Ever since Darwin the tree has been the unifying principle for understanding the history of life on Earth. At its base is LUCA, the Last Universal Common Ancestor of all living things, and out of LUCA grows a trunk, which splits again and again to create a vast, bifurcating tree. Each branch represents a single species; branching points are where one species becomes two. Most branches eventually come to a dead end as species go extinct, but some reach right to the top - these are living species. The tree is thus a record of how every species that ever lived is related to all others right back to the origin of life. ...The green and budding twigs may represent existing species, and those produced during each former year may represent the long succession of extinct species. For much of the past 150 years, biology has largely concerned itself with filling in the details of the tree. "For a long time the holy grail was to build a tree of life," says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. "We have no evidence at all that the tree of life is a reality," says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.
So what happened? In a nutshell, DNA. The discovery of the structure of DNA in 1953 opened up new vistas for evolutionary biology. Here, at last, was the very stuff of inheritance into which was surely written the history of life, if only we knew how to decode it. Thus was born the field of molecular evolution, and as techniques became available to read DNA sequences and those of other biomolecules such as RNA and proteins, its pioneers came to believe that it would provide proof positive of Darwin's tree of life. The basic idea was simple: the more closely related two species are (or the more recently their branches on the tree split), the more alike their DNA, RNA and protein sequences ought to be. It started well. The first molecules to be sequenced were RNAs found in ribosomes, the cell's protein-making machines. In the 1970s, by comparing RNA sequences from various plants, animals and microorganisms, molecular biologists began to sketch the outlines of a tree. This led to, among other successes, the unexpected discovery of a previously unknown major branch of the tree of life, the unicellular archaea, which were previously thought to be bacteria.
By the mid-1980s there was great optimism that molecular techniques would finally reveal the universal tree of life in all its glory. Ironically, the opposite happened. The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse. Which was correct? Paradoxically, both - but only if the main premise underpinning Darwin's tree was incorrect. Darwin assumed that descent was exclusively "vertical", with organisms passing traits down to their offspring. But what if species also routinely swapped genetic material with other species, or hybridised with them? Then that neat branching pattern would quickly degenerate into an impenetrable thicket of interrelatedness, with species being closely related in some respects but not others.
February 10, 2009
Original web page at New Scientist