Baum, Etal. (2005) the Tree-Thinking Challenge

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DOI: 10.1126/science.1117727, 979 (2005);310Science

et al.David A. BaumThe Tree-Thinking Challenge

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The central claim of the theory of evo-lution as laid out in 1859 by CharlesDarwin in The Origin of Species is

that living species, despite their diversity inform and way of life, are the products ofdescent (with modification) from commonancestors. To communicate this ide a,Darwin developed the metaphor of thetree of life. In this comparison, livingspecies trace backward in time to commonancestors in the same way that separatetwigs on a tree trace back to the same majorbranches. Coincident with improved meth-ods for uncovering evolutionaryrelationships, evolutionary trees,or phylogenies, have become anessential element of modern biol-ogy (1) . Consider the case of HIV/AIDS, where phylogenieshave been used to identify thesource of the virus, to date theonset of the epidemic, to detectviral recombination, to track viralevolution within a patient, and toidentify modes of potential trans-mission (2). Phylogenetic analysiswas even used to solve a murdercase involving HIV (3). Yet treethinking remains widely prac-ticed only by professional evolu-tionary biologists. This is a partic-ular cause for concern at a timewhen the teaching of evolution isbeing chal lenged, because evolutionarytrees serve not only as tools for biologicalresearchers across disciplines but also asthe main framework within which evidencefor evolution is evaluated (4, 5).

At the outset, it is important to clarifythat tree thinking does not necessarilyentail knowing how phylogenies areinferred by practicing systematists. Anyonewho has looked into phylogenetics from

outside the f ield of evolutionary biologyknows that it is complex and rapidly chang-ing, replete with a dense statistical litera-ture, impassioned philosophical debates,and an abundance of highly technical com-puter programs. Fortunately, one can inter-

pr et tr ee s and use them fo r organizingknowledge of biodiversity without know-ing the details of phylogenetic inference.The reverse is, however, not true. One can-not really understand phylogenetics if oneis not clear what an evolutionary tree is.

The preferred interpretation of a phylo-genetic tree is as a depiction of lines ofdescent. That is, trees communicate theevolutionary relationships among ele-ments, such as genes or species, that con-nect a sample of branch tips. Under thisinterpretation, the nodes (branching points)

on a tree are taken to correspond to actualbiological entities that existed in the past:ancestral populations or ancestral genes.However, tree diagrams are also used inmany nonevolutionary contexts, which cancause confusion. For example, trees candepict the clustering of genes on the basisof their expression profiles from microar-rays, or the clustering of ecological com-munities by species composition. The

prevalence of such cluster diag rams mayexplain why phylogenetic trees are oftenmisinterpreted as depictions of the similar-ity among the branch tips. Phylogenetictrees show historical relationships, not sim-ilarities. Although closely related speciestend to be similar to one another, this is notnecessarily the case if the rate of evolutionis not uniform: Crocodiles are more closelyrelated to birds than they are to lizards, eventhough crocodiles are indisputably moresimilar in external appearance to lizards.

But what does it mean to be moclosely related? Relatedness should bunderstood in terms of common ancestrythe more recently species share a commoancestor, the more closely related they arThis can be seen by reference to pedigree

You are more closely related to your fircousin than to your second cousin becauyour last common ancestor with your fircousin lived two generations ago (granparents), whereas your last common ancetor with your second cousin lived thregenerations ago (great-grandparentsNonetheless, many introductory studenand even professionals do not find it easy read a tree diagram as a depiction of evoltionary relationships. For example, whpresented with a particular phylogenettree (see the figure, left), people often err

neously conclude that a frog is more closerelated to a fish than to a human. A frog actually more closely related to a humathan to a fish because the last commoancestor of a frog and a human (see the f iure, label x) is a descendant of the last common ancestor of a frog and a fish (see thfigure, label y), and thus lived morecently. [To evaluate your tree-thinkinskills, take the quizzes (6)].

Why are trees liable to misinterprettion? Some evolutionary biologists havproposed that nonspecialists are prone read trees along the tips (1, 7), which in thcase yields an ordered sequence from fito frogs and ultimately to humans. Thincorrect way to read a phylogeny maexplain the widely held but erroneous viethat evolution is a linear progression froprimitive to advanced species (8), evethough a moments reflection will revethat a living frog cannot be the ancestor

EVOLUT ION

The Tree-Thinking ChallengeDavid A.Baum, Stacey DeWitt Smith, Samuel S. S. Donovan

D. A. Baum and S. D. Smith are in the Department ofBotany, University of Wisconsin, 430 Lincoln Drive,Madison,WI 53706, USA. E-mail: [email protected];[email protected] S. S. Donovan is in the Departmentof Instruction and Learning, University of Pittsburgh,Pittsburgh, PA 15260, USA. E-mail:[email protected]

PERSPECTIVES

CREDIT:P.

