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Uprooting the
Tree of Life
by W. Ford Doolittle
harles Darwin contended more than a century ago that all modern species diverged from a more limited set of ancestral groups, which themselves evolved from still fewer progenitors and so on back to the beginning of life. In principle, then, the relationships among all living and extinct organisms could be represented as a single genealogicaltree. Most contemporary researchers agree. Many would even argue that the general features of this tree are already known, all the way down to the root— a solitary cell, termed life’s last universal common ancestor, that lived roughly 3.5 to 3.8 billion years ago. The consensus view did not come easily but has been widely accepted for more than a decade. Yet ill winds are blowing. To everyone’ssurprise, discoveries made in the past few years have begun to cast serious doubt on some aspects of the tree, especially on the depiction of the relationships near the root. The First Sketches

About 10 years ago scientists finally worked out the basic outline of how modern life-forms evolved. Now parts of their tidy scheme are unraveling


Instead of looking just at anatomy or physiology, theyasked, why not base family trees on differences in the order of the building blocks in selected genes or proteins? Their approach, known as molecular phylogeny, is eminently logical. Individual genes, composed of unique sequences of nucleotides, typically serve as the blueprints for making specific proteins, which consist of particular strings of amino acids. All genes, however, mutate (change insequence), sometimes altering the encoded protein. Genetic mutations that have no effect on protein function or that improve it will inevitably accumulate over time. Thus, as two species diverge from an ancestor, the sequences of the genes they share will also diverge. And as time passes, the genetic divergence will increase. Investigators can therefore recon-

Other bacteriaCyanobacteria


cientists could not even begin to contemplate constructing a universal tree until about 35 years ago. From the time of Aristotle to the 1960s, researchers deduced the relatedness of organisms by comparing their anatomy or physiology, or both. For complex organisms, they were frequently able to draw reasonable genealogical inferences in this way. Detailed analyses of innumerable traitssuggested, for instance, that hominids shared a common ancestor with apes, that this common ancestor shared an earlier one with monkeys, and that that precursor shared an even earlier forebear with prosimians, and so forth. Microscopic single-celled organisms, however, often provided too little information for defining relationships. That paucity was disturbing because microbes were the onlyinhabitants of the earth for the first half to two thirds of the planet’s history; the absence of a clear phylogeny (family tree) for microorganisms left scientists unsure about the sequence in which some of the most radical innovations in cellular structure and function occurred. For example, between the birth of the first cell and the appearance of multicellular fungi, plants and animals, cells grewbigger and more complex, gained a nucleus and a cytoskeleton (internal scaffolding), and found a way to eat other cells. In the mid-1960s Emile Zuckerkandl and Linus Pauling of the California Institute of Technology conceived of a revolutionary strategy that could supply the missing information.
90 Scientific American February 2000

Hyperthermophilic bacteria

CONSENSUS VIEW of the universal treeof life holds that the early descendants of life’s last universal common ancestor—a small cell with no nucleus—divided into two prokaryotic (nonnucleated) groups: the bacteria and the archaea. Later, the archaea gave rise to organisms having complex cells containing a nucleus: the eukaryotes. Eukaryotes gained valuable energy-generating organelles—mitochondria and, in the case of plants,...
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