Molecular dating of phylogenies by likelihood methods: a comparison of models and a new information criterion.
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Summary
The improvements are the introduction of alternative models, including one with non-correlated rates of molecular substitution ("relaxed" model), a completely reworked fitting algorithm that considers the high-dimensionality of the optimisation problem, and the development of a new information criterion for model selection in the presence of a penalised term.
- Type
- article
- Published
- 2013-05-01
- Cited by
- 168
- References
- 37
- Access
- Open access
- OpenAlex
- https://openalex.org/W1997408815
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:205837792
Keywords
Molecular clock, Substitution (logic), Divergence (linguistics), Model selection, Estimator
References
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- Information Criteria and Statistical Modeling
- Analysis of Phylogenetics and Evolution with R
- A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy
- Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach.
- Phylogenetic dating with confidence intervals using mean path lengths.
- A modular system of algorithms for unconstrained minimization
- Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inference.
- Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks
- Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds.
- Estimating the rate of evolution of the rate of molecular evolution.
- Rate Tests for Phenotypic Evolution Using Phylogenetically Independent Contrasts
- Relaxed Phylogenetics and Dating with Confidence
- PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
- PAML 4: phylogenetic analysis by maximum likelihood.
- A general comparison of relaxed molecular clock models.
- Analyses of Phylogenetics and Evolution
- Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
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- Does vocal learning accelerate acoustic diversification? Evolution of contact calls in Neotropical parrots
- Monocot fossils suitable for molecular dating analyses
- Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life
- Species Selection Favors Dispersive Life Histories in Sea Slugs, but Higher Per-Offspring Investment Drives Shifts to Short-Lived Larvae.
- Host abundance, durability, basidiome form and phylogenetic isolation determine fungivore species richness
- To move or to evolve: contrasting patterns of intercontinental connectivity and climatic niche evolution in “Terebinthaceae” (Anacardiaceae and Burseraceae)
- Dispersal has inhibited avian diversification in Australasian archipelagoes
- Molecular‐clock methods for estimating evolutionary rates and timescales
- The impact of calibration and clock-model choice on molecular estimates of divergence times.
- The changing face of the molecular evolutionary clock.
- A practical guide to molecular dating
- Near‐to‐nature logging influences fungal community assembly processes in a temperate forest
- Amplified fragment length polymorphisms, the evolution of the land snail genus Theba (Stylommatophora: Helicidae), and an objective approach for relating fossils to internal nodes of a phylogenetic tree using geometric morphometrics
- Simulating and detecting autocorrelation of molecular evolutionary rates among lineages
- Puzzling rocks and complicated clocks: how to optimize molecular dating approaches in historical phytogeography.
- Evolution of the Selenoproteome in Helicobacter pylori and Epsilonproteobacteria
- Phylogeny of Dictyoptera: Dating the Origin of Cockroaches, Praying Mantises and Termites with Molecular Data and Controlled Fossil Evidence
- Bulk De Novo Mitogenome Assembly from Pooled Total DNA Elucidates the Phylogeny of Weevils (Coleoptera: Curculionoidea)
- Molecular Phylogenetics and Temporal Diversification in the Genus Aeromonas Based on the Sequences of Five Housekeeping Genes
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