ArticlePLoS computational biology2021
Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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73 citing papers in PubMed.
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- Characteristics of Mitochondrial Genomes and Phylogenetic Analysis of Three Species of Littorinimorpha Snails.Animals : an open access journal from MDPI · 2026Article
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- Mixed Support for Pleistocene Sea-Level Fluctuations in Promoting the Diversification of Anole Lizards in the Northern Lesser Antilles.Molecular ecology · 2026Article
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- The Phylodynamic Threshold of Measurably Evolving Populations.Molecular biology and evolution · 2026Article
- Phylogeny ofPersoonia · 2026Article
- Taxonomy, biogeography and evolution of thirty-four taxa inStudies in mycology · 2026Article
- VINE: Variational inference for scalable Bayesian reconstruction of species and cell-lineage phylogenies.bioRxiv : the preprint server for biology · 2026Article
- Evolutionary origin and demographic trajectory of tomato spotted wilt virus (Orthotospovirus tomatomaculae).Archives of virology · 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
- Uncovering a neglected canine filarioid in Asia: First evidence ofCurrent research in parasitology & vector-borne diseases · 2026Article
- Tick-associated microorganisms (Current research in parasitology & vector-borne diseases · 2026Article
- A morphologically generalized EurasianPeerJ · 2026Article
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- Exploring the matrilineal ancestry of swamp buffaloes (Open veterinary journal · 2025Article
13 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Relaxed clock models enable estimation of molecular substitution rates across lineages and are widely used in phylogenetics for dating evolutionary divergence times. Under the (uncorrelated) relaxed clock model, tree branches are associated with molecular substitution rates which are independently and identically distributed. In this article we delved into the internal complexities of the relaxed clock model in order to develop efficient MCMC operators for Bayesian phylogenetic inference. We compared three substitution rate parameterisations, introduced an adaptive operator which learns the weights of other operators during MCMC, and we explored how relaxed clock model estimation can benefit from two cutting-edge proposal kernels: the AVMVN and Bactrian kernels. This work has produced an operator scheme that is up to 65 times more efficient at exploring continuous relaxed clock parameters compared with previous setups, depending on the dataset. Finally, we explored variants of the standard narrow exchange operator which are specifically designed for the relaxed clock model. In the most extreme case, this new operator traversed tree space 40% more efficiently than narrow exchange. The methodologies introduced are adaptive and highly effective on short as well as long alignments. The results are available via the open source optimised relaxed clock (ORC) package for BEAST 2 under a GNU licence (https://github.com/jordandouglas/ORC).
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