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The Tree-Thinking Challenge

December 2005
Science 310(5750):979-980

December 2005
310(5750):979-980

DOI:10.1126/science.1117727

Authors:

David A Baum

University of Wisconsin–Madison

Stacey Dewitt Smith

University of Nebraska at Lincoln

Sam Donovan

BioQUEST Curriculum Consortium

The preferred interpretation of a phylogenetic tree is as a depiction of lines of descent. That is, trees communicate the evolutionary relationships among elements, such as genes or species, that connect a sample of branch tips. Under this interpretation, the nodes (branching points) on a tree are taken to correspond to actual biological entities that existed in the past: ancestral populations or ancestral genes. However, tree diagrams are also used in many nonevolutionary contexts, which can cause confusion. For example, trees can depict the clustering of genes on the basis of their expression profiles from microarrays, or the clustering of ecological communities by species composition. The prevalence of such cluster diagrams may explain why phylogenetic trees are often misinterpreted as depictions of the similarity among the branch tips. Phylogenetic trees show historical relationships, not similarities.

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Papers in the Biological Sciences

Faculty Publications in the Biological Sciences

University of Nebraska - Lincoln Year 

The Tree-Thinking Challenge

David A. Baum∗Stacey DeWitt Smith†

Samuel S.S. Donovan‡

∗University of Wisconsin - Madison, dbaum@wisc.edu

†University of Nebraska - Lincoln, ssmith19@unl.edu

‡University of Pittsburgh - Main Campus, sdonovan@pitt.edu

This paper is posted at DigitalCommons@University of Nebraska - Lincoln.

http://digitalcommons.unl.edu/bioscifacpub/105

The central claim of the theory of evolu-

tion as laid out in 1859 by Charles Darwin

in The Origin of Species is that living species,

despite their diversity in form and way of

life, are the products of descent (with mod-

ication) from common ancestors. To com-

municate this idea, Darwin developed the

metaphor of the “tree of life.” In this com-

parison, living species trace backward in

time to common ancestors in the same way

that separate twigs on a tree trace back to

the same major branches. Coincident with

improved methods for uncovering evolu-

tionary relationships, evolutionary trees, or

phylogenies, have become an essential ele-

ment of modern biology (1). Consider the

case of HIV/AIDS, where phylogenies have

been used to identify the source of the virus,

to date the onset of the epidemic, to detect

viral recombination, to track viral evolu-

tion within a patient, and to identify modes

of potential transmission (2). Phylogenetic

analysis was even used to solve a murder

case involving HIV (3). Yet “tree thinking”

remains widely practiced only by profes-

sional evolutionary biologists. This is a par-

ticular cause for concern at a time when the

teaching of evolution is being challenged,

because evolutionary trees serve not only

as tools for biological researchers across

disciplines but also as the main framework

within which evidence for evolution is eval-

uated (4, 5).

At the outset, it is important to clarify that

tree thinking does not necessarily entail

knowing how phylogenies are inferred by

practicing systematists. Anyone who has

looked into phylogenetics from outside the

eld of evolutionary biology knows that it

is complex and rapidly changing, replete

with a dense statistical literature, impas-

sioned philosophical debates, and an abun-

dance of highly technical computer pro-

grams. Fortunately, one can interpret trees

and use them for organizing knowledge of

biodiversity without knowing the details of

phylogenetic inference. The reverse is, how-

ever, not true. One cannot really under-

stand phylogenetics if one is not clear what

an evolutionary tree is.

The preferred interpretation of a phyloge-

netic tree is as a depiction of lines of descent.

That is, trees communicate the evolution-

ary relationships among elements, such as

genes or species, that connect a sample of

branch tips. Under this interpretation, the

nodes (branching points) on a tree are taken

to correspond to actual biological entities

that existed in the past: ancestral popula-

tions or ancestral genes. However, tree dia-

grams are also used in many nonevolution-

ary contexts, which can cause confusion.

For example, trees can depict the cluster-

ing of genes on the basis of their expression

proles from microarrays, or the clustering

of ecological communities by species com-

position. The prevalence of such cluster dia-

grams may explain why phylogenetic trees

are often misinterpreted as depictions of the

similarity among the branch tips. Phyloge-

netic trees show historical relationships, not

similarities. Although closely related spe-

cies tend to be similar to one another, this

is not necessarily the case if the rate of evo-

lution is not uniform: Crocodiles are more

closely related to birds than they are to liz-

ards, even though crocodiles are indisput-

ably more similar in external appearance to

lizards.

