062759/v5openalex-snapshot

Epi-Clock: A sensitive platform to help understand pathogenic disease outbreaks and facilitate the response to future outbreaks of concern.

inferred← citeshttps://doi.org/10.21203/rs.3.rs-2062759/v6openalex-snapshot

Epi-Clock: A sensitive platform to help understand pathogenic disease outbreaks and facilitate the response to future outbreaks of concern.

inferred← citeshttps://doi.org/10.21203/rs.3.rs-3263845/v1openalex-snapshot

Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates

inferred← citeshttps://doi.org/10.21203/rs.3.rs-604881/v1openalex-snapshot

Genetic mechanisms underlying East Asian and European Facial differentiation

inferred← citeshttps://doi.org/10.21203/rs.3.rs-8780717/v1openalex-snapshot

Evolutionary persistence governs transmitted prediction across generations in hyper-diverse genomes

inferred← citeshttps://doi.org/10.2174/0113892029301969240708094053openalex-snapshot

Melocular Evolution on Cold Temperature Adaptation of Chinese Rhesus Macaques

inferred← citeshttps://doi.org/10.24072/pci.genomics.100251openalex-snapshot

Natural variation and adaptation in Brachypodium distachyon

inferred← citeshttps://doi.org/10.24072/pcjournal.319openalex-snapshot

The demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological niches

inferred← citeshttps://doi.org/10.3233/blc-230010openalex-snapshot

Historical Pathogen-Driven Selection May Contribute to Contemporary Ethnic Difference in Bladder Cancer Susceptibility

inferred← citeshttps://doi.org/10.3233/jpd-230250openalex-snapshot

The Etiology of Parkinson’s Disease: New Perspectives from Gene-Environment Interactions

inferred← citeshttps://doi.org/10.3390/cancers18101671openalex-snapshot

Elevated Allele Frequency of a Common Germline LAG3 Variant Associated with Anemia, Thrombocytopenia and Peripheral Blast Percentage in Acute Myeloid Leukemia

inferred← citeshttps://doi.org/10.3390/genes15121650openalex-snapshot

Federated Learning: Breaking Down Barriers in Global Genomic Research

inferred← citeshttps://doi.org/10.3390/genes17080951openalex-snapshot

HFE p.S65C (rs1800730) in Europe: A Geographic Study

inferred← citeshttps://doi.org/10.3390/ijms27167356openalex-snapshot

Clinical Impact of a Common PDCD1 Germline Variant in DLBCL Patients Treated with CAR-T Cell Therapy

inferred← citeshttps://doi.org/10.6084/m9.figshare.12432260openalex-snapshot

Additional file 1 of Origins and characterization of variants shared between databases of somatic and germline human mutations

inferred← citeshttps://doi.org/10.6084/m9.figshare.12432269openalex-snapshot

Additional file 2 of Origins and characterization of variants shared between databases of somatic and germline human mutations

inferred← citeshttps://doi.org/10.6084/m9.figshare.12432275openalex-snapshot

Additional file 3 of Origins and characterization of variants shared between databases of somatic and germline human mutations

inferred← citeshttps://doi.org/10.6084/m9.figshare.12432284openalex-snapshot

Additional file 4 of Origins and characterization of variants shared between databases of somatic and germline human mutations

inferred← citeshttps://doi.org/10.6084/m9.figshare.14509506openalex-snapshot

Additional file 1 of Variants at the ASIP locus contribute to coat color darkening in Nellore cattle

inferred← citeshttps://doi.org/10.6084/m9.figshare.14509518openalex-snapshot

Additional file 5 of Variants at the ASIP locus contribute to coat color darkening in Nellore cattle

inferred← citeshttps://doi.org/10.6084/m9.figshare.25459520openalex-snapshot

Additional file 1 of Diversity of CFTR variants across ancestries characterized using 454,727 UK biobank whole exome sequences

