ArticlePLoS computational biology2020
Locally adaptive Bayesian birth-death model successfully detects slow and rapid rate shifts.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 48 citations in OpenAlex.
- Atlantic forest origins and Amazon connections: the evolutionary history of Adenocalymma.Annals of botany · 2026Article
- Inferring Branch-Specific Rates of Lineage Diversification Under the Birth-Death-Shift Process.Systematic biology · 2026Article
- Habitat-specific temporal variation in the pace of fish diversification.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Out of the tropics and adaptation in the Asian subtropics of Dendrobium section Dendrobium (Orchidaceae).Communications biology · 2026Article
- Practical Guide and Review of Fossil Tip-Dating in Phylogenetics.Systematic biology · 2026Review
- Non-adaptive Radiation Promotes Phenotypic Diversification and Convergent Evolution of Aposematic Mimicry in a Highly Diverse Genus of Megaloptera.Systematic biology · 2025Article
- Bayesian StairwayPlot for Inferring Single Population Demographic Histories From Site Frequency Spectra.Molecular ecology resources · 2025Article
- A multiscale stochastic cellular automata model for dispersion of mountain pine beetles.Royal Society open science · 2025Article
- The effects of cryptic diversity on diversification dynamics analyses in Crocodylia.Proceedings. Biological sciences · 2025Article
- Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations.Systematic biology · 2024Article
- Tropical Origin, Global Diversification, and Dispersal in the Pond Damselflies (Coenagrionoidea) Revealed by a New Molecular Phylogeny.Systematic biology · 2024Article
- Comparison of Bayesian Coalescent Skyline Plot Models for Inferring Demographic Histories.Molecular biology and evolution · 2024Article
- Commonly used Bayesian diversification methods lead to biologically meaningful differences in branch-specific rates on empirical phylogenies.Evolution letters · 2024Article
- Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.PLoS computational biology · 2024Article
- Climatic and biogeographic processes underlying the diversification of the pantropical flowering plant family Annonaceae.Frontiers in plant science · 2024Article
- Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.bioRxiv : the preprint server for biology · 2023Article
- Rapidly changing speciation and extinction rates can be inferred in spite of nonidentifiability.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Diversification dynamics in the Neotropics through time, clades, and biogeographic regions.eLife · 2022Article
- Macroevolutionary dynamics in the transition of angiosperms to aquatic environments.The New phytologist · 2022Article
- Cyphoderia ampulla (Cyphoderiidae: Rhizaria), a tale of freshwater sailors: The causes and consequences of ecological transitions through the salinity barrier in a family of benthic protists.Molecular ecology · 2022Article
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5 authors at 4 institutions in 3 countries.
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Abstract
Birth-death processes have given biologists a model-based framework to answer questions about changes in the birth and death rates of lineages in a phylogenetic tree. Therefore birth-death models are central to macroevolutionary as well as phylodynamic analyses. Early approaches to studying temporal variation in birth and death rates using birth-death models faced difficulties due to the restrictive choices of birth and death rate curves through time. Sufficiently flexible time-varying birth-death models are still lacking. We use a piecewise-constant birth-death model, combined with both Gaussian Markov random field (GMRF) and horseshoe Markov random field (HSMRF) prior distributions, to approximate arbitrary changes in birth rate through time. We implement these models in the widely used statistical phylogenetic software platform RevBayes, allowing us to jointly estimate birth-death process parameters, phylogeny, and nuisance parameters in a Bayesian framework. We test both GMRF-based and HSMRF-based models on a variety of simulated diversification scenarios, and then apply them to both a macroevolutionary and an epidemiological dataset. We find that both models are capable of inferring variable birth rates and correctly rejecting variable models in favor of effectively constant models. In general the HSMRF-based model has higher precision than its GMRF counterpart, with little to no loss of accuracy. Applied to a macroevolutionary dataset of the Australian gecko family Pygopodidae (where birth rates are interpretable as speciation rates), the GMRF-based model detects a slow decrease whereas the HSMRF-based model detects a rapid speciation-rate decrease in the last 12 million years. Applied to an infectious disease phylodynamic dataset of sequences from HIV subtype A in Russia and Ukraine (where birth rates are interpretable as the rate of accumulation of new infections), our models detect a strongly elevated rate of infection in the 1990s.
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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.