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About 10 years ago scientists finally worked out Uprooting the basic outline of how the modern life-forms evolved. Now parts of their tidy Tree of Life scheme are unraveling by W.Ford Doolittle Instead of looking just at anatomy or physiology, they asked, why not base family trees on differences in the order of the building blocks in selected genes or proteins? harles Darwin contended more than a century Their approach, known as molecular phylogeny, is emi- ago that all modern species diverged from a nently logical. Individual genes, composed of unique se- more limited set of ancestral groups, which quences of nucleotides, typically serve as the blueprints for themselves evolved from still fewer progeni- making specific proteins, which consist of particular strings tors and so on back to the beginning of life. In of amino acids. All genes, however, mutate (change in se- C principle, then, the relationships among all liv- quence), sometimes altering the encoded protein. Genetic mu- ing and extinct organisms could be represented as a single ge- tations that have no effect on protein function or that im- nealogical tree. prove it will inevitably accumulate over time. Thus, as two Most contemporary researchers agree. Many would even species diverge from an ancestor, the sequences of the genes argue that the general features of this tree are already known, they share will also diverge. And as time passes, the genetic all the way down to the root—a solitary cell, termed life’s last divergence will increase. Investigators can therefore recon- universal common ancestor, that lived roughly 3.5 to 3.8 bil- lion years ago. The consensus view did not come easily but has been widely accepted for more than a decade. BACTERIA Yet ill winds are blowing. To everyone’s surprise, discover- Other bacteria Cyanobacteria ies 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 cientists could not even begin to contemplate constructing Sa 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 traits suggested, 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 pro- vided too little information for defining relationships. That Hyperthermophilic paucity was disturbing because microbes were the only in- bacteria habitants 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 struc- ture and function occurred. For example, between the birth CONSENSUS VIEW of the universal tree of life holds that the of the first cell and the appearance of multicellular fungi, early descendants of life’s last universal common ancestor—a plants and animals, cells grew bigger and more complex, small cell with no nucleus—divided into two prokaryotic (non- gained a nucleus and a cytoskeleton (internal scaffolding), nucleated) groups: the bacteria and the archaea. Later, the ar- chaea gave rise to organisms having complex cells containing a and found a way to eat other cells. nucleus: the eukaryotes. Eukaryotes gained valuable energy-gen- In the mid-1960s Emile Zuckerkandl and Linus Pauling of erating organelles—mitochondria and, in the case of plants, the California Institute of Technology conceived of a revolu- chloroplasts—by taking up, and retaining, certain bacteria. tionary strategy that could supply the missing information. 90 Scientific American February 2000 Copyright 2000 Scientific American, Inc. struct the evolutionary past of living species—can construct data to draw some important inferences. Since then, phyloge- their phylogenetic trees—by assessing the sequence diver- neticists studying microbial evolution, as well as investigators gence of genes or proteins isolated from those organisms. concerned with higher sections of the universal tree, have Thirty-five years ago scientists were just becoming profi- based many of their branching patterns on sequence analyses cient at identifying the order of amino acids in proteins and of SSU rRNA genes. This accumulation of rRNA data helped could not yet sequence genes. Protein studies completed in the greatly to foster consensus about the universal tree in the late 1960s and 1970s demonstrated the general utility of molecu- 1980s. Today investigators have rRNA sequences for several lar phylogeny by confirming and then extending the family thousands of species. trees of well-studied groups such as the vertebrates. They also From the start, the rRNA results corroborated some already lent support to some hypotheses about the links among cer- accepted ideas, but they also produced an astonishing surprise. tain bacteria—showing, for instance, that bacteria capable of By the 1960s microscopists had determined that the world of producing oxygen during photosynthesis form a group of living things could be divided into two separate groups, eukary- their own (cyanobacteria). otes