Tree Thinking: An Introduction to Phylogenetic Biology

  • Baum, David (University of Wisconsin, Madison)
  • Smith, Stacey (University of Colorado, Boulder)
Copyright Year:2013
Specifications:496 pages, hardback, printed in black and white
Publication Status:Published June 15, 2012.

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Tree Thinking: An Introduction to Phylogenetic Biology

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About this Title

Baum and Smith, both professors evolutionary biology and researchers in the field of systematics, present this highly accessible introduction to phylogenetics and its importance in modern biology. Ever since Darwin, the evolutionary histories of organisms have been portrayed in the form of branching trees or “phylogenies.”  However, the broad significance of the phylogenetic trees has come to be appreciated only quite recently. Phylogenetics has myriad applications in biology, from discovering the features present in ancestral organisms, to finding the sources of invasive species and infectious diseases, to identifying our closest living (and extinct) hominid relatives.  Taking a conceptual approach, Tree Thinking introduces readers to the interpretation of phylogenetic trees, how these trees can be reconstructed, and how they can be used to answer biological questions. Examples and vivid metaphors are incorporated throughout, and each chapter concludes with a set of problems, valuable for both students and teachers. Tree Thinking is must-have textbook for any student seeking a solid foundation in this fundamental area of evolutionary biology.

About the Authors

David A. Baum is a professor at the University of Wisconsin, where he conducts research in plant systematics, systematic theory, and plant evolutionary developmental genetics.  He earned his Ph.D. in Population and Evolutionary Biology from Washington University in 1991, conducted postdoctoral research at the University of Wisconsin, and then served as Assistant and Associate Professor of Organismic and Evolutionary Biology at Harvard University.  He returned to the University of Wisconsin in 2001, and is now Professor and Chair of Botany and Director of the James F. Wright Institute for the Study of Evolution. Baum’s research has earned him awards including an Alfred P. Sloan Foundation Young Investigator Award, an NSF Career Award, and a John Simon Guggenheim Foundation Fellowship. In 2006 he was elected Fellow of the American Association for the Advancement of Science for “outstanding contributions in the investigation of plant evolution and for excellence in teaching and mentoring in phylogenetics and evolutionary biology.”  Baum teaches phylogenetic biology at both the introductory and advanced levels and has been offering workshops on phylogenies and tree thinking for K-12 teachers since 1999.

Stacey D. Smith is professor at the University of Colorado, Boulder. Her research focuses on the evolution of floral diversity and spans the fields of phylogenetics, evolutionary genetics, comparative methods and pollination ecology. Supported by a British Marshall fellowship, she earned an M.Phil in Botanical Diversity from the Universities of Reading and Birmingham in the United Kingdom in 2001.  She returned to the United States to pursue a doctoral degree in Systematic Botany at the University of Wisconsin-Madison.  After obtaining her Ph.D. in 2006, she conducted postdoctoral research at Duke University through a National Institutes of Health Ruth L. Kirschstein Fellowship before joining the faculty at the University of Nebraska in 2010.  She teaches introductory organismal biology and phylogenetic biology for undergraduate and graduate students and sponsors outreach events to promote public understanding of plant biology and evolution. 

Table of Contents

1. Introduction to phylogenetic trees and their importance in modern biology

2. Tree thinking and its importance in the development of evolutionary thought

3. What a phylogenetic tree represents

4. Trait evolution

5. Relatedness and biological classification

6. Gene trees and species trees

7. Phylogenetic inference with parsimony

8. Phylogenetic inference with distance, maximum likelihood and Bayesian methods

9. Statistical tests of phylogenetic hypotheses

10. Using trees to reconstruct evolutionary history

Answers to chapter quizzes

Literature cited




“Phylogenetics has had a revolutionary impact on biology in the last few decades, but few books convey the power and beauty of the field at an introductory level like this one does. It will help fill a long empty niche in undergraduate curricula and serve as a good prerequisite to more technical treatments at the graduate level.” —Michael Sanderson, University of Arizona

“This book is perfect for the kind of phylogeny course that we should be teaching everywhere.”  —Michael J. Donoghue, Sterling Professor of Ecology and Evolutionary Biology, Yale University

“We can’t expect students and the general public to understand the big idea of evolution—common ancestry—if we neglect to teach them the basic skills necessary to understand and interpret evolutionary trees. Tree Thinking is an exceptional resource for scientists, graduate students, and science educators.” —Louise Mead, Education Director at BEACON Center for the Study of Evolution in Action, Michigan State University

“Baum and Smith’s Tree Thinking is an admirably clear introduction to building and interpreting trees.” —Mark Pagel, FRS, Professor of Evolutionary Biology, University of Reading

“Phylogenetic analysis has become a fundamental element of 21st century biology, impacting all disciplines from molecular biology to ecosystem structure, from population genetics to the Tree of Life. Tree Thinking will help educators and students develop the skills crucial to understanding the evolutionary concepts underlying modern biology.” —Richard Olmstead, Professor of Biology and Herbarium Curator, University of Washington

“Tree thinking is not intuitive; it doesn’t come easily to most people. Yet it’s an essential tool for understanding how organisms—and their traits—evolve. Baum and Smith have provided a helpful guide to learning how to think like an evolutionary biologist. Their treatment is accessible, balanced, and well informed.” —James Hanken, Alexander Agassiz Professor of Zoology, Curator in Herpetology, and Director, Museum of Comparative Zoology, Harvard University

“Baum and Smith have produced a book that hits its target squarely. Tree thinking will be a critical tool in the arsenal of those of us who train the next generation of evolutionary biologists.” —Jack Sullivan, President of the Society of Systematic Biologists, and Professor of Biology, University of Idaho

“A timely and well-written primer. Highly recommended for anyone interested in taking a phylogenetic approach to study evolution.” —Jonathan B. Losos, Curator in Herpetology, and Monique and Philip Lehner Professor for the Study of Latin America, Harvard University

“Kudos to Baum and Smith, two highly accomplished phylogeneticists, for this clear and concise book, which is truly a much needed text for the field of phylogenetic biology. Both plant and animal examples are used throughout to show how an evolutionary tree depicts the relationships among organisms through time. Tree Thinking will be a required text for when I next teach Phylogenetic Plant Systematics.” —Kathleen Pryer, Professor of Biology, Duke University

"Where was this book when I taught my first phylogentics course 10 years ago?! But better late than never. Baum and Smith have provided the first general text for teaching a difficult to grasp subject, what is a phylogenetic tree and how best to infer one, in a non-technical framework." —Sydney Cameron, Professor of Biology, University of Illinois

Art for Teaching Purposes

For qualified instructors, we are pleased to offer all of the figures in JPEG format. Please contact the editor, Ben Roberts, at for a link to download the images. We can also send a CD-ROM, if necessary.

Pretest Files

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