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Evaluating the Impact of Purifying Selection on Species-level Molecular Dating

https://doi.org/10.1101/622209
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Relative rates of nucleotide substitution at the rbcl locus of monocotyledonous plants
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Evolutionary trees from DNA sequences: A maximum likelihood approach
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Evolutionary Divergence and Convergence in Proteins
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Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny
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Molecular clocks: when timesare a-changin'
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High mitogenomic evolutionary rates and time dependency
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The changing face of the molecular evolutionary clock
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An index of substitution saturation and its application
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The root of the mammalian tree inferred from whole mitochondrial genomes
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Evolutionary Rate at the Molecular Level
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Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution
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Bayesian molecular clock dating of species divergences in the genomics era
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Mutation rates in mammalian genomes
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Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas
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Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary
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The timescale of early land plant evolution
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PRIMARY STRUCTURE AND EVOLUTION OF CYTOCHROME C
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Extensive variation in evolutionary rate of rbcL gene sequences among seed plants.
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Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL.
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Divergence Time and Evolutionary Rate Estimation with Multilocus Data
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Identifying and Removing Fast-Evolving Sites Using Compatibility Analysis: An Example from the Arthropoda
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Inferring Speciation Times under an Episodic Molecular Clock
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Biopython: freely available Python tools for computational molecular biology and bioinformatics
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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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Time Dependency of Molecular Evolutionary Rates? Yes and No
inferredcites →https://doi.org/10.1093/gbe/evs092openalex-snapshot
Selective Constraints Determine the Time Dependency of Molecular Rates for Human Nuclear Genomes
inferredcites →https://doi.org/10.1093/genetics/116.1.169openalex-snapshot
On the Overdispersed Molecular Clock
inferredcites →https://doi.org/10.1093/genetics/146.1.393openalex-snapshot
Comparing Patterns of Nucleotide Substitution Rates Among Chloroplast Loci Using the Relative Ratio Test
inferredcites →https://doi.org/10.1093/molbev/msi145openalex-snapshot
Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times
inferredcites →https://doi.org/10.1093/molbev/msj024openalex-snapshot
Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds
inferredcites →https://doi.org/10.1093/molbev/msl107openalex-snapshot
Can Deleterious Mutations Explain the Time Dependency of Molecular Rate Estimates?
inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msq132openalex-snapshot
A Method to Correct for the Effects of Purifying Selection on Genealogical Inference
inferredcites →https://doi.org/10.1093/molbev/msr045openalex-snapshot
Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times
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Exploring Patterns and Extent of Bias in Estimating Divergence Time from Mitochondrial DNA Sequence Data in a Particular Lineage: A Case Study of Salamanders (Order Caudata)
inferredcites →https://doi.org/10.1093/molbev/mss140openalex-snapshot
The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates
inferredcites →https://doi.org/10.1093/molbev/mss170openalex-snapshot
Distortions in Genealogies Due to Purifying Selection
inferredcites →https://doi.org/10.1093/molbev/msu132openalex-snapshot
OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals
inferredcites →https://doi.org/10.1093/nar/gkh935openalex-snapshot
Identification of genes with fast-evolving regions in microbial genomes
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025892openalex-snapshot
Estimating the rate of evolution of the rate of molecular evolution
inferredcites →https://doi.org/10.1093/sysbio/syq045openalex-snapshot
Accommodating Heterogenous Rates of Evolution in Molecular Divergence Dating Methods: An Example Using Intercontinental Dispersal of Plestiodon (Eumeces) Lizards
inferredcites →https://doi.org/10.1093/sysbio/syu020openalex-snapshot
The Impact of the Rate Prior on Bayesian Estimation of Divergence Times with Multiple Loci
inferredcites →https://doi.org/10.1093/sysbio/syu109openalex-snapshot
Characterization of the Uncertainty of Divergence Time Estimation under Relaxed Molecular Clock Models Using Multiple Loci
inferredcites →https://doi.org/10.1093/sysbio/syv061openalex-snapshot
Enlarged Multilocus Data set Provides Surprisingly Younger Time of Origin for the Plethodontidae, the Largest Family of Salamanders
inferredcites →https://doi.org/10.1093/sysbio/syw018openalex-snapshot
Gene Tree Discordance Causes Apparent Substitution Rate Variation
inferredcites →https://doi.org/10.1093/sysbio/syx061openalex-snapshot
An Evaluation of Different Partitioning Strategies for Bayesian Estimation of Species Divergence Times
inferredcites →https://doi.org/10.1098/rspb.2012.0683openalex-snapshot
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
inferredcites →https://doi.org/10.1109/mcse.2007.55openalex-snapshot
Matplotlib: A 2D Graphics Environment
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2D Principal Component Analysis for Face and Facial-Expression Recognition
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Python for Scientists and Engineers
inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05178.xopenalex-snapshot
Time-dependent rates of molecular evolution
inferredcites →https://doi.org/10.1111/mec.13450openalex-snapshot
Time‐dependent estimates of molecular evolutionary rates: evidence and causes
inferredcites →https://doi.org/10.1126/science.1211028openalex-snapshot
Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification
inferredcites →https://doi.org/10.1126/science.1253451openalex-snapshot
Whole-genome analyses resolve early branches in the tree of life of modern birds
inferredcites →https://doi.org/10.1126/science.147.3653.68openalex-snapshot
Evolving Genes and Proteins
inferredcites →https://doi.org/10.1128/jvi.00593-16openalex-snapshot
Time-Dependent Rate Phenomenon in Viruses
inferredcites →https://doi.org/10.1146/annurev-ecolsys-102710-145119openalex-snapshot
The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates
inferredcites →https://doi.org/10.1146/annurev-genom-082908-150129openalex-snapshot
The Neutral Theory of Molecular Evolution in the Genomic Era
inferredcites →https://doi.org/10.1146/annurev.ecolsys.23.1.263openalex-snapshot
The Nearly Neutral Theory of Molecular Evolution
inferredcites →https://doi.org/10.1146/annurev.ecolsys.33.010802.150500openalex-snapshot
Estimating Divergence Times from Molecular Data on Phylogenetic and Population Genetic Timescales
inferredcites →https://doi.org/10.1186/1471-2105-13-209openalex-snapshot
Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython
inferredcites →https://doi.org/10.1186/1471-2148-10-58openalex-snapshot
Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective
inferredcites →https://doi.org/10.1186/1471-2148-11-177openalex-snapshot
Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation
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Environmental variation and rivers govern the structure of chimpanzee genetic diversity in a biodiversity hotspot
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Time dependency of foamy virus evolutionary rate estimates
inferredcites →https://doi.org/10.1534/genetics.104.75135openalex-snapshot
Molecular Clock: An Anti-neo-Darwinian Legacy
inferredcites →https://doi.org/10.1534/genetics.113.152025openalex-snapshot
Why Do More Divergent Sequences Produce Smaller Nonsynonymous/Synonymous Rate Ratios in Pairwise Sequence Comparisons?

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