Tree Thinking


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Tree Thinking

  1. 1. E VO L U T I O N PERSPECTIVES But what does it mean to be “more closely related”? Relatedness should be The Tree-Thinking Challenge understood in terms of common ancestry— the more recently species share a common David A. Baum, Stacey DeWitt Smith, Samuel S. S. Donovan ancestor, the more closely related they are. This can be seen by reference to pedigrees: he central claim of the theory of evo- pret trees and use them for organizing You are more closely related to your first T lution as laid out in 1859 by Charles knowledge of biodiversity without know- Darwin in The Origin of Species is ing the details of phylogenetic inference. that living species, despite their diversity in The reverse is, however, not true. One can- cousin than to your second cousin because your last common ancestor with your first cousin lived two generations ago (grand- form and way of life, are the products of not really understand phylogenetics if one parents), whereas your last common ances- descent (with modification) from common is not clear what an evolutionary tree is. tor with your second cousin lived three ancestors. To communicate this idea, The preferred interpretation of a phylo- generations ago (great-grandparents). Darwin developed the metaphor of the genetic tree is as a depiction of lines of Nonetheless, many introductory students “tree of life.” In this comparison, living descent. That is, trees communicate the and even professionals do not find it easy to species trace backward in time to common evolutionary relationships among ele- read a tree diagram as a depiction of evolu- ancestors in the same way that separate ments, such as genes or species, that con- tionary relationships. For example, when twigs on a tree trace back to the same major nect a sample of branch tips. Under this presented with a particular phylogenetic branches. Coincident with improved meth- interpretation, the nodes (branching points) tree (see the figure, left), people often erro- ods for uncovering evolutionary relationships, evolutionary trees, or phylogenies, have become an essential element of modern biol- ogy (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 evolution within a patient, and to identify modes of potential trans- mission (2). Phylogenetic analysis was even used to solve a murder x case involving HIV (3). Yet “tree thinking” remains widely prac- y ticed only by professional evolu- Which phylogenetic tree is accurate? On the basis of the tree on the left, is the frog more closely related to tionary biologists. This is a partic- the fish or the human? Does the tree on the right change your mind? See the text for how the common ances- ular cause for concern at a time tors (x and y) indicate relatedness. when the teaching of evolution is being challenged, because evolutionary on a tree are taken to correspond to actual neously conclude that a frog is more closely trees serve not only as tools for biological biological entities that existed in the past: related to a fish than to a human. A frog is researchers across disciplines but also as ancestral populations or ancestral genes. actually more closely related to a human the main framework within which evidence However, tree diagrams are also used in than to a f ish because the last common for evolution is evaluated (4, 5). many nonevolutionary contexts, which can ancestor of a frog and a human (see the fig- At the outset, it is important to clarify cause confusion. For example, trees can ure, label x) is a descendant of the last com- that tree thinking does not necessarily depict the clustering of genes on the basis mon ancestor of a frog and a fish (see the entail knowing how phylogenies are of their expression profiles from microar- f igure, label y), and thus lived more inferred by practicing systematists. Anyone rays, or the clustering of ecological com- recently. [To evaluate your tree-thinking who has looked into phylogenetics from munities by species composition. The skills, take the quizzes (6)]. outside the field of evolutionary biology prevalence of such cluster diagrams may Why are trees liable to misinterpreta- knows that it is complex and rapidly chang- explain why phylogenetic trees are often tion? Some evolutionary biologists have ing, replete with a dense statistical litera- misinterpreted as depictions of the similar- proposed that nonspecialists are prone to ture, impassioned philosophical debates, ity among the branch tips. Phylogenetic read trees along the tips (1, 7), which in this and an abundance of highly technical com- trees show historical relationships, not sim- case yields an ordered sequence from fish puter programs. Fortunately, one can inter- ilarities. Although closely related species to frogs and ultimately to humans. This tend to be similar to one another, this is not incorrect way to read a phylogeny may CREDIT: P. HUEY/SCIENCE D. A. Baum and S. D. Smith are in the Department of necessarily the case if the rate of evolution explain the widely held but erroneous view Botany, University of Wisconsin, 430 Lincoln Drive, is not uniform: Crocodiles are more closely that evolution is a linear progression from Madison, WI 53706, USA. E-mail:; S. S. Donovan is in the Department related to birds than they are to lizards, even primitive to advanced species (8), even of Instruction and Learning, University of Pittsburgh, though crocodiles are indisputably more though a moment’s reflection will reveal Pittsburgh, PA 15260, USA. E-mail: similar in external appearance to lizards. that a living frog cannot be the ancestor of SCIENCE VOL 310 11 NOVEMBER 2005 979 Published by AAAS
