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Evolution and Paleontology Studies
Research Guide
What is Evolution and Paleontology Studies?
Evolution and Paleontology Studies is the scientific study of how life changes through time using fossil evidence and evolutionary models to infer phylogeny, diversification, trait evolution, and biogeographic history.
The Evolution and Paleontology Studies literature comprises 257,771 works focused on evolutionary dynamics, diversification rates, and adaptive radiations, with particular emphasis on mammals and their ancestors. Core analytical practice in this area is phylogenetic inference and model-based comparison across molecular and morphological data, using methods such as neighbor-joining, maximum likelihood, and Bayesian MCMC. Widely used research infrastructure includes general phylogenetic programs and quantitative paleontology toolkits, including "PAST: PALEONTOLOGICAL STATISTICAL SOFTWARE PACKAGE FOR EDUCATION AND DATA ANALYSIS" (2001) and large-phylogeny engines such as "RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies" (2014).
Topic Hierarchy
Research Sub-Topics
Phylogenetic Comparative Methods
This sub-topic develops statistical models for trait evolution analysis controlling for phylogenetic non-independence. Researchers innovate independent contrasts, phylogenetic GLS, and OU models for macroevolutionary hypothesis testing.
Mammalian Diversification Rates
This sub-topic estimates lineage accumulation, extinction probabilities, and diversification shifts across mammal clades. Researchers apply birth-death models and boundary-crossing approaches to fossil-calibrated phylogenies.
Adaptive Radiation in Mammals
This sub-topic examines ecological opportunity exploitation, trait disparification, and clade packing in mammal radiations. Researchers study placental ordinal radiations post-K-Pg and island endemic diversification patterns.
Mammalian Body Size Evolution
This sub-topic models allometric scaling, Cope's rule violations, and size selection across geological timescales. Researchers analyze dwarfism/giantism extremes and miniaturization in early mammal evolution.
Cenozoic Mammalian Biogeography
This sub-topic reconstructs dispersal corridors, vicariance events, and range dynamics driving mammal distributions. Researchers integrate fossils, phylogenies, and paleoenvironments to model post-Gondwanan biogeographic history.
Why It Matters
Evolution and Paleontology Studies matters because it provides operational methods for reconstructing evolutionary relationships and testing evolutionary hypotheses that directly support specimen-based systematics, comparative biology, and fossil-based rate estimation. For example, Saitou and Nei (1987) introduced "The neighbor-joining method: a new method for reconstructing phylogenetic trees.", enabling fast tree reconstruction from evolutionary distance data that is still used for exploratory analyses and large datasets. Stamatakis (2006) described "RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models", and Stamatakis (2014) extended this with "RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies", supporting maximum-likelihood inference at scales relevant to macroevolutionary questions. Ronquist and Huelsenbeck (2003) presented "MrBayes 3: Bayesian phylogenetic inference under mixed models" and Ronquist et al. (2012) expanded it in "MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space", which are routinely used to integrate heterogeneous partitions (e.g., different character sets) under explicit probabilistic models. In quantitative paleontology workflows, Hammer et al. (2001) introduced "PAST: PALEONTOLOGICAL STATISTICAL SOFTWARE PACKAGE FOR EDUCATION AND DATA ANALYSIS", a free Windows package that supports common numerical analyses used in paleontology education and research. These methods and tools have practical downstream uses in building reproducible phylogenies for comparative analyses, assembling time-scaled evolutionary hypotheses, and quantifying uncertainty for inferences about speciation, extinction, and trait change.
Reading Guide
Where to Start
Start with Saitou and Nei (1987), "The neighbor-joining method: a new method for reconstructing phylogenetic trees.", because it clearly states the tree-reconstruction problem and provides an accessible distance-based solution that helps readers understand later likelihood and Bayesian approaches.
Key Papers Explained
A practical progression is: Saitou and Nei (1987) "The neighbor-joining method: a new method for reconstructing phylogenetic trees." for distance-based reconstruction; Ronquist and Huelsenbeck (2003) "MrBayes 3: Bayesian phylogenetic inference under mixed models" for Bayesian MCMC with partitioned data; Stamatakis (2006) "RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models" for scalable maximum-likelihood inference; Ronquist et al. (2012) "MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space" for expanded Bayesian model choice; and Kalyaanamoorthy et al. (2017) "ModelFinder: fast model selection for accurate phylogenetic estimates" alongside Minh et al. (2020) "IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era" to connect model selection with fast, model-rich inference on genomic-scale datasets.
