ArticleJournal of theoretical biology2021
The probability distribution of the ancestral population size conditioned on the reconstructed phylogenetic tree with occurrence data.
Article in Journal of theoretical biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data.Molecular biology and evolution · 2025Article
- Estimating epidemic dynamics with genomic and time series data.Journal of the Royal Society, Interface · 2025Article
- EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering.PLoS computational biology · 2024Article
- The Occurrence Birth-Death Process for Combined-Evidence Analysis in Macroevolution and Epidemiology.Systematic biology · 2022Article
- Statistical Challenges in Tracking the Evolution of SARS-CoV-2.Statistical science : a review journal of the Institute of Mathematical Statistics · 2022Article
- A computationally tractable birth-death model that combines phylogenetic and epidemiological data.PLoS computational biology · 2022Article
- Fundamental Identifiability Limits in Molecular Epidemiology.Molecular biology and evolution · 2021Article
- Additional Analytical Support for a New Method to Compute the Likelihood of Diversification Models.Bulletin of mathematical biology · 2020Article
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4 authors.
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Abstract
We consider a homogeneous birth-death process with three different sampling schemes. First, individuals can be sampled through time and included in a reconstructed phylogenetic tree. Second, they can be sampled through time and only recorded as a point 'occurrence' along a timeline. Third, extant individuals can be sampled and included in the reconstructed phylogenetic tree with a fixed probability. We further consider that sampled individuals can be removed or not from the process, upon sampling, with fixed probability. We derive the probability distribution of the population size at any time in the past conditional on the joint observation of a reconstructed phylogenetic tree and a record of occurrences not included in the tree. We also provide an algorithm to simulate ancestral population size trajectories given the observation of a reconstructed phylogenetic tree and occurrences. This distribution can be readily used to draw inferences about the ancestral population size in the field of epidemiology and macroevolution. In epidemiology, these results will allow data from epidemiological case count studies to be used in conjunction with molecular sequencing data (yielding reconstructed phylogenetic trees) to coherently estimate prevalence through time. In macroevolution, it will foster the joint examination of the fossil record and extant taxa to reconstruct past biodiversity.
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