ArticleEvolutionary bioinformatics online2007
Estimating population parameters using the structured serial coalescent with Bayesian MCMC inference when some demes are hidden.
Article in Evolutionary bioinformatics online, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed.
- When migration leaves a clean trace: Decoupling migration from coalescence in the structured serial coalescent.bioRxiv : the preprint server for biology · 2025Article
- Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations.Virus evolution · 2023Article
- Identification of diffusion routes of O/EA-3 topotype of foot-and-mouth disease virus in Africa and Western Asia between 1974 and 2019 - a phylogeographic analysis.Transboundary and emerging diseases · 2022Article
- Accounting for spatial sampling patterns in Bayesian phylogeography.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- A brief history and popularity of methods and tools used to estimate micro-evolutionary forces.Ecology and evolution · 2021Review
- Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk.PLoS computational biology · 2021Article
- Phylodynamic analysis and evaluation of the balance between anthropic and environmental factors affecting IBV spreading among Italian poultry farms.Scientific reports · 2020Article
- Evolutionary Dynamics in Structured Populations Under Strong Population Genetic Forces.G3 (Bethesda, Md.) · 2019Article
- Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data.Molecular biology and evolution · 2016Article
- New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation.PLoS genetics · 2015Article
- Phylogenetic and epidemic modeling of rapidly evolving infectious diseases.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2011Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Using the structured serial coalescent with Bayesian MCMC and serial samples, we estimate population size when some demes are not sampled or are hidden, ie ghost demes. It is found that even with the presence of a ghost deme, accurate inference was possible if the parameters are estimated with the true model. However with an incorrect model, estimates were biased and can be positively misleading. We extend these results to the case where there are sequences from the ghost at the last time sample. This case can arise in HIV patients, when some tissue samples and viral sequences only become available after death. When some sequences from the ghost deme are available at the last sampling time, estimation bias is reduced and accurate estimation of parameters associated with the ghost deme is possible despite sampling bias. Migration rates for this case are also shown to be good estimates when migration values are low.
Indexed as
Identifiers
19455215PMC2674663What OpenQuestion holds
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.