HUEY/SCIENCE

y

x

Which phylogenetic tree is accurate? On the basis of the tree on the left, is the frog more closely related the fish or the human? Does the tree on the right change your mind? See the text for how the common ancetors (x and y) indicate relatedness.

Published by AAAS


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a living human. The correct way to read a treeis as a set of hierarchically nested groups,known as clades. In this example, there arethree meaningful clades: human-mouse,human-mouse-lizard, and human-mouse-lizard-frog. The difference between readingbranch tips and reading clades becomesapparent if the branches are rotated so thatthe tip order is changed (see the figure,right). Although the order across the branch

tips is different, the branching pattern of evo-lutionary descent and clade composition isidentical. A focus on clade structure helps toemphasize that there is no single, linear nar-rative of evolutionary progress (1, 7).

There are other problems in reading rela-tionships from trees (9). For example, thereis a common assumption that trait evolutionhappens only at nodes. But nodes simplyrepresent places where populations becamegenetically isolated, permitting them toaccumulate differences in their subsequentevolution. Similarly, living species may bemistakenly projected backward to occupyinternal nodes of a tree. But it is incorrect toread a tree as saying that humans descendedfrom mice when all that is implied is that

humans and mice shared a common ances-tor. Thus, for all its importance, tree think-ing is fraught with challenges.

Tree thinking belongs alongside naturalselection as a major theme in evolutiontraining. Further, trees could be usedthroughout biological training as an effi-cient way to present information on the dis-tribution of trai ts among species. To thisend, what is needed are more resources:

computer programs (10), educational strate-gies (11, 12), and accessible presentationsof current phylogenetic knowledge (1315).

Phylogenetic trees are the most direct rep-resentation of the principle of commonancestrythe very core of evolutionarytheoryand thus they must find a moreprominent place in the general publics under-standing of evolution. As philosopher of sci-ence Robert OHara (16) stated, just asbeginning students in geography need to betaught how to read maps, so beginning stu-dents in biology should be taught how to readtrees and to understand what trees communi-cate. Among other benefits, as the concept oftree thinking becomes better understood bythose in the sciences, we can hope that a wider

segment of society will come to appreciate toverwhelming evidence for common ancestand the scientific rigor of evolutionary biolog

References1. R. J. OHara,Syst.Zool. 37, 142 (1988).2. K. A. Crandall, The Evolution of HIV(Johns Hopk

Univ. Press, Baltimore,1999).3. M. L. Metzger et al. Proc.Natl.Acad.Sci. U.S.A.

14292 (2002).4. D. Penny, L. R. Foulds, M. D. Hendy, Nature 297,1

(1982).

5. E. Sober, M. Steel,J.Theor. Biol. 218, 395 (2002).6. See the two quizzes on Science Online.7. S.Nee, Nature 435, 429 (2005).8. J.L.Rudolph,J.Stewart,J.Res.Sci.Teach. 35, 1069 (1999. M. D.Crisp,L. G.Cook, Trends Ecol. Evol.20, 122 (200

10. J. Herron et al., EvoBeaker 1.0 (SimBiotic SoftwaIthaca, NY,2005).

11. D.W. Goldsmith,Am. Biol.Teach. 65, 679 (2003).12. S.F. Gilbert, Nat.Rev.Genet. 4, 735 (2003).13. J. Cracraft, M. J. Donoghue,Assembling the Tree of L

(Oxford Univ. Press, Oxford, 2004).14. R. Dawkins, The Ancestors Tale: A Pilgrimage to

Dawn of Evolution (Houghton Mifflin,New York, 20015. Tree-Thinking Group (www.tree-thinking.org).16. R. J. OHara,Zool.Scripta 26, 323 (1997).

Supporting Online Materialwww.sciencemag.org/cgi/content/full/310/5750/979/DCTree-Thinking Quizzes I and II

10.1126/science.11177

Some biological molecules, such as thosein visual or photosynthetic systems,have evolved to efficiently convert

energy from one form to another. How dothese molecules channel energy rapidly andefficiently so that useful work can be per-formed without this energy being dissipatedineffectively into the surroundings?Dissipation of molecular vibrational excita-tion energy typically takes place on picosec-ond time scales, so biological molecules mustbe able to channel energy rapidly and effi-ciently if they are to be able to direct it in a use-ful manner. In biological systems excited bylight, the nonradiative electronic transitions

can occur on time scales (

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Baum, Etal. (2005) the Tree-Thinking Challenge