Paper Timeline
Most-cited paper highlighted in red. Papers ordered chronologically.
Advanced Directions
Advanced work increasingly focuses on scaling inference and model choice to very large datasets while maintaining rigorous uncertainty quantification across many candidate models and partitions, as emphasized by "RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies" (2014), "MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space" (2012), "ModelFinder: fast model selection for accurate phylogenetic estimates" (2017), and "IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era" (2020). A parallel advanced direction is building reproducible quantitative paleontology pipelines that pair phylogenies with standard statistical analyses as supported by "PAST: PALEONTOLOGICAL STATISTICAL SOFTWARE PACKAGE FOR EDUCATION AND DATA ANALYSIS" (2001).
Papers at a Glance
In the News
This 2.6-million-year-old jawbone changes the human story
Culture Bureau. Funding for the project was provided by Margaret and Will Hearst and the University of Chicago.
Fossil study rewrites timeline of evolution of hearing in mammals
The study, “ Biomechanics of the mandibular middle ear of the cynodont Thrinaxodon and the evolution of mammal hearing ,” was supported by UChicago, the National Institutes of Health and the Nation...
Betiton Celebrates Scientific Advancement with New Fossil ...
Plea\_deal\_reached\_in\_Des\_Moines\_murder\_t\_0\_20180308045359 Author:Orko Manna Published:2:56 PM CST March 7, 2018 Updated:12:31 AM CST March 8, 2018 Facebook
New fossil study illuminates on the evolutionary success of ...
The study is part of a research cooperation between UCC, Martin-Luther-University Halle-Wittenberg (Germany), Natural History Museum Bamberg (Germany) and Stanford Synchrotron Radiation Lightsource...
Chicago Archaeopteryx informs on the early evolution of the avian bauplan
Here we report on the nearly complete and uncrushed 14th specimen of*Archaeopteryx*. Exceptional preservation and preparation guided by micro-computed tomographic data make this one of the best exe...
Code & Tools
`paleotree`is an R package for transforming, 'a posteriori' time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages. In p...
## About paleobuddy: an R package for simulating diversification dynamics, fossil records and phylogenies in R. ### Topics
PyRate is a program to estimate speciation, extinction, and preservation rates from fossil occurrence data using a Bayesian framework. ### License...
FossilBM uses phylogenies of extant and extinct species (typically obtained through tip-dating) and quantitative traits to infer the mode of evolut...
# Search code, repositories, users, issues, pull requests... Search Clear Search syntax tips # Provide feedback We read every piece of feedba...
Recent Preprints
Journal of Paleontology | Cambridge Core
The Journal of Paleontology publishes original articles and notes on the systematics, phylogeny, paleoecology, paleogeography, and evolution of fossil organisms. It emphasizes specimen-based resear...
Palaeontology - Latest research and news
Palaeontology is the study of prehistoric species, mostly ones that are extinct. It focuses primarily on fossil data, using a variety of physical, chemical and biological techniques to analyse them...
Palaeontology
As an official journal of The Palaeontological Association, _Palaeontology_ includes innovative and timely hypothesis-driven research that significantly advances our understanding of the history of...
Journal of Vertebrate Paleontology
_The Journal of Vertebrate Paleontology_ publishes original contributions on all aspects of vertebrate paleobiology, including vertebrate origins, evolution, functional morphology, taxonomy, biostr...
Paleontology - Frontiers in Ecology and Evolution
- [Original Research\ \ Published on 17 Dec 2025\ \ **Imaging and spectroscopy techniques applied to characterise fossilisation processes and biomineralisation** \ \ in Paleontology\ \ - Gabriel La...
Latest Developments
Recent developments in paleontology and evolutionary studies include the discovery and explanation of soft-bodied fossils from the Cambrian period due to ancient ocean chemistry (ScienceDaily), the identification of over 150 species that survived a mass extinction event in China (Phys.org), and new research on rapid evolution following the asteroid impact that caused the dinosaurs' extinction (Astrobiology). Additionally, studies have provided insights into the early evolution of birds through fossil analysis (Nature), and the creation of a comprehensive evolutionary tree of all birds based on phylogenetic estimates (PNAS).
