Interpretation of Phylogenetic Trees

by

Stacey D. Smith

• LAST REVIEWED: 14 April 2023
• LAST MODIFIED: 26 August 2014
• DOI: 10.1093/obo/9780199941728-0052

Introduction

At first glance, a phylogenetic tree appears to be a relatively simple diagram, beginning at some single starting point and giving rise to a set of tips through a series of branching events. Trees have long served as models for relating different species, even before the advent of Charles Darwin’s theory of evolution. However, correctly interpreting phylogenetic trees can be challenging, especially given the pervasiveness of alternative depictions of the history of life (e.g., Aristotle’s Scala naturae). Most biologists interpret phylogenetic trees as representations of the branching evolutionary history of the organisms at the tips. Because of the relevance of evolutionary history to understanding many biological patterns (e.g., in ecology, biogeography, and epidemiology), developing a clear understanding of how to read and interpret phylogenetic trees has become paramount for all biology students and practitioners. This article will cover the core literature related to understanding the information communicated by phylogenetic trees, and, to some extent, how this information is applied to address broader questions. Related topics, such as phylogenetic inference, comparative methods, and the use of phylogenies to create classifications, are covered by other articles. The author would like to thank Joseph Felsenstein and one anonymous reviewer for helpful comments on an earlier version.

Books

Although there are quite a few texts that cover phylogenetic inference, relatively few deal explicitly with interpreting phylogenetic trees or applying them to address broader evolutionary questions. In this section, some of the classic books that cover areas of phylogenetics beyond tree inference itself are listed. Of these, Baum and Smith 2013 provides the most in-depth introduction to reading phylogenetic trees, while the others (Brooks and McLennan 1991, Eldredge and Cracraft 1980, Harvey and Pagel 1991, Wiley and Lieberman 2011) discuss some of the ways that phylogenies are important for addressing questions about evolutionary patterns and processes.

• Baum, D. A., and S. D. Smith. 2013. Tree thinking: An introduction to phylogenetic biology. Greenwood Village, CO: Roberts.

  This textbook provides a broad introduction to tree thinking, with several chapters devoted to interpreting evolutionary relatedness and patterns of trait evolution using phylogenies. It is written to be accessible to undergraduates and biologists in fields outside of phylogenetics.

• Brooks, D. R., and D. A. McLennan. 1991. Phylogeny, ecology, and behavior: A research program in comparative biology. Chicago: Univ. of Chicago Press.

  This book focuses on interpreting patterns of speciation and adaptation in a parsimony framework and includes many fascinating biological examples. It is important to note that many of the trees are based on morphological characters, which are not commonly used today for phylogenetic studies of adaptation because of the potential for circularity.

• Eldredge, N., and J. Cracraft. 1980. Phylogenetic patterns and the evolutionary process: Method and theory in comparative biology. New York: Columbia Univ. Press.

  The authors cover the basics of cladistics but also devote special attention to how phylogenetic analysis can be applied to addressing macroevolutionary questions, such as the role of adaptation to new niches in diversification. Recent advances in statistical methods have resulted in renewed interest in applying phylogenies to testing such questions.

• Harvey, P. H., and M. D. Pagel. 1991. The comparative method in evolutionary biology. Oxford Series in Ecology and Evolution. Oxford: Oxford Univ. Press.

  A classic book in comparative biology that lays out the need for incorporating phylogenetic history in any analysis that spans multiple taxa. It describes how phylogenetic approaches can be used to test adaptive hypotheses by using both discrete and continuous data.

• Wiley, E. O., and B. S. Lieberman. 2011. Phylogenetics: The theory and practice of phylogenetic systematics. 2d ed. Hoboken, NJ: Wiley.

  DOI: 10.1002/9781118017883

  An updated version of Wiley’s 1981 book (New York: Wiley), this text covers many concepts relevant to interpreting trees. For example, the authors discuss different kinds of trees and different ways that character evolution is represented graphically on trees.