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The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1016/j.jtbi.2008.04.005openalex-snapshot
The conditioned reconstructed process
inferredcites →https://doi.org/10.1016/j.tree.2007.06.013openalex-snapshot
Estimating diversification rates from phylogenetic information
inferredcites →https://doi.org/10.1016/j.tree.2013.09.007openalex-snapshot
Phylogenetic estimates of speciation and extinction rates for testing ecological and evolutionary hypotheses
inferredcites →https://doi.org/10.1016/s0025-5564(00)00061-4openalex-snapshot
Properties of phylogenetic trees generated by Yule-type speciation models
inferredcites →https://doi.org/10.1016/s0169-5347(01)02161-9openalex-snapshot
Phylogenetics and speciation
inferredcites →https://doi.org/10.1038/nature22897openalex-snapshot
Speciation gradients and the distribution of biodiversity
inferredcites →https://doi.org/10.1073/pnas.0811087106openalex-snapshot
Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates
inferredcites →https://doi.org/10.1073/pnas.1518659113openalex-snapshot
Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures
inferredcites →https://doi.org/10.1073/pnas.89.17.8322openalex-snapshot
Tempo and mode of evolution revealed from molecular phylogenies.
inferredcites →https://doi.org/10.1080/10635150500234641openalex-snapshot
Resolving Deep Phylogenetic Relationships in Salamanders: Analyses of Mitochondrial and Nuclear Genomic Data
inferredcites →https://doi.org/10.1080/10635150500354647openalex-snapshot
Under-parameterized Model of Sequence Evolution Leads to Bias in the Estimation of Diversification Rates from Molecular Phylogenies
inferredcites →https://doi.org/10.1080/10635150701607033openalex-snapshot
Estimating a Binary Character's Effect on Speciation and Extinction
inferredcites →https://doi.org/10.1086/284325openalex-snapshot
Phylogenies and the Comparative Method
inferredcites →https://doi.org/10.1086/667574openalex-snapshot
A Conceptual and Statistical Framework for Adaptive Radiations with a Key Role for Diversity Dependence
inferredcites →https://doi.org/10.1086/703055openalex-snapshot
Revisiting a Key Innovation in Evolutionary Biology: Felsenstein’s “Phylogenies and the Comparative Method”
inferredcites →https://doi.org/10.1093/bioinformatics/13.3.235openalex-snapshot
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/19.2.301openalex-snapshot
r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot
APE: Analyses of Phylogenetics and Evolution in R language
inferredcites →https://doi.org/10.1093/bioinformatics/bts492openalex-snapshot
treePL: divergence time estimation using penalized likelihood for large phylogenies
inferredcites →https://doi.org/10.1093/gbe/evt048openalex-snapshot
Rewriting Evolution—“Been There, Done That”
inferredcites →https://doi.org/10.1093/genetics/161.3.1307openalex-snapshot
Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data
inferredcites →https://doi.org/10.1093/molbev/msi103openalex-snapshot
Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences
inferredcites →https://doi.org/10.1093/molbev/msi125openalex-snapshot
Accuracy of Rate Estimation Using Relaxed-Clock Models with a Critical Focus on the Early Metazoan Radiation
inferredcites →https://doi.org/10.1093/molbev/msm178openalex-snapshot
The Problem of Rooting Rapid Radiations
inferredcites →https://doi.org/10.1093/molbev/msm193openalex-snapshot
A General Comparison of Relaxed Molecular Clock Models
inferredcites →https://doi.org/10.1093/molbev/mss075openalex-snapshot
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
inferredcites →https://doi.org/10.1093/molbev/msy103openalex-snapshot
Undersampling Genomes has Biased Time and Rate Estimates Throughout the Tree of Life
inferredcites →https://doi.org/10.1093/oso/9780198546412.001.0001openalex-snapshot
The Comparative Method in Evolutionary Biology
inferredcites →https://doi.org/10.1093/sysbio/syp067openalex-snapshot
Estimating Trait-Dependent Speciation and Extinction Rates from Incompletely Resolved Phylogenies
inferredcites →https://doi.org/10.1093/sysbio/syp082openalex-snapshot
Bayesian Dating of Shallow Phylogenies with a Relaxed Clock
inferredcites →https://doi.org/10.1093/sysbio/syq032openalex-snapshot
Slowdowns in Diversification Rates from Real Phylogenies May Not be Real
inferredcites →https://doi.org/10.1093/sysbio/syq053openalex-snapshot
Quantitative Traits and Diversification
inferredcites →https://doi.org/10.1093/sysbio/sys029openalex-snapshot
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
inferredcites →https://doi.org/10.1093/sysbio/sys073openalex-snapshot
How Can We Improve Accuracy of Macroevolutionary Rate Estimates?
