Understanding Evolutionary Trees

Evo Edu Outreach (2008) 1:121–137 DOI 10.1007/s12052-008-0035-x ORIGINAL SCIENCE/EVOLUTION REVIEW Understanding Evolutionary Trees T. Ryan Gregory Published online: 12 February 2008 # Springer Science + Business Media, LLC 2008 Abstract Charles Darwin sketched his first evolutionary tree in 1837, and trees have remained a central metaphor in evolutionary biology up to the present. Today, phylogenetics—the science of constructing and evaluating hypotheses about historical patterns of descent in the form of evolutionary trees—has become pervasive within and increasingly outside evolutionary biology. Fostering skills in “tree thinking” is therefore a critical component of biological education. Conversely, misconceptions about evolutionary trees can be very detrimental to one’s understanding of the patterns and processes that have occurred in the history of life. This paper provides a basic introduction to evolutionary trees, including some guidelines for how and how not to read them. Ten of the most common misconceptions about evolutionary trees and their implications for understanding evolution are addressed. Keywords Branch . Clade . Common ancestor . Evolution . Node . Phylogeny . Sister taxa . Topology . Trend Introduction: The Importance of Tree Thinking In a flourish indicative of both his literary style and perceptive understanding of nature, Darwin (1859) offered the following arboreal metaphor to describe the diversification and extinction of species: As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been T. R. Gregory (*) Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada e-mail: with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever-branching and beautiful ramifications. Darwin clearly considered this Tree of Life as an important organizing principle in understanding the concept of “descent with modification” (what we now call evolution), having used a branching diagram of relatedness early in his exploration of the question (Fig. 1) and including a tree-like diagram as the only illustration in On the Origin of Species (Darwin 1859). Indeed, the depiction of historical relationships among living groups as a pattern of branching predates Darwin; Lamarck (1809), for example, used a similar type of illustration (see Gould 1999). Today, evolutionary trees are the subject of detailed, rigorous analysis that seeks to reconstruct the patterns of branching that have led to the diversity of life as we know it (e.g., Cracraft and Donoghue 2004; Hodkinson and Parnell 2007; Lecointre and Le Guyader 2007; Maddison and Schultz 2007). An entire discipline known as phylogenetics (Gr. phyle, tribe + genesis, birth) has emerged, complete with professional societies, dedicated scientific journals, and a complex technical literature that can be impenetrable to many nonspecialists. The output of this profession has become prodigious: It has been suggested that phylogeneticists as a group publish an average of 15 new evolutionary trees per day (Rokas 2006). Little surprise, then, that it has been argued that evolutionary biology as a whole has undergone a shift to “tree thinking” (O’Hara 1988), akin to the earlier movement toward “population thinking” that helped to shape the Neo-Darwinian synthesis around the mid-twentieth century (Mayr and Provine 1980). Whereas tree thinking has permeated much of professional evolutionary biology, it has yet to exert its full 122 Fig. 1 The first evolutionary tree sketched by Darwin (1837) in one of his notebooks. It is also of note that the only illustration in On the Origin of Species (Darwin 1859) was an evolutionary tree. Other early evolutionists before and after Darwin, including Lamarck (1809), also drew branching diagrams to indicate relatedness (see Gould 1999) influence among nonscientists. As Baum et al. (2005) recently pointed out, “Phylogenetic trees are the most direct representation of the principle of common ancestry—the very core of evolutionary theory—and thus they must find a more prominent place in the general public’s understanding of evolution.” In this regard, it is not so much the technical aspects of phylogenetic analysis1 that are of interest but a more practical understanding of what evolutionary trees represent and, at least as important, what they do not represent. As Baum et al. (2005) continued, Tree thinking does not necessarily entail knowing how phylogenies are inferred by practicing systematists. Anyone who has looked into phylogenetics from outside the field of evolutionary biology knows that it is complex and rapidly changing, replete with a dense statistical literature, impassioned philosophical debates, and an abundance of highly technical computer programs. Fortunately, one can interpret trees and use them for organizing knowledge of biodiversity without knowing the details of phylogenetic inference. Unfortunately, it is becoming clear that many readers lack a sufficient level of phylogenetic literacy to properly interpret evolutionary patterns and processes. For example, a recent study of undergraduate students who had received at least introductory instruction in evolutionary science 1 A discussion of phylogenetic methods is well beyond the scope of this article. Introductions to the technical aspects of phylogenetic analysis are provided by Hillis et al. (1996), Page and Holmes (1998), Nei and Kumar (2000), Felsenstein (2003), Salemi and Vandamme (2003), and Hall (2007). Evo Edu Outreach (2008) 1:121–137 revealed a range of common misconceptions about phylogenetic trees that represent “fundamental barriers to understanding how evolution operates” (Meir et al. 2007).2 Early correction of these misconceptions would be of obvious benefit, and it has been suggested that the importance for biology students of learning how to interpret evolutionary trees is on par with that of geography students being taught how to read maps (O’Hara 1997). Given the growing significance of phylogenetic analyses in forensic, medical, and other applications (e.g., Vogel 1997; Rambaut et al. 2001; Mace et al. 2003; Mace and Holden 2005) in addition to their pervasive influence in evolutionary studies, this claim does not appear to be overstated. This paper aims to provide a brief introduction to evolutionary trees and some basic details on how they should and should not be read and interpreted. This is followed by a discussion of ten of the most common misconceptions about evolutionary trees, many of which are held simultaneously and any of which can severely impede one’s understanding of evolution. The Basics of Phylogenetic Literacy What is an Evolutionary Tree? In the most general terms, an evolutionary tree—also known as a phylogeny3—is a diagrammatic depiction of biological entities that a (...truncated)