ArticlePLoS genetics2019
An estimator of first coalescent time reveals selection on young variants and large heterogeneity in rare allele ages among human populations.
Article in PLoS genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- Tracing the evolutionary histories of ultra-rare variants using variational dating of large ancestral recombination graphs.bioRxiv : the preprint server for biology · 2026Article
- Multi-centric origins and gene flow shape the diversity of β-thalassemia mutations in Southern East Asia.Nature communications · 2025Article
- Allele age estimators designed for whole-genome datasets show only a moderate reduction in performance when applied to whole-exome datasets.G3 (Bethesda, Md.) · 2025Article
- CINner: Modeling and simulation of chromosomal instability in cancer at single-cell resolution.PLoS computational biology · 2025Article
- A molecular mechanism for bright color variation in parrots.Science (New York, N.Y.) · 2024Article
- CINner: modeling and simulation of chromosomal instability in cancer at single-cell resolution.bioRxiv : the preprint server for biology · 2024Article
- Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank.Nature genetics · 2023Article
- Genetic architecture and evolution of color variation in American black bears.Current biology : CB · 2023Article
- Article
- Identifying rare variants inconsistent with identity-by-descent in population-scale whole-genome sequencing data.Methods in ecology and evolution · 2022Article
- Article
- Detecting Selection on Segregating Gene Duplicates in a Population.Journal of molecular evolution · 2021Article
- Characterizing Amino Acid Substitution with Complete Linkage of Sites on a Lineage.Genome biology and evolution · 2021Article
- Characterizing the demographic history and prion protein variation to infer susceptibility to chronic wasting disease in a naïve population of white-tailed deer (Evolutionary applications · 2021Article
- A variant-centric perspective on geographic patterns of human allele frequency variation.eLife · 2020Article
- Article
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Authors and funding
4 authors.
Funding
Abstract
Allele age has long been a focus of population genetic research, primarily because it can be an important clue to the fitness effects of an allele. By virtue of their effects on fitness, alleles under directional selection are expected to be younger than neutral alleles of the same frequency. We developed a new coalescent-based estimator of a close proxy for allele age, the time when a copy of an allele first shares common ancestry with other chromosomes in a sample not carrying that allele. The estimator performs well, including for the very rarest of alleles that occur just once in a sample, with a bias that is typically negative. The estimator is mostly insensitive to population demography and to factors that can arise in population genomic pipelines, including the statistical phasing of chromosomes. Applications to 1000 Genomes Data and UK10K genome data confirm predictions that singleton alleles that alter proteins are significantly younger than those that do not, with a greater difference in the larger UK10K dataset, as expected. The 1000 Genomes populations varied markedly in their distributions for singleton allele ages, suggesting that these distributions can be used to inform models of demographic history, including recent events that are only revealed by their impacts on the ages of very rare alleles.
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