A Dirichlet process prior for estimating lineage-specific substitution rates
Open accessAbstract
We introduce a new model for relaxing the assumption of a strict molecular clock for use as a prior in Bayesian methods for divergence time estimation. Lineage-specific rates of substitution are modeled using a Dirichlet process prior (DPP), a type of stochastic process that assumes lineages of a phylogenetic tree are distributed into distinct rate classes. Under the Dirichlet process, the number of rate classes, assignment of branches to rate classes, and the rate value associated with each class are treated as random variables. The performance of this model was evaluated by conducting analyses on data sets simulated under a range of different models. We compared the Dirichlet process model with two alternative models for rate variation: the strict molecular clock and the independent rates model. Our results show that divergence time estimation under the DPP provides robust estimates of node ages and branch rates without significantly reducing power. Further analyses were conducted on a biological data set, and we provide examples of ways to summarize Markov chain Monte Carlo samples under this model.
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Our model is more specific in its goals than those implemented in more general phylogenetic packages.
“Without doubt, our model is more specific in its goals than those implemented in more general phylogenetic packages (Drummond et al. 2006; Drummond and Suchard 2010; Heath et al. 2012; Ogilvie et al. 2017).”
From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Heath et al. 2012
The DPP on Branch Rates section identifies a phylogenetic model implemented in the C++ program DPPDiv, so the paper supports the citation as an example of another implemented model. It does not establish that DPPDiv is a general phylogenetic package; that description is not supported for this citation. (LLM, conf=0.84)
Experimental — accuracy not yet measuredSeveral existing relaxed clock models explicitly model substitution rate variation across phylogeny.
“Several existing relaxed clock models (Drummond and Suchard 2010; Heath et al. 2012) explicitly model substitution rate variation across phylogeny.”
From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Heath et al. 2012
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Cites
Relaxed Phylogenetics and Dating with Confidence
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“This model was first described by Drummond et al. (2006), and variants of the uncorrelated rates model are commonly used for divergence time estimation in the program BEAST (Drummond and Rambaut 2007).”
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“Change in the rate of substitution occurs gradually over the tree and closely related lineages have similar rates under the model presented by Thorne et al. (1998) and Kishino et al. (2001).”
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“…stepping stone method (Xie et al. 2011) to perform Bayes factor comparisons of three different relaxedclock models: the independent gamma rates model also called the “white noise” model by Lepage et al. (2007), the CPP model (Huelsenbeck et al. 2000), and the AR-LN model (Thorne and Kishino 2002).”
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Sorted by citations
The fossilized birth-death process for coherent calibration of divergence-time estimates
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Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees
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Relative Time Constraints Improve Molecular Dating
Szöllõsi, G. J., Höhna, S., Williams, T. A., Schrempf, D., Daubin, V., & Boussau, B. (2022) · Systematic Biology · doi:10.1093/sysbio/syab084 · Cited by 23 · see citing works
- Authors
- Heath, T. A., Holder, M. T., & Huelsenbeck, J. P.
- Affiliations
- University of Kansas (US)
- University of California, Berkeley (US)
- Corresponding author
- Heath, T. A.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-11-02
- Volume
- 29
- Issue
- 3
- Pages
- 939-955
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC3350323
- OpenAlex
- W2130931762
- Cited by
- 105
- References
- 11
- Citations by year
- 2025: 3 · 2024: 5 · 2023: 3 · 2022: 4 · 2021: 3 · 2020: 11 · 2019: 6 · 2018: 6 · 2017: 4 · 2016: 12 · 2015: 7 · 2014: 34 · 2013: 4 · 2012: 3
- FWCI
- 5.00
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Molecular Biology and Evolution (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (5r01gm069801-09)
- National Institute of General Medical Sciences (R01 GM-069801, GM069801, GM086887, R01GM086887)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- Dirichlet process prior, relaxed molecular clock, divergence time estimation, Bayesian phylogenetics, rate heterogeneity, node age estimation, Markov chain Monte Carlo
- MeSH terms
- Bayes Theorem, Computer Simulation, Markov Chains, Models, Genetic, Monte Carlo Method, Phylogeny, Stochastic Processes, Evolution, Molecular, Mutation Rate
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