ArticleSystematic biology2022
An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference.
Article in Systematic biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed.
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- MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions.PLoS computational biology · 2025Article
- The sandfish identity: phylogeographic reconstructions uncover a species complex within the Indo-Pacific distribution of Holothuria (Metriatyla) scabra.BMC ecology and evolution · 2025Article
- Evolution is coupled with branching across many granularities of life.Proceedings. Biological sciences · 2025Article
- How to Validate a Bayesian Evolutionary Model.Systematic biology · 2025Article
- AARS Online: A collaborative database on the structure, function, and evolution of the aminoacyl-tRNA synthetases.IUBMB life · 2024Article
- Spatial and temporal transmission dynamics of respiratory syncytial virus in New Zealand before and after the COVID-19 pandemic.Nature communications · 2024Article
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- An independent base composition of each rate class for improved likelihood-based phylogeny estimation; the 5rf model.bioRxiv : the preprint server for biology · 2024Article
- Species distribution models predict genetic isolation ofEcology and evolution · 2024Article
- Interrogating Genomes and Geography to Unravel Multiyear Vesicular Stomatitis Epizootics.Viruses · 2024Article
- Enzymic recognition of amino acids drove the evolution of primordial genetic codes.Nucleic acids research · 2024Article
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- Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia.Communications medicine · 2023Article
- Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru.Nature communications · 2023Article
- Phylogenetic Diversity of the Red Swamp CrayfishBiology · 2023Article
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Abstract
We present a two-headed approach called Bayesian Integrated Coalescent Epoch PlotS (BICEPS) for efficient inference of coalescent epoch models. Firstly, we integrate out population size parameters, and secondly, we introduce a set of more powerful Markov chain Monte Carlo (MCMC) proposals for flexing and stretching trees. Even though population sizes are integrated out and not explicitly sampled through MCMC, we are still able to generate samples from the population size posteriors. This allows demographic reconstruction through time and estimating the timing and magnitude of population bottlenecks and full population histories. Altogether, BICEPS can be considered a more muscular version of the popular Bayesian skyline model. We demonstrate its power and correctness by a well-calibrated simulation study. Furthermore, we demonstrate with an application to SARS-CoV-2 genomic data that some analyses that have trouble converging with the traditional Bayesian skyline prior and standard MCMC proposals can do well with the BICEPS approach. BICEPS is available as open-source package for BEAST 2 under GPL license and has a user-friendly graphical user interface.[Bayesian phylogenetics; BEAST 2; BICEPS; coalescent model.].
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