ArticleMolecular biology and evolution2015
Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations.
Article in Molecular biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Review
- DiagnoDating: diagnostics for dated phylogenies in microbial population genetics.Molecular biology and evolution · 2026Article
- Article
- Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock.Genome biology and evolution · 2024Review
- TiDeTree: a Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data.Proceedings. Biological sciences · 2022Article
- Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches.Molecular ecology resources · 2021Article
- Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics.Molecular biology and evolution · 2020Article
- Testing adequacy for DNA substitution models.BMC bioinformatics · 2019Article
- Phylodynamic Model Adequacy Using Posterior Predictive Simulations.Systematic biology · 2019Article
- Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence.Virus evolution · 2018Article
- Differences in Performance among Test Statistics for Assessing Phylogenomic Model Adequacy.Genome biology and evolution · 2018Article
- Impact of the tree prior on estimating clock rates during epidemic outbreaks.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Unravelling the complicated evolutionary and dissemination history of HIV-1M subtype A lineages.Virus evolution · 2018Article
- Strategies for Partitioning Clock Models in Phylogenomic Dating: Application to the Angiosperm Evolutionary Timescale.Genome biology and evolution · 2017Article
- Cross-validation to select Bayesian hierarchical models in phylogenetics.BMC evolutionary biology · 2016Article
- Advances in Time Estimation Methods for Molecular Data.Molecular biology and evolution · 2016Article
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4 authors.
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Abstract
Molecular clock models are commonly used to estimate evolutionary rates and timescales from nucleotide sequences. The goal of these models is to account for rate variation among lineages, such that they are assumed to be adequate descriptions of the processes that generated the data. A common approach for selecting a clock model for a data set of interest is to examine a set of candidates and to select the model that provides the best statistical fit. However, this can lead to unreliable estimates if all the candidate models are actually inadequate. For this reason, a method of evaluating absolute model performance is critical. We describe a method that uses posterior predictive simulations to assess the adequacy of clock models. We test the power of this approach using simulated data and find that the method is sensitive to bias in the estimates of branch lengths, which tends to occur when using underparameterized clock models. We also compare the performance of the multinomial test statistic, originally developed to assess the adequacy of substitution models, but find that it has low power in identifying the adequacy of clock models. We illustrate the performance of our method using empirical data sets from coronaviruses, simian immunodeficiency virus, killer whales, and marine turtles. Our results indicate that methods of investigating model adequacy, including the one proposed here, should be routinely used in combination with traditional model selection in evolutionary studies. This will reveal whether a broader range of clock models to be considered in phylogenetic analysis.
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