Rachel C. M. Warnock
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View article: Identifying the Big Questions in paleontology: a community-driven project
Identifying the Big Questions in paleontology: a community-driven project Open
Paleontology provides insights into the history of the planet, from the origins of life billions of years ago to the biotic changes of the Recent. The scope of paleontological research is as vast as it is varied, and the field is constantl…
View article: Combining fossil taxa with and without morphological data improves dated phylogenetic analyses
Combining fossil taxa with and without morphological data improves dated phylogenetic analyses Open
The fossilized birth–death (FBD) model has become an increasingly popular method for inferring dated phylogenies. It is especially useful for incorporating fossil data into such analyses, integrating fossils along with their age informatio…
View article: “A history of the world imperfectly kept”: Will we ever know how biodiversity has changed over deep time?
“A history of the world imperfectly kept”: Will we ever know how biodiversity has changed over deep time? Open
The fossil record is our only direct source of evidence for how life on Earth has waxed and waned over its long history. However, the fossil record is also incomplete and biased in many ways, after passing through biological, geological, a…
View article: Combining fossil taxa with and without morphological data improves dated phylogenetic analyses
Combining fossil taxa with and without morphological data improves dated phylogenetic analyses Open
The fossilized birth-death (FBD) model has become an increasingly popular method for inferring dated phylogenies. This is because it is especially useful for incorporating fossil data into such analyses, integrating fossils along with thei…
View article: From fossils to phylogenies: exploring the integration of paleontological data into Bayesian phylogenetic inference
From fossils to phylogenies: exploring the integration of paleontological data into Bayesian phylogenetic inference Open
Incorporating paleontological data into phylogenetic inference can greatly enrich our understanding of evolutionary relationships by providing insights into the diversity and morphological evolution of a clade over geological timescales. P…
View article: Practical guidelines for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC)
Practical guidelines for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) Open
Phylogenetic estimation is, and has always been, a complex endeavor. Estimating a phylogenetic tree involves evaluating many possible solutions and possible evolutionary histories that could explain a set of observed data, typically by usi…
View article: The FossilSimShiny app for simulating under the fossilized birth–death process and plotting the results
The FossilSimShiny app for simulating under the fossilized birth–death process and plotting the results Open
Phylogenetic inferences using combined datasets of both extant and extinct species have grown increasingly popular, in part thanks to the development of the fossilized birth–death (FBD) process. The FBD process provides a powerful model fo…
View article: A macroevolutionary analysis of European Late Upper Palaeolithic stone tool shape using a Bayesian phylodynamic framework
A macroevolutionary analysis of European Late Upper Palaeolithic stone tool shape using a Bayesian phylodynamic framework Open
Phylogenetic models are commonly used in palaeobiology to study the patterns and processes of organismal evolution. In the human sciences, phylogenetic methods have been deployed for reconstructing ancestor–descendant relationships using l…
View article: Challenges in estimating species' age from phylogenetic trees
Challenges in estimating species' age from phylogenetic trees Open
Aim Species age, the elapsed time since origination, can give insight into how species longevity might influence eco‐evolutionary dynamics, which has been hypothesized to influence extinction risk. Traditionally, species' ages have been es…
View article: Practical guidelines for Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC)
Practical guidelines for Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC) Open
Phylogenetic estimation is, and has always been, a complex endeavor. Estimating a phylogenetic tree involves evaluating many possible solutions and possible evolutionary histories that could explain a set of observed data, typically by usi…
View article: Decision: Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction — R2/PR9
Decision: Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction — R2/PR9 Open
Phylodynamic models can be used to estimate diversification trajectories from time-calibrated phylogenies. Here we apply two such models to phylogenies of non-avian dinosaurs, a clade whose evolutionary history has been widely debated. Alt…
View article: A macroevolutionary analysis of European Late Upper Palaeolithic stone tool shape using a Bayesian phylodynamic framework
A macroevolutionary analysis of European Late Upper Palaeolithic stone tool shape using a Bayesian phylodynamic framework Open
Phylogenetic models are commonly used in paleobiology to study the patterns and processes of organismal evolution. In the human sciences, phylogenetic methods have been deployed for reconstructing ancestor-descendant relationships using li…
View article: Recommendation: Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction — R2/PR8
Recommendation: Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction — R2/PR8 Open
Phylodynamic models can be used to estimate diversification trajectories from time-calibrated phylogenies. Here we apply two such models to phylogenies of non-avian dinosaurs, a clade whose evolutionary history has been widely debated. Alt…
View article: Decision: Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction — R1/PR6
Decision: Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction — R1/PR6 Open
Phylodynamic models can be used to estimate diversification trajectories from time-calibrated phylogenies. Here we apply two such models to phylogenies of non-avian dinosaurs, a clade whose evolutionary history has been widely debated. Alt…
View article: Assessing the Adequacy of Morphological Models used in Palaeobiology
Assessing the Adequacy of Morphological Models used in Palaeobiology Open