Sources
Frequently Asked Questions
What is the core goal of Evolution and Paleontology Studies?
The core goal is to infer how lineages are related and how they changed through time by combining fossil evidence with evolutionary inference methods. In practice, this often means estimating phylogenetic trees and then using them to study diversification, trait evolution, and biogeography in deep time.
How do researchers reconstruct phylogenetic trees in this field?
Common approaches include distance-based clustering, maximum likelihood, and Bayesian inference. "The neighbor-joining method: a new method for reconstructing phylogenetic trees." (1987) formalized a distance-based method, while "RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models" (2006) and "MrBayes 3: Bayesian phylogenetic inference under mixed models" (2003) represent maximum-likelihood and Bayesian MCMC approaches, respectively.
Why do Bayesian methods like MrBayes matter for paleontology and evolution?
Bayesian phylogenetics provides a probabilistic framework for estimating trees and model parameters while representing uncertainty via posterior distributions. Ronquist and Huelsenbeck (2003) in "MrBayes 3: Bayesian phylogenetic inference under mixed models" emphasized combining information across data partitions, and Ronquist et al. (2012) in "MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space" expanded efficiency and model choice across many candidate models.
Which tools are commonly used for maximum-likelihood phylogenetic inference on large datasets?
RAxML is a standard tool for large maximum-likelihood analyses. Stamatakis (2006) introduced "RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models", and Stamatakis (2014) described "RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies" for phylogenetic analysis and post-analysis workflows.
How is model selection handled in modern phylogenetic workflows?
Model choice is often treated as an explicit optimization step because substitution/model misfit can bias phylogenetic estimates. "ModelFinder: fast model selection for accurate phylogenetic estimates" (2017) describes a dedicated approach to fast model selection, and "IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era" (2020) integrates expanded models and efficient inference methods for genomic-scale analyses.
Which software supports quantitative paleontology data analysis beyond tree inference?
"PAST: PALEONTOLOGICAL STATISTICAL SOFTWARE PACKAGE FOR EDUCATION AND DATA ANALYSIS" (2001) describes a free Windows software package implementing standard numerical analyses used in quantitative paleontology. It is commonly used for education and for routine exploratory and statistical analyses of paleontological datasets.
Open Research Questions
- ? How can phylogenetic inference methods be made both scalable and statistically robust when analyses involve thousands of taxa and mixed/partitioned models, as targeted by "RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models" (2006) and "RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies" (2014)?
- ? How should researchers choose among large spaces of evolutionary models and partitioning schemes without overfitting while maintaining accurate phylogenetic estimates, as framed by "MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space" (2012) and "ModelFinder: fast model selection for accurate phylogenetic estimates" (2017)?
- ? How can heterogeneous datasets (e.g., different character subsets evolving under different stochastic processes) be integrated in a single coherent inference framework while keeping MCMC and likelihood computations stable, as described in "MrBayes 3: Bayesian phylogenetic inference under mixed models" (2003)?
- ? Which combinations of inference engine (e.g., RAxML, MrBayes, IQ-TREE) and model-selection strategy produce the most reliable phylogenies for downstream macroevolutionary analyses, given the expanding model sets described in "IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era" (2020)?
- ? How should distance-based reconstructions such as "The neighbor-joining method: a new method for reconstructing phylogenetic trees." (1987) be used or validated in modern workflows dominated by likelihood and Bayesian methods, especially for large exploratory analyses?
Recent Trends
The field’s methods emphasis has shifted toward scalable maximum-likelihood and Bayesian inference with explicit model selection and expanded model spaces, reflected by the prominence of "RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies" , "ModelFinder: fast model selection for accurate phylogenetic estimates" (2017), and "IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era" (2020).
2014The topic cluster is large (257,771 works), and its most-cited methodological foundations include "The neighbor-joining method: a new method for reconstructing phylogenetic trees." (1987; 60,110 citations) and major inference platforms such as "MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space" (2012; 26,647 citations) and "RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies" (2014; 33,002 citations), indicating sustained reliance on general-purpose phylogenetic computation as a backbone for evolutionary and paleontological research.
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