Into the Woods

The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum

Eugene V Koonin and Yuri I.Wolf

Biology Direct (2009), 4:33

Human communication and thought is largely shaped by metaphors. Metaphors allow man to think about concepts and facts in new ways and to make connections that otherwise might have been left undiscovered. However, if one becomes too committed to a particular metaphor there is the danger of the opposite-of stifling creativity and having a distorted view of individual facts or even the world at large.

"The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. .... The limbs divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was small, budding twigs; and this connexion of the former and present buds by ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups."

The authors of this article begin with this quote from Charles Darwin(1) in order to assert that the very roots of evolutionary theory are grounded in the metaphor of a “Tree of Life.” In this metaphor all living organisms are the budding tips of living branches in the Tree of Life (TOL), whose trunk was the original organism from which all life derived. While this metaphor has served scientists well for centuries, our increased understanding of horizontal gene transfer has led to a “crisis of the TOL.”

The authors argue that individual viruses, plasmids, transposons, individual genes, and the like, rather than organisms or species, should be considered as the true fundamental units of evolution (FUEs). The evolutionary history of each individual FUE is still accurately represented by a tree in that an ancestral gene can be altered such that a new version “branches off,” with this process continuing until a full tree is formed. An organism, therefore, is made up of many such FUE trees, and so is more properly a “forest of life.”

The more we learn about the importance of horizontal gene transfer among organisms, species, or even kingdoms, the more clear it becomes that the metaphor of a Tree of Life ignores much of the complexity of true evolutionary histories, especially among prokaryotes. We therefore might benefit from reevaluating our metaphor and perhaps, as the authors suggest, acknowledge the true complexity of the Forest of Life.

References\Further Reading:

1. Darwin C: On the Origin of Species. 1st edition. London: Murray; 1859.

2. Hilario E, Gogarten JP: Horizontal transfer of ATPase genes--the tree of life becomes a net of life. Biosystems31(2-3):111-119. 1993,

3. Doolittle WF: Uprooting the tree of life. Sci Am 2000, 282(2):90-95

4. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, et al.: Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 1999, 399(6734):323-329.

Julie M. Hughes

University of Idaho