1 Abstract Reconstructing the evolutionary history of different groups of organisms provides insight into how life originated and diversified on Earth. Phylogenetic trees are commonly used to estimate this evolutionary history, providing a…
View article: Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction
Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction Open
Phylodynamic models can be used to estimate diversification trajectories from time-calibrated phylogenies. Here we apply two such models to phylogenies of non-avian dinosaurs, a clade whose evolutionary history has been widely debated. Alt…
View article: Increasing the equitability of data citation in paleontology: capacity building for the big data future
Increasing the equitability of data citation in paleontology: capacity building for the big data future Open
Data compilations expand the scope of research; however, data citation practice lags behind advances in data use. It remains uncommon for data users to credit data producers in professionally meaningful ways. In paleontology, databases lik…
View article: Recommendation: Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction — R1/PR5
Recommendation: Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction — R1/PR5 Open
Phylodynamic models can be used to estimate diversification trajectories from time-calibrated phylogenies. Here we apply two such models to phylogenies of non-avian dinosaurs, a clade whose evolutionary history has been widely debated. Alt…
View article: Practical guidelines for Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC)
Practical guidelines for Bayesian phylogenetic inference using Markov Chain Monte Carlo (MCMC) Open
Phylogenetic estimation is, and has always been, a complex endeavor. Estimating a phylogenetic tree involves evaluating many possible solutions and possible evolutionary histories that could explain a set of observed data, typically by usi…
View article: Challenges in estimating species age from phylogenetic trees
Challenges in estimating species age from phylogenetic trees Open
Aim Species age, the elapsed time since origination, can give an insight into how species longevity might influence eco-evolutionary dynamics and has been hypothesized to influence extinction risk. Traditionally, species ages have been mea…
View article: Putting the F into <scp>FBD</scp> analysis: tree constraints or morphological data?
Putting the F into <span>FBD</span> analysis: tree constraints or morphological data? Open
The fossilized birth–death (FBD) process provides an ideal model for inferring phylogenies from both extant and fossil taxa. Using this approach, fossils are directly integrated into the tree, leading to a statistically coherent prior on d…
View article: Supplementary materials for "Putting the F into FBD analysis: tree constraints or morphological data ?"
Supplementary materials for "Putting the F into FBD analysis: tree constraints or morphological data ?" Open
This dataset contains the R code, simulated datasets and configuration files used to run the analyses presented in the manuscript "Putting the F into FBD analysis: tree constraints or morphological data ?".
View article: Supplementary materials for "Putting the F into FBD analysis: tree constraints or morphological data ?"
Supplementary materials for "Putting the F into FBD analysis: tree constraints or morphological data ?" Open
This dataset contains the R code, simulated datasets and configuration files used to run the analyses presented in the manuscript "Putting the F into FBD analysis: tree constraints or morphological data ?".
View article: Decision: Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction — R0/PR3
Decision: Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction — R0/PR3 Open
Phylodynamic models can be used to estimate diversification trajectories from time-calibrated phylogenies. Here we apply two such models to phylogenies of non-avian dinosaurs, a clade whose evolutionary history has been widely debated. Alt…
View article: Code and Data: Increasing the equitability of data citation in paleontology: Capacity building for the big data future
Code and Data: Increasing the equitability of data citation in paleontology: Capacity building for the big data future Open
Data compilations expand the scope of research; however, data citation practice lags behind advances in data use. It remains uncommon for data users to credit data producers in professionally meaningful ways. In paleontology, databases lik…
View article: Code and Data: Increasing the equitability of data citation in paleontology: Capacity building for the big data future
Code and Data: Increasing the equitability of data citation in paleontology: Capacity building for the big data future Open
Data compilations expand the scope of research; however, data citation practice lags behind advances in data use. It remains uncommon for data users to credit data producers in professionally meaningful ways. In paleontology, databases lik…
View article: Supplementary materials for "Putting the F into FBD analysis: tree constraints or morphological data ?"
Supplementary materials for "Putting the F into FBD analysis: tree constraints or morphological data ?" Open
This dataset contains the R code, simulated datasets and configuration files used to run the analyses presented in the manuscript "Putting the F into FBD analysis: tree constraints or morphological data ?".
View article: Recommendation: Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction — R0/PR2
Recommendation: Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction — R0/PR2 Open
Phylodynamic models can be used to estimate diversification trajectories from time-calibrated phylogenies. Here we apply two such models to phylogenies of non-avian dinosaurs, a clade whose evolutionary history has been widely debated. Alt…
View article: Where traditional extinction estimates fall flat: using novel cophylogenetic methods to estimate extinction risk in platyhelminths
Where traditional extinction estimates fall flat: using novel cophylogenetic methods to estimate extinction risk in platyhelminths Open
Today parasites comprise a huge proportion of living biodiversity and play a major role in shaping community structure. Given their ecological significance, parasite extinctions could result in massive cascading effects across ecosystems. …