ArticleeLife2024
Improved inference of population histories by integrating genomic and epigenomic data.
Article in eLife, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Distance-Limited Larval Replenishment in the Deep-Sea Mussel Gigantidas platifrons Challenges Connectivity-Based Conservation Planning.Molecular ecology · 2026Article
- Coalescence and translation: A language model for population genetics.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Centromeres are hotspots of cytosine methylation epimutations in a filamentous fungus.bioRxiv : the preprint server for biology · 2026Article
- Not Just Ne Ne-More: New Applications for SMC from Ecology to Phylogenies.Genome biology and evolution · 2026Review
- Genomic perspectives on the inference of evolutionary changes in ecological life-history traits.Quantitative plant biology · 2026Review
- High-quality genome assembly of Chironomus riparius and its population history in European populations.G3 (Bethesda, Md.) · 2025Article
- The interplay of recombination landscape and a transposable element in European populations of Chironomus riparius.BMC genomics · 2025Article
- Adaptive epigenetic divergence can facilitate ecological speciation.Proceedings. Biological sciences · 2025Article
- Methylomes Reveal Recent Evolutionary Changes in Populations of Two Plant Species.Genome biology and evolution · 2025Article
- Epigenetic variation in light of population genetic practice.Nature communications · 2025Review
- High germline mutation rates, but not extreme population outbreaks, influence genetic diversity in a keystone coral predator.PLoS genetics · 2024Article
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Authors and funding
3 authors.
Funding
Abstract
With the availability of high-quality full genome polymorphism (SNPs) data, it becomes feasible to study the past demographic and selective history of populations in exquisite detail. However, such inferences still suffer from a lack of statistical resolution for recent, for example bottlenecks, events, and/or for populations with small nucleotide diversity. Additional heritable (epi)genetic markers, such as indels, transposable elements, microsatellites, or cytosine methylation, may provide further, yet untapped, information on the recent past population history. We extend the Sequential Markovian Coalescent (SMC) framework to jointly use SNPs and other hyper-mutable markers. We are able to (1) improve the accuracy of demographic inference in recent times, (2) uncover past demographic events hidden to SNP-based inference methods, and (3) infer the hyper-mutable marker mutation rates under a finite site model. As a proof of principle, we focus on demographic inference in
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Registered trials
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.