Manometro

PERSPECTIVES
E VO L U T I O N

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

he central claim of the theory of evo- pret trees and use them for organizing lution as laid out in 1859 by Charles knowledge of biodiversity without knowDarwin in The Origin of Species is ing the details of phylogenetic inference. that living species, despite theirdiversity in The reverse is, however, not true. One canform and way of life, are the products of not really understand phylogenetics if one descent (with modification) from common is not clear what an evolutionary tree is. ancestors. To communicate this idea, The preferred interpretation of a phyloDarwin developed the metaphor of the genetic tree is as a depiction of lines of “tree of life.” In thiscomparison, living descent. That is, trees communicate the species trace backward in time to common evolutionary relationships among eleancestors in the same way that separate ments, such as genes or species, that contwigs on a tree trace back to the same major nect a sample of branch tips. Under this branches. Coincident with improved meth- interpretation, the nodes (branching points) ods foruncovering evolutionary relationships, evolutionary trees, or phylogenies, have become an essential element 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 evolution within a patient, and to identify modes of potential transmission (2).Phylogenetic analysis was even used to solve a murder x case involving HIV (3). Yet “tree y thinking” remains widely practiced 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 commonancesular 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 disciplinesbut 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 figAt the outset, it is important to clarify cause confusion. Forexample, trees can ure, label x) is a descendant of the last comthat 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 misinterpretaknows that it is complex and rapidly chang- explain why phylogenetic trees are often tion? Some evolutionary biologists have ing, repletewith 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....