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A Bayesian Approach for Estimating Branch-Specific Speciation and Extinction Rates

https://doi.org/10.1101/555805
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What this work says

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

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Phylogenetic Inference Using RevBayes
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Detecting Diversification Rate Variation in Supertrees
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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
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The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events
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10.2 Maximum Likelihood from Incomplete Data
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Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates
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Mammalian phylogeny reveals recent diversification rate shifts
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Reconciling molecular phylogenies with the fossil record
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Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures
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The Calculation of Posterior Distributions by Data Augmentation
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Sampling-Based Approaches to Calculating Marginal Densities
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Mapping Mutations on Phylogenies
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Frequentist Properties of Bayesian Posterior Probabilities of Phylogenetic Trees Under Simple and Complex Substitution Models
inferredcites →https://doi.org/10.1080/10635150701607033openalex-snapshot
Estimating a Binary Character's Effect on Speciation and Extinction
inferredcites →https://doi.org/10.1086/282070openalex-snapshot
Homage to Santa Rosalia or Why Are There So Many Kinds of Animals?
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Linking the Investigations of Character Evolution and Species Diversification
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A Conceptual and Statistical Framework for Adaptive Radiations with a Key Role for Diversity Dependence
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SYMMETREE: whole-tree analysis of differential diversification rates
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A Compound Poisson Process for Relaxing the Molecular Clock
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A Multitype Birth–Death Model for Bayesian Inference of Lineage-Specific Birth and Death Rates
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Estimating Trait-Dependent Speciation and Extinction Rates from Incompletely Resolved Phylogenies
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Quantitative Traits and Diversification
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Phylogenetic Inference of Reciprocal Effects between Geographic Range Evolution and Diversification
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Bayesian Analysis of Biogeography when the Number of Areas is Large
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A Novel Bayesian Method for Inferring and Interpreting the Dynamics of Adaptive Landscapes from Phylogenetic Comparative Data
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RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language
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Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction
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How Well Can We Detect Lineage-Specific Diversification-Rate Shifts? A Simulation Study of Sequential AIC Methods
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Evaluating the Impact of Genomic Data and Priors on Bayesian Estimates of the Angiosperm Evolutionary Timescale
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Is BAMM Flawed? Theoretical and Practical Concerns in the Analysis of Multi-Rate Diversification Models
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Cladogenetic and Anagenetic Models of Chromosome Number Evolution: A Bayesian Model Averaging Approach
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Testing the Role of the Red Queen and Court Jester as Drivers of the Macroevolution of Apollo Butterflies
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Stochastic Character Mapping of State-Dependent Diversification Reveals the Tempo of Evolutionary Decline in Self-Compatible Onagraceae Lineages
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Extinction rates can be estimated from molecular phylogenies
inferredcites →https://doi.org/10.1098/rstb.1994.0068openalex-snapshot
The reconstructed evolutionary process
inferredcites →https://doi.org/10.1098/rstb.2016.0020openalex-snapshot
The evolution of methods for establishing evolutionary timescales
inferredcites →https://doi.org/10.1111/2041-210x.12563openalex-snapshot
A Bayesian approach for detecting the impact of mass‐extinction events on molecular phylogenies when rates of lineage diversification may vary
inferredcites →https://doi.org/10.1111/ele.12062openalex-snapshot
Macroevolutionary perspectives to environmental change
inferredcites →https://doi.org/10.1111/ele.12251openalex-snapshot
Phylogenetic approaches for studying diversification
inferredcites →https://doi.org/10.1111/evo.13378openalex-snapshot
Estimating diversification rates for higher taxa: BAMM can give problematic estimates of rates and rate shifts
inferredcites →https://doi.org/10.1111/evo.13566openalex-snapshot
BAMM at the court of false equivalency: A response to Meyer and Wiens
inferredcites →https://doi.org/10.1111/evo.13574openalex-snapshot
BAMM gives misleading rate estimates in simulated and empirical datasets
inferredcites →https://doi.org/10.1111/evo.13594openalex-snapshot
Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeographic uncertainty
inferredcites →https://doi.org/10.1111/j.1558-5646.2012.01730.xopenalex-snapshot
TEMPO AND MODE IN PLANT BREEDING SYSTEM EVOLUTION
inferredcites →https://doi.org/10.1111/j.2041-210x.2012.00234.xopenalex-snapshot
Diversitree: comparative phylogenetic analyses of diversification in R
inferredcites →https://doi.org/10.1111/j.2517-6161.1977.tb01600.xopenalex-snapshot
Maximum Likelihood from Incomplete Data Via the EM Algorithm
inferredcites →https://doi.org/10.1126/science.1065889openalex-snapshot
Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
inferredcites →https://doi.org/10.1186/s12862-015-0347-8openalex-snapshot
Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating
inferredcites →https://doi.org/10.1214/aoms/1177730285openalex-snapshot
On the Generalized "Birth-and-Death" Process
inferredcites →https://doi.org/10.1371/journal.pone.0049521openalex-snapshot
Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix
inferredcites →https://doi.org/10.1371/journal.pone.0084184openalex-snapshot
Likelihood Inference of Non-Constant Diversification Rates with Incomplete Taxon Sampling
inferredcites →https://doi.org/10.1371/journal.pone.0089543openalex-snapshot
Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees
inferredcites →https://doi.org/10.2307/2289776openalex-snapshot
Sampling-Based Approaches to Calculating Marginal Densities

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Comprehensive phylogeny of Pieridae butterflies reveals strong correlation between diversification and temperature
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Genome-wide macroevolutionary signatures of key innovations in butterflies colonizing new host plants
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Palaeoclimate ocean conditions shaped the evolution of corals and their skeletons through deep time
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Universal probabilistic programming offers a powerful approach to statistical phylogenetics
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Commonly used Bayesian diversification methods lead to biologically meaningful differences in branch-specific rates on empirical phylogenies
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The nature and prevalence of diversification rate shifts across the Tree of Life
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Modeling Phylogenetic Biome Shifts on a Planet with a Past
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Detecting Lineage-Specific Shifts in Diversification: A Proper Likelihood Approach
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Is Sexual Conflict a Driver of Speciation? A Case Study With a Tribe of Brush-footed Butterflies
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Ecological Opportunity from Innovation, not Islands, Drove the Anole Lizard Adaptive Radiation
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Fast and Accurate Estimation of Species-Specific Diversification Rates Using Data Augmentation
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Diversification Models Conflate Likelihood and Prior, and Cannot be Compared Using Conventional Model-Comparison Tools
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The ClaDS rate-heterogeneous birth–death prior for full phylogenetic inference in BEAST2
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Deep Learning from Phylogenies for Diversification Analyses
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The Limits of the Constant-rate Birth–Death Prior for Phylogenetic Tree Topology Inference
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Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model
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Testing Relationships between Multiple Regional Features and Biogeographic Processes of Speciation, Extinction, and Dispersal
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How to Validate a Bayesian Evolutionary Model
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Phylogenetic Estimation of Branch-Specific Shifts in the Tempo of Origination
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An Evolving View of Lineage Diversification
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Integrating Fossils Samples with Heterogeneous Diversification Rates: A Combined Multi-Type Fossilized Birth-Death model
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Diversification dynamics of hypermetamorphic blister beetles (Meloidae): Are homoplastic host shifts and phoresy key factors of a rushing forward strategy to escape extinction?
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Evolution and Diversification Dynamics of Butterflies
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