Phylogenetic Biology
2025-10-07
Preface
0.1 Approach
Models are at the core of modern phylogenetic biology. Models are usually taught in the context of phylogenetic inference, where they are used to look backward in time. This seems to me a bit like teaching students to master driving in reverse before you show them how to drive forward down a road. Phylogenetic models are generative - they explain how data are created under specific evolutionary processes. They are therefore more intuitive to understand in the context of generating data, proceeding in time from ancestral states forward to future states. I therefore focus first on building an intuitive understanding of models in the context of simulation, and only after that apply models to inference and other tasks that look back in time.
This book is not a comprehensive treatment of phylogenetic biology, it is focused on teaching some of the key concepts and methods at the core of the field. This will provide a foundation for the many other rich areas of the field, from its interfaces with population genetics to comparative genomics to comparative methods at a macroevolutionary scale.
0.2 Using this book
This book is intended both for the self directed learner, and for use in a course.
I wrote it as a text for my course, Phylogenetic Biology (Yale EEB354). We read one chapter a week. We review and discuss the reading on Tuesdays, and then on Thursdays do hands-on work, read papers from the literature, or share student projects.
0.3 Distribution
There are several ways you can get this book:
You can read an html version for free at https://dunnlab.org/phylogenetic_biology/
The book is rendered from source code available at https://github.com/caseywdunn/phylogenetic_biology, with
bookdown(Xie 2016). If you are curious about how any of the figures or analyses were done you can examine the source code there and rerun it yourself.Snapshots of source code for each edition are also available on Zenodo via the the book’s DOI at https://doi.org/10.5281/zenodo.17267993.
You can purchase a paperback from your favorite book retailer. Search for ISBN 979-8-9934524-0-1.
You can purchase a hardback from your favorite book retailer. Search for ISBN 979-8-9934524-1-8.
Please submit any errors you find, typos, or suggestions that you have for improving the manuscript to the issue tracker at https://github.com/caseywdunn/phylogenetic_biology/issues.
You are currently reading Edition 0.9.0 of the book. Please cite it as follows:
Dunn CW. Phylogenetic Biology. Edition 0.9.0. New Haven, CT: Casey W. Dunn; 2025. ISBN 979-8-9934524-0-1. doi:10.5281/zenodo.17267993
0.4 Other resources
The following sites have a wide variety of material that is relevant to the theory and and practice of phylogenetic biology.
An extensive list of tools, tutorials, and examples of phylogenetic tools in the programming language R maintained by Briam O’Meara. https://cran.r-project.org/web/views/Phylogenetics.html
Liam Revell has an excellent blog on phylogenetic methods. https://blog.phytools.org/
The Workshop on Molecular Evolution at Woods Hole. This is an intensive summer course on phylogenetics, with an emphasis on building phylogenetic trees. https://molevolworkshop.github.io
The Applied Phylogenetics Workshop in Bodega Bay. This is another summer course on phylogenetics, but with a bit more emphasis on using phylogenies to test evolutionary questions. http://treethinkers.org/tutorials/
The following are some of the many great books for learning more about phylogenetic methods:
Baum, D. and Smith, S. (2012). Tree Thinking. An Introduction to Phylogenetic Biology. Roberts Publishers.
Felsenstein, J. (2004) Inferring phylogenies. Sinauer Associates.
Garamszegi, LZ. (2014) Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology. Springer
Paradis, E. (2011) Analysis of Phylogenetics and Evolution with R. Springer
Revell, LJ, Harmon, LJ (2022) Phylogenetic Comparative Methods in R. Princeton
Swofford, D. L., Olsen, G. J., Waddell, P. J., & Hillis, D. M. (1996). Phylogenetic inference. In: Molecular Systematics, Second Edition. eds: D. M. Hillis, C Moritz, & B. K. Mable. Sinauer Associates
The following books provide general computational background for the topics covered here:
Wickham, H., Grolemund, G (2017) R for Data Science. https://r4ds.had.co.nz
Haddock, S. H. D. and Dunn, C. W. (2010). Practical Computing for Biologists. http://practicalcomputing.org
0.5 Acknowledgements
Thanks in particular to the students of Yale EEB354 in the falls of 2020 (the first course I taught fully online), 2022, and 2024. This book started as a collection of lecture notes for this course. The students provided invaluable motivation and feedback. Thanks in particular to Lauren Mellenthin (graduate teaching fellow for the course in 2020), Namrata Ahuja (teaching fellow in 2022), and Dalila Destanovic (teaching fellow in 2024). Other lab members provided very helpful feedback when I posted new chapters. Steve Haddock and Felipe Zapata also provided close reads of most chapters, often within hours of completing first drafts. Thanks to Richard Hammack, author of Book of Proof, for his helpful advice on self publishing to facilitate student access. I am also very grateful to the students and faculty of the Workshop on Molecular Evolution at Woods Hole.
0.6 License
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. It is available to read online for free at http://dunnlab.org/phylogenetic_biology/, ensuring access to all students worldwide. Commercial use by others (e.g., the sale of printed copies by anyone other than the author) are not allowed.