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baum et al 2005 treethinking

baum et al 2005 treethinking - PERSPECTIVES E VO L U T I O...

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www.sciencemag.org SCIENCE VOL 310 11 NOVEMBER 2005 979 T he central claim of the theory of evo- lution 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 modification) from common ancestors. To communicate this idea, Darwin developed the metaphor of the “tree of life.” In this comparison, 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 meth- 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 case involving HIV ( 3 ). Yet “tree thinking” remains widely prac- ticed only by professional evolu- tionary biologists. This is a partic- ular 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 evaluated ( 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 field of evolutionary biology knows 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- pret trees and use them for organizing knowledge of biodiversity without know- ing the details of phylogenetic inference. The reverse is, however, not true. One can- not really understand phylogenetics if one is not clear what an evolutionary tree is. The preferred interpretation of a phylo- genetic tree is as a depiction of lines of descent. That is, trees communicate the evolutionary relationships among ele- ments, such as genes or species, that con- nect 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 microar- rays, or the clustering of ecological com- munities by species composition. The prevalence of such cluster diagrams may explain why phylogenetic trees are often misinterpreted as depictions of the similar- ity among the branch tips. Phylogenetic
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