and prokaryotes, depending on the structure of the cells As this protein work was progressing, Carl R. Woese of the that composed them. Eukaryotic organisms (animals, plants, University of Illinois was turning his attention to a powerful fungi and many unicellular life-forms) were defined as those new yardstick of evolutionary distances: small subunit riboso- composed of cells that contained a true nucleus—a membrane- mal RNA (SSU rRNA). This genetically specified molecule is a bound organelle housing the chromosomes. Eukaryotic cells key constituent of ribosomes, the “factories” that construct proteins in cells, and cells throughout time have needed it to survive. These features suggested to Woese in the late 1960s EUKARYOTES that variations in SSU rRNA (or more precisely in the genes encoding it) would reliably indicate the relatedness among Animals Fungi Plants any life-forms, from the plainest bacteria to the most complex animals. Small subunit ribosomal RNA could thus serve, in Woese’s words, as a “universal molecular chronometer.” Initially the methods available for the project were indirect and laborious. By the late 1970s, though, Woese had enough ARCHAEA Algae Crenarchaeota Euryarchaeota Proteobacteria Ciliates loroplasts Bacteria that gave rise to ch Other single- }cell eukaryotes t gave rise to mitochondria Bacteria tha Korarchaeota G N I N N E R B A N Last Universal Common Ancestor A J (single cell) Scientific American February 2000 91 Copyright 2000 Scientific American, Inc. ENDOSYMBIONT HYPOTHESIS proposes CHLOROPLAST that mitochondria formed after a prokaryote MITOCHONDRION that had evolved into an early eukaryote en- gulfed (a) and then kept (b) one or more al- pha-proteobacteria cells. Eventually, the d Cell acquires second symbiont, bacterium gave up its ability to live on which becomes the chloroplast its own and transferred some of its genes to the nucleus of the host CYANOBACTERIAL (c), becoming a mitochondri- FOOD on. Later, some mitochondri- SYMBIONT on-bearing eukaryote ingest- c Symbiont loses many ed a cyanobacterium that genes, and some genes became the chloroplast (d). transfer to nucleus H C encode SSU rRNA. Hence, once the I R M right tools became available in the mid- U L B H 1970s, investigators decided to see if P O T S those RNA genes were inherited from I R H alpha-proteobacteria and cyanobacteria, C b Eukaryote retains bacterium PRIMITIVE as a symbiont respectively—as the endosymbiont hy- EUKARYOTE pothesis would predict. They were. CHROMOSOME One deduction, however, introduced NUCLEUS a discordant note into all this harmony. INTERNAL MEMBRANE In the late 1970s Woese asserted that CYTOSKELETON BACTERIAL FOOD (ALPHA-PROTEOBACTERIUM) the two-domain view of life, dividing the world into bacteria and eukaryotes, was no longer tenable; a three-domain construct had to take its place. PROKARYOTE a Cell loses wall, grows, acquires other eukaryotic features and ingests a bacterium Certain prokaryotes classified as bac- DNA RIBOSOME teria might look like bacteria but, he in- MEMBRANE sisted, were genetically much different. CELL WALL In fact, their rRNA supported an early cient anaerobic prokaryote (unable to separation. Many of these species had use oxygen for energy) lost its cell wall. already been noted for displaying unusu- also displayed other prominent features, The more flexible membrane under- al behavior, such as favoring extreme en- among them a cytoskeleton, an intricate neath then began to grow and fold in vironments, but no one had disputed system of internal membranes and, usu- on itself. This change, in turn, led to their status as bacteria. Now Woese ally, mitochondria (organelles that per- formation of a nucleus and other inter- claimed that they formed a third primary form respiration, using oxygen to ex- nal membranes and also enabled the group—the archaea—as different from tract energy from nutrients). In the case cell to engulf and digest neighboring bacteria as bacteria are from eukaryotes. of algae and higher plants, the cells also prokaryotes, instead of gaining nour- contained chloroplasts (photosynthetic ishment entirely by absorbing small Acrimony, Then Consensus organelles). molecules from its environment. Prokaryotes, thought at the time to be At some point, one of the descen- t first, the claim met enormous resis- synonymous with bacteria, were noted to dants of this primitive eukaryote took Atance. Yet eventually most scientists consist of smaller and simpler nonnucle- up bacterial cells of the type known as became convinced, in part because the ated cells. They are usually enclosed by alpha-proteobacteria, which are profi- overall structures of certain molecules both a membrane and a rigid outer wall.

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