ArticleSystematic biology2020
A Multitype Birth-Death Model for Bayesian Inference of Lineage-Specific Birth and Death Rates.
Article in Systematic biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 1 of them a synthesis that pooled it.
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34 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference.Systematic biology · 2024Pooled it
- Estimating Divergence Times and Diversification Rates with the Unresolved Fossilized Birth-Death Process.bioRxiv : the preprint server for biology · 2026Article
- Rapid Phylogeographic Inference of Regional Epidemic Dynamics for Routine Genomic Surveillance.Research square · 2026Article
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- Inferring Branch-Specific Rates of Lineage Diversification Under the Birth-Death-Shift Process.Systematic biology · 2026Article
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- The nature and prevalence of diversification rate shifts across the Tree of Life.Evolution letters · 2026Article
- Quantifying the real-world impact of antibiotic use and genetic determinants of resistance on gonococcal dynamics.Nature microbiology · 2026Article
- Introduction and inter-species transmission dynamics of high pathogenicity avian influenza H5N1 viruses in Japan 2021-25.Virus evolution · 2026Article
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- Bayesian Phylodynamic Inference of Multitype Population Trajectories Using Genomic Data.Molecular biology and evolution · 2025Article
- Bayesian phylodynamic inference of population dynamics with dormancy.Proceedings of the National Academy of Sciences of the United States of America · 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
- Bayesian phylodynamic inference of population dynamics with dormancy.bioRxiv : the preprint server for biology · 2025Article
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- Three evolutionary radiations shaped the evolution of global religious diversity.Evolutionary human sciences · 2025Article
- PhyloJunction: A Computational Framework for Simulating, Developing, and Teaching Evolutionary Models.Systematic biology · 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
- Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.bioRxiv : the preprint server for biology · 2023Article
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3 authors.
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Abstract
Heterogeneous populations can lead to important differences in birth and death rates across a phylogeny. Taking this heterogeneity into account is necessary to obtain accurate estimates of the underlying population dynamics. We present a new multitype birth-death model (MTBD) that can estimate lineage-specific birth and death rates. This corresponds to estimating lineage-dependent speciation and extinction rates for species phylogenies, and lineage-dependent transmission and recovery rates for pathogen transmission trees. In contrast with previous models, we do not presume to know the trait driving the rate differences, nor do we prohibit the same rates from appearing in different parts of the phylogeny. Using simulated data sets, we show that the MTBD model can reliably infer the presence of multiple evolutionary regimes, their positions in the tree, and the birth and death rates associated with each. We also present a reanalysis of two empirical data sets and compare the results obtained by MTBD and by the existing software BAMM. We compare two implementations of the model, one exact and one approximate (assuming that no rate changes occur in the extinct parts of the tree), and show that the approximation only slightly affects results. The MTBD model is implemented as a package in the Bayesian inference software BEAST 2 and allows joint inference of the phylogeny and the model parameters.[Birth-death; lineage specific rates, multi-type model.].
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