inferredcites →https://doi.org/10.1093/sysbio/syw095openalex-snapshot
The Impact of the Tree Prior on Molecular Dating of Data Sets Containing a Mixture of Inter- and Intraspecies Sampling
inferredcites →https://doi.org/10.1098/rspb.2000.1278openalex-snapshot
Testing macro–evolutionary models using incomplete molecular phylogenies
inferredcites →https://doi.org/10.1098/rspb.2011.1439openalex-snapshot
Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record
inferredcites →https://doi.org/10.1098/rstb.1925.0002openalex-snapshot
II.—A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis, F. R. S
inferredcites →https://doi.org/10.1098/rstb.1994.0054openalex-snapshot
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/10.1111/evo.12820openalex-snapshot
Challenges in the estimation of extinction from molecular phylogenies: A response to Beaulieu and O'Meara
inferredcites →https://doi.org/10.1111/j.0014-3820.2001.tb00826.xopenalex-snapshot
ABSOLUTE DIVERSIFICATION RATES IN ANGIOSPERM CLADES
inferredcites →https://doi.org/10.1111/j.1558-5646.2009.00926.xopenalex-snapshot
EXTINCTION RATES SHOULD NOT BE ESTIMATED FROM MOLECULAR PHYLOGENIES
inferredcites →https://doi.org/10.1111/j.1558-5646.2010.01159.xopenalex-snapshot
ESTIMATING DIVERSIFICATION RATES: HOW USEFUL ARE DIVERGENCE TIMES?
inferredcites →https://doi.org/10.1111/jeb.13148openalex-snapshot
Phylogenetic estimates of diversification rate are affected by molecular rate variation
inferredcites →https://doi.org/10.1126/science.1065889openalex-snapshot
Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
inferredcites →https://doi.org/10.1146/annurev-ecolsys-110411-160331openalex-snapshot
Evolutionary Inferences from Phylogenies: A Review of Methods
inferredcites →https://doi.org/10.1146/annurev.ecolsys.37.091305.110035openalex-snapshot
Birth-Death Models in Macroevolution
inferredcites →https://doi.org/10.1186/s12862-014-0274-0openalex-snapshot
Environmental variation and rivers govern the structure of chimpanzee genetic diversity in a biodiversity hotspot
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.pbio.0040088openalex-snapshot
Relaxed Phylogenetics and Dating with Confidence
inferredcites →https://doi.org/10.1371/journal.pone.0043348openalex-snapshot
Trees of Unusual Size: Biased Inference of Early Bursts from Large Molecular Phylogenies
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/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.32942/osf.io/e3xnropenalex-snapshot
Phylogenetic Comparative Methods: Learning From Trees
inferredcites →https://doi.org/10.5860/choice.29-5104openalex-snapshot
The comparative method in evolutionary biology
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Geography and ecology structure diversification in Ziziphus Mill. (Rhamnaceae)
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Six Impossible Things before Breakfast: Assumptions, Models, and Belief in Molecular Dating
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Limitations of molecular dating using constant birth–death rate priors in deep time reflected in Brachiopoda evolution
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Isolation by distance and past climate resistance shaped the distribution of genealogical lineages of a neotropical lizard
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Dispersal from Africa to the Neotropics was followed by multiple transitions across Neotropical biomes facilitated by frugivores
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Biogeography and diversification of the Caribbean clade of Miconia (Melastomataceae): a Cuban origin underlies one of the largest Antillean radiations
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Historical biogeography of Vellozia (Velloziaceae) reveals range expansion in South American mountaintops after climatic cooling events and increased diversification rates after the occupation of Southern Espinhaço Province
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The Limits of the Constant-rate Birth–Death Prior for Phylogenetic Tree Topology Inference
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Evolutionary Tempo, Supertaxa, and Living Fossils
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A rapid and parallel Late Pleistocene/Holocene morphological radiation in a predaceous planktonic water flea: the case of Bythotrephes (Cladocera: Cercopagididae)
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Biogeographic history and ecological divergence of cat skinks ( Ristella : Scincidae) in the Western Ghats Mountains of India
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Their fates intertwined: diversification patterns of the Asian gliding vertebrates may have been forged by dipterocarp trees
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Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates
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Additional file 1 of The roles of vicariance and isolation by distance in shaping biotic diversification across an ancient archipelago: evidence from a Seychelles caecilian amphibian
inferred← citeshttps://doi.org/10.7287/peerj.10804v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.10804v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere (v0.1)"
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Peer Review #1 of "Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere (v0.2)"
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Peer Review #2 of "Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere (v0.2)"
inferred← citeshttps://doi.org/10.7717/peerj.10804openalex-snapshot
Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere
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A morphologically generalized Eurasian Pleuroxus aduncus species group (Cladocera: Chydoridae) is paraphyletic and contains denticulated P. truncatus , with an analog in the American Pleuroxus
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