ArticleBMC evolutionary biology2020
Improving the performance of Bayesian phylogenetic inference under relaxed clock models.
Article in BMC evolutionary 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.
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- Navigating the mysterious space of evolutionary histories.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Comprehensive genomic analysis of rabies virus in India reveals distinct lineages and evolutionary stability.Virus genes · 2026Article
- Biological causes and impacts of rugged tree landscapes in phylodynamic inference.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Biological causes and impacts of rugged tree landscapes in phylodynamic inference.bioRxiv : the preprint server for biology · 2025Article
- Evolution is coupled with branching across many granularities of life.Proceedings. Biological sciences · 2025Article
- Why the Long "Horns"? Fine-Scale Morphology Suggests Tactile Demands Contributed to the Exaggeration of Male Longhorned Beetle Antennae (Coleoptera: Cerambycidae).Ecology and evolution · 2025Article
- Cryptic diversity on the genusPeerJ · 2025Article
- Paleopteran molecular clock: Time drift and recent acceleration.Ecology and evolution · 2024Article
- Central African dwarf crocodiles found in syntopy are comparably divergent to South American dwarf caimans.Biology letters · 2024Article
- Dated Phylogeny ofBiology · 2023Article
- Integrative species delimitation helps to find the hidden diversity of the leaf-litter frogPeerJ · 2023Article
- Lexical phylogenetics of the Tupí-Guaraní family: Language, archaeology, and the problem of chronology.PloS one · 2023Article
- An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference.Systematic biology · 2022Article
- Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation.Systematic biology · 2022Article
- Quantitatively defining species boundaries with more efficiency and more biological realism.Communications biology · 2022Article
- Relative Time Constraints Improve Molecular Dating.Systematic biology · 2022Article
- StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent.Systematic biology · 2022Article
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2 authors.
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Abstract
backgroundBayesian MCMC has become a common approach for phylogenetic inference. But the growing size of molecular sequence data sets has created a pressing need to improve the computational efficiency of Bayesian phylogenetic inference algorithms.
resultsThis paper develops a new algorithm to improve the efficiency of Bayesian phylogenetic inference for models that include a per-branch rate parameter. In a Markov chain Monte Carlo algorithm, the presented proposal kernel changes evolutionary rates and divergence times at the same time, under the constraint that the implied genetic distances remain constant. Specifically, the proposal operates on the divergence time of an internal node and the three adjacent branch rates. For the root of a phylogenetic tree, there are three strategies discussed, named Simple Distance, Small Pulley and Big Pulley. Note that Big Pulley is able to change the tree topology, which enables the operator to sample all the possible rooted trees consistent with the implied unrooted tree. To validate its effectiveness, a series of experiments have been performed by implementing the proposed operator in the BEAST2 software.
conclusionsThe results demonstrate that the proposed operator is able to improve the performance by giving better estimates for a given chain length and by using less running time for a given level of accuracy. Measured by effective samples per hour, use of the proposed operator results in overall mixing more efficient than the current operators in BEAST2. Especially for large data sets, the improvement is up to half an order of magnitude.
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