ArticleGenetics2012
Complex population dynamics and the coalescent under neutrality.
Article in Genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 100 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
100 citing papers in PubMed.
- Untangling the effects of within-host and between-host natural selection in viruses with applications to evolution of HIV-1 co-receptor usage.Journal of the Royal Society, Interface · 2026Article
- Hidden Burden of a Measles Outbreak Revealed by Genomic and Transmission Models.medRxiv : the preprint server for health sciences · 2026Article
- Viral introductions and return to baseline sexual behaviors maintain low-level mpox incidence in Los Angeles.Nature communications · 2026Article
- Optimizing genomic sampling for demographic and epidemiological inference with Markov decision processes.Genetics · 2026Article
- Phylogenetics and molecular evolution to understand and curb the HIV pandemic.Nature reviews. Microbiology · 2026Review
- When migration leaves a clean trace: Decoupling migration from coalescence in the structured serial coalescent.bioRxiv : the preprint server for biology · 2025Article
- MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions.PLoS computational biology · 2025Article
- Robust phylodynamic inference and model specification for HIV transmission dynamics.Epidemics · 2025Article
- Viral introductions and return to baseline sexual behaviors maintain low-level mpox incidence in Los Angeles County, USA, 2023-2024.medRxiv : the preprint server for health sciences · 2025Article
- Evolution and transmission dynamics of wild poliovirus in Pakistan and Afghanistan (2012-2023).Nature communications · 2025Article
- Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model.PLoS computational biology · 2025Article
- Phylodynamics beyond neutrality: the impact of incomplete purifying selection on viral phylogenies and inference.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal.PLoS computational biology · 2024Article
- EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering.PLoS computational biology · 2024Article
- Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong.Systematic biology · 2024Article
- Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England.PLoS pathogens · 2024Article
- Congruity of genomic and epidemiological data in modelling of local cholera outbreaks.Proceedings. Biological sciences · 2024Article
- Estimates of early outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- ReMASTER: improved phylodynamic simulation for BEAST 2.7.Bioinformatics (Oxford, England) · 2024Article
- A phylogenetic assessment of HIV-1 transmission trends among people who inject drugs from Coastal and Nairobi, Kenya.Virus evolution · 2024Article
40 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
1 author.
Funding
Abstract
Estimates of the coalescent effective population size N(e) can be poorly correlated with the true population size. The relationship between N(e) and the population size is sensitive to the way in which birth and death rates vary over time. The problem of inference is exacerbated when the mechanisms underlying population dynamics are complex and depend on many parameters. In instances where nonparametric estimators of N(e) such as the skyline struggle to reproduce the correct demographic history, model-based estimators that can draw on prior information about population size and growth rates may be more efficient. A coalescent model is developed for a large class of populations such that the demographic history is described by a deterministic nonlinear dynamical system of arbitrary dimension. This class of demographic model differs from those typically used in population genetics. Birth and death rates are not fixed, and no assumptions are made regarding the fraction of the population sampled. Furthermore, the population may be structured in such a way that gene copies reproduce both within and across demes. For this large class of models, it is shown how to derive the rate of coalescence, as well as the likelihood of a gene genealogy with heterochronous sampling and labeled taxa, and how to simulate a coalescent tree conditional on a complex demographic history. This theoretical framework encapsulates many of the models used by ecologists and epidemiologists and should facilitate the integration of population genetics with the study of mathematical population dynamics.
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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.