ArticleMolecular biology and evolution2012
A dirichlet process prior for estimating lineage-specific substitution rates.
Article in Molecular biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed.
- Practical Guide and Review of Fossil Tip-Dating in Phylogenetics.Systematic biology · 2026Review
- Infinite Mixture Models for Improved Modeling of Across-Site Evolutionary Variation.Molecular biology and evolution · 2025Article
- Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model.Systematic biology · 2024Article
- Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock.Genome biology and evolution · 2024Review
- Detecting Episodic Evolution through Bayesian Inference of Molecular Clock Models.Molecular biology and evolution · 2023Article
- Latent functional diversity may accelerate microbial community responses to temperature fluctuations.eLife · 2022Article
- Generalizing Bayesian phylogenetics to infer shared evolutionary events.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Relative Time Constraints Improve Molecular Dating.Systematic biology · 2022Article
- Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary.BMC ecology and evolution · 2022Article
- An Unbiased Molecular Approach Using 3'-UTRs Resolves the Avian Family-Level Tree of Life.Molecular biology and evolution · 2021Article
- Adaptive evolution shapes the present-day distribution of the thermal sensitivity of population growth rate.PLoS biology · 2020Article
- Phytoplankton thermal responses adapt in the absence of hard thermodynamic constraints.Evolution; international journal of organic evolution · 2020Article
- Rates and Rocks: Strengths and Weaknesses of Molecular Dating Methods.Frontiers in genetics · 2020Article
- Full Bayesian Comparative Phylogeography from Genomic Data.Systematic biology · 2019Article
- Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees.Molecular biology and evolution · 2019Article
- The Estimated Pacemaker for Great Apes Supports the Hominoid Slowdown Hypothesis.Evolutionary bioinformatics online · 2019Article
- Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case.Systematic biology · 2018Article
- Efficient Detection of Repeating Sites to Accelerate Phylogenetic Likelihood Calculations.Systematic biology · 2017Article
- Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins.Systematic biology · 2017Article
- A mixed relaxed clock model.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.