ArticleGenetics2019
Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions.
Article in Genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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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.
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Who cites it
24 citing papers in PubMed.
- Recent Insights Into the Evolutionary Genomics of the Critically Endangered Aye-Aye (Daubentonia madagascariensis).American journal of primatology · 2025Review
- Selection Estimation from Genetic Time-Series Data: Effects of Limited Sampling and Genetic Drift.Molecular biology and evolution · 2025Article
- Accounting for Chimerism in Demographic Inference: Reconstructing the History of Common Marmosets (Callithrix jacchus) from High-Quality, Whole-Genome, Population-Level Data.Molecular biology and evolution · 2025Article
- Inferring demographic and selective histories from population genomic data using a 2-step approach in species with coding-sparse genomes: an application to human data.G3 (Bethesda, Md.) · 2025Article
- Inferring the Demographic History of Aye-Ayes (Daubentonia madagascariensis) from High-Quality, Whole-Genome, Population-Level Data.Genome biology and evolution · 2025Article
- Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data.bioRxiv : the preprint server for biology · 2024Article
- Inferring the demographic history of aye-ayes (bioRxiv : the preprint server for biology · 2024Article
- Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples.PLoS pathogens · 2023Review
- Interpreting the pervasive observation of U-shaped Site Frequency Spectra.PLoS genetics · 2023Article
- Article
- Population genetic models for the spatial spread of adaptive variants: A review in light of SARS-CoV-2 evolution.PLoS genetics · 2022Review
- How Can We Resolve Lewontin's Paradox?Genome biology and evolution · 2022Article
- The impact of frequently neglected model violations on bacterial recombination rate estimation: a case study in Mycobacterium canettii and Mycobacterium tuberculosis.G3 (Bethesda, Md.) · 2022Article
- Recommendations for improving statistical inference in population genomics.PLoS biology · 2022Article
- Inferring the distribution of fitness effects in patient-sampled and experimental virus populations: two case studies.Heredity · 2022Article
- Article
- Effects of Selection at Linked Sites on Patterns of Genetic Variability.Annual review of ecology, evolution, and systematics · 2021Article
- Review
- Imposed mutational meltdown as an antiviral strategy.Evolution; international journal of organic evolution · 2020Review
- Considering Genomic Scans for Selection as Coalescent Model Choice.Genome biology and evolution · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The recent increase in time-series population genomic data from experimental, natural, and ancient populations has been accompanied by a promising growth in methodologies for inferring demographic and selective parameters from such data. However, these methods have largely presumed that the populations of interest are well-described by the Kingman coalescent. In reality, many groups of organisms, including viruses, marine organisms, and some plants, protists, and fungi, typified by high variance in progeny number, may be best characterized by multiple-merger coalescent models. Estimation of population genetic parameters under Wright-Fisher assumptions for these organisms may thus be prone to serious mis-inference. We propose a novel method for the joint inference of demography and selection under the Ψ-coalescent model, termed Multiple-Merger Coalescent Approximate Bayesian Computation, or MMC-ABC. We first demonstrate mis-inference under the Kingman, and then exhibit the superior performance of MMC-ABC under conditions of skewed offspring distributions. In order to highlight the utility of this approach, we reanalyzed previously published drug-selection lines of influenza A virus. We jointly inferred the extent of progeny-skew inherent to viral replication and identified putative drug-resistance mutations.
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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.