inferred← citeshttps://doi.org/10.6084/m9.figshare.25459666openalex-snapshot

Additional file 2 of Diversity of CFTR variants across ancestries characterized using 454,727 UK biobank whole exome sequences

inferred← citeshttps://doi.org/10.6084/m9.figshare.26640037openalex-snapshot

Additional file 1 of The role of admixture in the rare variant contribution to inflammatory bowel disease

inferred← citeshttps://doi.org/10.64898/2025.12.22.25342816openalex-snapshot

Genetic and functional evidence implicates a CRIP3 non-synonymous variant in age-related hearing loss

inferred← citeshttps://doi.org/10.64898/2026.01.07.698223openalex-snapshot

Tracing the evolutionary histories of ultra-rare variants using variational dating of large ancestral recombination graphs

inferred← citeshttps://doi.org/10.64898/2026.01.20.700628openalex-snapshot

Evidence of Adaptation in Structural Variants among Wild Populations of the purple sea urchin, Strongylocentrotus purpuratus

inferred← citeshttps://doi.org/10.64898/2026.02.01.703099openalex-snapshot

The genetic architecture of local adaptation is historically contingent

inferred← citeshttps://doi.org/10.64898/2026.02.26.708176openalex-snapshot

Tracing the origin of non-brittle rachis alleles in wheat

inferred← citeshttps://doi.org/10.64898/2026.05.05.722510openalex-snapshot

Rhodopsin moonlights as a tunable capacitor buffering the toxic, desensitizing retinoids of the vertebrate eye

inferred← citeshttps://doi.org/10.70675/c760e78az1e76z470cza3a1za00d79b1f954openalex-snapshot

The legacy of human disease : paleogenomic insights into genetic disease endurance in France and selection in wider Europe

inferred← citeshttps://doi.org/10.7554/elife.60107openalex-snapshot

A variant-centric perspective on geographic patterns of human allele frequency variation

inferred← citeshttps://doi.org/10.7554/elife.73767openalex-snapshot

Modeling the spatiotemporal spread of beneficial alleles using ancient genomes

inferred← citeshttps://doi.org/10.7554/elife.75464openalex-snapshot

The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals

inferred← citeshttps://doi.org/10.7554/elife.79111openalex-snapshot

Balancing selection on genomic deletion polymorphisms in humans

inferred← citeshttps://doi.org/10.7554/elife.89470openalex-snapshot

Improved inference of population histories by integrating genomic and epigenomic data

inferred← citeshttps://doi.org/10.7554/elife.89470.1openalex-snapshot

Improved inference of population histories by integrating genomic and epigenomic data

inferred← citeshttps://doi.org/10.7554/elife.89470.2openalex-snapshot

Improved inference of population histories by integrating genomic and epigenomic data

inferred← citeshttps://doi.org/10.7554/elife.89470.3openalex-snapshot

Improved inference of population histories by integrating genomic and epigenomic data

inferred← citeshttps://doi.org/10.7554/elife.89470.3.sa2openalex-snapshot

Reviewer #1 (Public Review): Improved inference of population histories by integrating genomic and epigenomic data

inferred← citeshttps://doi.org/10.7554/elife.89470.3.sa3openalex-snapshot

eLife Assessment: Improved inference of population histories by integrating genomic and epigenomic data

inferred← citeshttps://doi.org/10.7554/elife.89470.4openalex-snapshot

Improved inference of population histories by integrating genomic and epigenomic data

inferred← citeshttps://doi.org/10.7554/elife.93258openalex-snapshot

Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls

inferred← citeshttps://doi.org/10.7554/elife.93258.1openalex-snapshot

Analyses of allele age and fitness impact reveal human beneficial alleles to be older than neutral controls

inferred← citeshttps://doi.org/10.7554/elife.93284openalex-snapshot

The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role

inferred← citeshttps://doi.org/10.7554/elife.93284.1openalex-snapshot

The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.