ArticleProceedings of the National Academy of Sciences of the United States of America2021
Nonparametric coalescent inference of mutation spectrum history and demography.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed.
- The dynamics of introgression and parallel adaptation across North AmericanProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Severe bottleneck of ancient Homo populations: insights from computational modeling and relevant fossil evidence.Molecular biology and evolution · 2026Article
- Characterization of de novo germline mutations suggests a strong male mutation bias in coppery titi monkeys (Plecturocebus cupreus).Molecular biology and evolution · 2026Article
- A general framework for branch length estimation in Ancestral Recombination Graphs.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A General Framework for Branch Length Estimation in Ancestral Recombination Graphs.bioRxiv : the preprint server for biology · 2025Article
- Identifying Single-Origin Rare Variants in Population Genomic Data.Molecular biology and evolution · 2025Article
- GHIST 2024: The First Genomic History Inference Strategies Tournament.Molecular biology and evolution · 2025Article
- Estimation of demography and mutation rates from one million haploid genomes.American journal of human genetics · 2025Article
- A structured coalescent model reveals deep ancestral structure shared by all modern humans.Nature genetics · 2025Article
- Estimating effective population size trajectories from time-series identity-by-descent segments.Genetics · 2025Article
- The population genetics of convergent adaptation in maize and teosinte is not locally restricted.eLife · 2025Article
- An Expanding Universe of Mutational Signatures and Its Rapid Evolution in Single-Stranded RNA Viruses.Molecular biology and evolution · 2025Article
- Insufficient Evidence for a Severe Bottleneck in Humans During the Early to Middle Pleistocene Transition.Molecular biology and evolution · 2025Article
- A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact.Genetics · 2025Article
- NeMu: a comprehensive pipeline for accurate reconstruction of neutral mutation spectra from evolutionary data.Nucleic acids research · 2024Article
- Reference Genome Choice and Filtering Thresholds Jointly Influence Phylogenomic Analyses.Systematic biology · 2024Article
- The Promise of Inferring the Past Using the Ancestral Recombination Graph.Genome biology and evolution · 2024Article
- Time-resolved, integrated analysis of clonally evolving genomes.PLoS genetics · 2023Article
- The divergence of mutation rates and spectra across the Tree of Life.EMBO reports · 2023Review
- Evolution of the Mutation Spectrum Across a Mammalian Phylogeny.Molecular biology and evolution · 2023Article
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4 authors.
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Abstract
As populations boom and bust, the accumulation of genetic diversity is modulated, encoding histories of living populations in present-day variation. Many methods exist to decode these histories, and all must make strong model assumptions. It is typical to assume that mutations accumulate uniformly across the genome at a constant rate that does not vary between closely related populations. However, recent work shows that mutational processes in human and great ape populations vary across genomic regions and evolve over time. This perturbs the mutation spectrum (relative mutation rates in different local nucleotide contexts). Here, we develop theoretical tools in the framework of Kingman's coalescent to accommodate mutation spectrum dynamics. We present mutation spectrum history inference (mushi), a method to perform nonparametric inference of demographic and mutation spectrum histories from allele frequency data. We use mushi to reconstruct trajectories of effective population size and mutation spectrum divergence between human populations, identify mutation signatures and their dynamics in different human populations, and calibrate the timing of a previously reported mutational pulse in the ancestors of Europeans. We show that mutation spectrum histories can be placed in a well-studied theoretical setting and rigorously inferred from genomic variation data, like other features of evolutionary history.
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