  2. 2. PERSPECTIVES a living human. The correct way to read a tree humans and mice shared a common ances- segment of society will come to appreciate the is as a set of hierarchically nested groups, tor. Thus, for all its importance, tree think- overwhelming evidence for common ancestry known as clades. In this example, there are ing is fraught with challenges. and the scientific rigor of evolutionary biology. three meaningful clades: human-mouse, Tree thinking belongs alongside natural human-mouse-lizard, and human-mouse- selection as a major theme in evolution References lizard-frog. The difference between reading training. Further, trees could be used 1. R. J. O’Hara, Syst. Zool. 37, 142 (1988). 2. K. A. Crandall, The Evolution of HIV (Johns Hopkins branch tips and reading clades becomes throughout biological training as an effi- Univ. Press, Baltimore, 1999). apparent if the branches are rotated so that cient way to present information on the dis- 3. M. L. Metzger et al. Proc. Natl. Acad. Sci. U.S.A. 99, the tip order is changed (see the f igure, tribution of traits among species. To this 14292 (2002). right). Although the order across the branch end, what is needed are more resources: 4. D. Penny, L. R. Foulds, M. D. Hendy, Nature 297,197 (1982). tips is different, the branching pattern of evo- computer programs (10), educational strate- 5. E. Sober, M. Steel, J. Theor. Biol. 218, 395 (2002). lutionary descent and clade composition is gies (11, 12), and accessible presentations 6. See the two quizzes on Science Online. identical. A focus on clade structure helps to of current phylogenetic knowledge (13–15). 7. S. Nee, Nature 435, 429 (2005). 8. J. L. Rudolph, J. Stewart, J.Res.Sci.Teach. 35, 1069 (1998). emphasize that there is no single, linear nar- Phylogenetic trees are the most direct rep- 9. M. D. Crisp, L. G. Cook, Trends Ecol. Evol. 20, 122 (2005). rative of evolutionary progress (1, 7). resentation of the principle of common 10. J. Herron et al., EvoBeaker 1.0 (SimBiotic Software, There are other problems in reading rela- ancestry—the very core of evolutionary Ithaca, NY, 2005). 11. D. W. Goldsmith, Am. Biol. Teach. 65, 679 (2003). tionships from trees (9). For example, there theory—and thus they must find a more 12. S. F. Gilbert, Nat. Rev. Genet. 4, 735 (2003). is a common assumption that trait evolution prominent place in the general public’s under- 13. J. Cracraft, M. J. Donoghue, Assembling the Tree of Life happens only at nodes. But nodes simply standing of evolution. As philosopher of sci- (Oxford Univ. Press, Oxford, 2004). represent places where populations became ence Robert O’Hara (16) stated, “just as 14. R. Dawkins, The Ancestor’s Tale: A Pilgrimage to the Dawn of Evolution (Houghton Mifflin, New York, 2004). genetically isolated, permitting them to beginning students in geography need to be 15. Tree-Thinking Group ( accumulate differences in their subsequent taught how to read maps, so beginning stu- 16. R. J. O’Hara, Zool. Scripta 26, 323 (1997). evolution. Similarly, living species may be dents in biology should be taught how to read Supporting Online Material mistakenly projected backward to occupy trees and to understand what trees communi- internal nodes of a tree. But it is incorrect to cate.” Among other benefits, as the concept of Tree-Thinking Quizzes I and II read a tree as saying that humans descended tree thinking becomes better understood by from mice when all that is implied is that those in the sciences, we can hope that a wider 10.1126/science.1117727 C H E M I S T RY spectral resolution associated with Raman spectra, without violating the uncertainty Following the Flow of Energy principle? Although not emphasized in the report by Kukura et al., these authors are in Biomolecules fully aware (9) that the underlying time scale for the generation of the Raman pho- ton is dictated by the dephasing time of the Paul M. Champion coherence between the initial and f inal vibrational levels of the material undergo- ome biological molecules, such as those Photoexcited biological molecules offer ing the Raman process. A typical time scale S in visual or photosynthetic systems, have evolved to eff iciently convert energy from one form to another. How do a unique opportunity to monitor the evolu- tion of excitation energy as it transforms a reactant molecule into its final products. for the vibrational dephasing time is on the order of 10−12 s, which translates to a 10 cm−1 Raman bandwidth. This means that these molecules channel energy rapidly and With the advent of appropriate femtosec- the FSRS experiment reads out Raman efficiently so that useful work can be per- ond laser techniques (5), it has become pos- radiation from the sample that is averaged formed without this energy being dissipated sible to examine the underlying dynamics over its vibrational dephasing time window ineffectively into the surroundings? of the elementary vibrational and electronic (that is, the stimulated Raman signals con- Dissipation of molecular vibrational excita- excitations that guide the structural changes tinue to appear at the detector, even after the tion energy typically takes place on picosec- and, ultimately, the function of a variety of probe pulse has passed through the sam- ond time scales, so biological molecules must biomolecules (6–8). The work presented by ple). Thus, there is no violation of the be able to channel energy rapidly and effi- Kukura et al. enhances our ability to moni- uncertainty principle. However, being able ciently if they are to be able to direct it in a use- tor rapid structural changes in such mole- to control the “gating” of the Raman coher- ful manner. In biological systems excited by cules by introducing the technique of fem- ence by changing the time delay between light, the nonradiative electronic transitions tosecond stimulated Raman spectroscopy the photochemical pump and the broadband can occur on time scales (<< 10–12 ps) that are (FSRS). In their report, Kukura et al. follow probe allows the dephasing time window to even faster than vibrational energy dissipation the evolution of the retinal chromophore as be moved so that rapid structural dynamics (1–3), hinting at how nature solves the problem it is excited to photorhodopsin and decays can be monitored. Changes in the vibra- of directing energy flow. On page 1006 of this into bathorhodopsin, all within the first tional frequencies that take place within the issue, Kukura et al. (4) take an important step picosecond of the visual process. They do dephasing time window affect the FSRS forward in defining the process of directed this by taking advantage of the broad spec- lineshape, and the authors have done a con- energy flow in the visual pigment rhodopsin. tral bandwidth of their probe pulse to obtain vincing job of simulating these lineshape very high quality time-resolved stimulated changes as shown in the supporting online Raman spectra over the range of 600 to material of their paper. The author is in the Physics Department and the Center for Interdisciplinary Research on Complex 2000 cm−1. A key conclusion of the work on Systems, Northeastern University, Boston, MA 02115, How does this experiment generate rhodopsin is that low-symmetry hydrogen USA. E-mail: ultrafast time resolution, as well as the high out-of-plane (HOOP) wagging motions 980 11 NOVEMBER 2005 VOL 310 SCIENCE Published by AAAS