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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
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Practical Guide and Review of Fossil Tip-Dating in Phylogenetics
Nicola S Heckeberg1,2, Alessio Capobianco1,2, Basanta Khakurel1,2
1Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333 Munich, Germany.
Systematic Biology
|September 24, 2025
Summary
Phylogenetic tip-dating revolutionizes evolutionary biology by placing fossils into phylogenies. This review details methods and models for this complex but increasingly vital approach.
Area of Science:
- Evolutionary Biology
- Phylogenetics
- Paleontology
Background:
- Phylogenetic tip-dating offers a principled method for time-calibrated phylogenies, surpassing traditional node-dating.
- Fossils integrated as tips in phylogenies are crucial for macroevolutionary studies, including diversification and phenotypic evolution.
- Despite advancements since 2011, phylogenetic tip-dating analyses remain complex and challenging.
Purpose of the Study:
- To provide a comprehensive review of methods and models for phylogenetic tip-dating analyses incorporating fossils.
- To survey published tip-dating studies, identifying common data and modeling choices and emerging trends.
- To offer practical recommendations for data collection, preparation, and modeling in tip-dating analyses.
Main Methods:
- Review of existing literature and published phylogenetic tip-dating studies.
- Detailed examination of models for molecular, morphological (discrete and continuous), and lineage evolution.
- Analysis of data collection, preparation, and modeling choices, including underlying assumptions.
Main Results:
- A survey of tip-dating studies reveals common data/modeling choices and evolving approaches.
- Detailed descriptions of standard models for different evolutionary data types are presented.
- The review highlights the importance of the fossilized-birth-death process in lineage evolution.
Conclusions:
- Phylogenetic tip-dating is a powerful, evolving tool for evolutionary biology, despite its complexity.
- This review provides a roadmap for researchers navigating data and modeling choices in tip-dating analyses.
- Practical recommendations are offered to facilitate the application and advancement of phylogenetic tip-dating methods.
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