But what does it mean to be “more closely

related”? Relatedness should be understood

in terms of common ancestry— the more

recently species share a common ances-

tor, the more closely related they are. This

can be seen by reference to pedigrees: You

are more closely related to your rst cousin

than to your second cousin because your

last common ancestor with your rst cousin

lived two generations ago (grandparents),

whereas your last common ancestor with

your second cousin lived three genera-

tions ago (great-grandparents). Nonethe-

less, many introductory students and even

professionals do not nd it easy to read a

tree diagram as a depiction of evolutionary

relationships. For example, when presented

with a particular phylogenetic tree (see the

gure, left), people often erroneously con-

clude that a frog is more closely related to

a sh than to a human. A frog is actually

more closely related to a human than to a

sh because the last common ancestor of a

frog and a human (see the gure, label x)

is a descendant of the last common ances-

tor of a frog and a sh (see the gure, label

science. Used by permission. DOI: 10.1126/science.1117727

PERSPECTIVES

EVOLUTION

The Tree-Thinking Challenge

David A. Baum, Stacey DeWitt Smith, Samuel S. S. Donovan

In 2005, D. A. Baum and S. D. Smith were in the Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madi-

son, WI 53706, USA. E-mail: dbaum@wisc.edu; ssmith19@unl.edu.

S. S. Donovan is in the Department of Instruction and Learning, University of Pittsburgh, Pittsburgh, PA 15260, USA. E-

mail: sdonovan@pitt.edu.

Which phylogenetic tree is accurate? On the basis of the tree on the left, is the frog more closely related

to the sh or the human? Does the tree on the right change your mind? See the text for how the common

ancestors (x and y) indicate relatedness.

y), and thus lived more recently. [To evalu-

ate your tree-thinking skills, take the quiz-

zes (6)].

Why are trees liable to misinterpretation?

Some evolutionary biologists have pro-

posed that nonspecialists are prone to read

trees along the tips (1, 7), which in this case

yields an ordered sequence from sh to

frogs and ultimately to humans. This incor-

rect way to read a phylogeny may explain

980 Baum, Smith & Donovan i n Science (novemBer 11, 2005) 310

the widely held but erroneous view that

evolution is a linear progression from prim-

itive to advanced species (8), even though

a moment’s reection will reveal that a liv-

ing frog cannot be the ancestor of a living

human. The correct way to read a tree is as

a set of hierarchically nested groups, known

as clades. In this example, there are three

meaningful clades: human-mouse, human-

mouse-lizard, and human-mouselizard-

frog. The difference between reading branch

tips and reading clades becomes appar-

ent if the branches are rotated so that the

tip order is changed (see the gure, right).

Although the order across the branch tips

is different, the branching pattern of evo-

lutionary descent and clade composition is

identical. A focus on clade structure helps

to emphasize that there is no single, linear

narrative of evolutionary progress (1, 7).

There are other problems in reading rela-

tionships from trees (9). For example, there

is a common assumption that trait evo-

lution happens only at nodes. But nodes

simply represent places where popula-

tions became genetically isolated, permit-

ting them to accumulate differences in their

subsequent evolution. Similarly, living spe-

cies may be mistakenly projected back-

ward to occupy internal nodes of a tree. But

it is incorrect to read a tree as saying that

humans descended from mice when all that

is implied is that humans and mice shared

a common ancestor. Thus, for all its impor-

tance, tree thinking is fraught with chal-

lenges.

Tree thinking belongs alongside natu-

ral selection as a major theme in evolu-

tion training. Further, trees could be used

throughout biological training as an ef-

cient way to present information on the dis-

tribution of traits among species. To this

end, what is needed are more resources:

computer programs (10), educational strat-

egies (11, 12), and accessible presentations

of current phylogenetic knowledge (13-15).

Phylogenetic trees are the most direct

representation of the principle of common

ancestry—the very core of evolutionary the-

ory—and thus they must nd a more prom-

inent place in the general public’s under-

standing of evolution. As philosopher of

science Robert O’Hara (16) stated, “just as

beginning students in geography need to

be taught how to read maps, so beginning

students in biology should be taught how

to read trees and to understand what trees

communicate.” Among other benets, as

the concept of tree thinking becomes better

understood by those in the sciences, we can

hope that a wider segment of society will

come to appreciate the overwhelming evi-

dence for common ancestry and the scien-

tic rigor of evolutionary biology.

References

1. R. J. O’Hara, Syst. Zool. 37, 142 (1988).

2. K. A. Crandall, The Evolution of HIV (Johns

Hopkins Univ. Press, Baltimore, 1999).

3. M. L. Metzger et al. Proc. Natl. Acad. Sci.

U.S.A. 99, 14292 (2002).

4. D. Penny, L. R. Foulds, M. D. Hendy,

Nature 297,197 (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 (1998).

9. M. D. Crisp, L. G. Cook, Trends Ecol. Evol.

20, 122 (2005).

10. J. Herron et al., EvoBeaker 1.0 (SimBiotic

Software, Ithaca, 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 Life (Oxford Univ. Press, Oxford,

2004).

14. R. Dawkins, The Ancestor’s Tale: A Pil-

grimage to the Dawn of Evolution (Houghton

Mifin, New York, 2004).

15. Tree-Thinking Group (www.tree-think-

ing.org).

16. R. J. O’Hara, Zool. Scripta 26, 323 (1997).

Supporting Online Material

www.sciencemag.org/cgi/content/full/310/5750/979/DC1

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