Thus the modern evolutionary scientist may not need to venture beyond a computer with access to data from the world's DNA databases. This information is allowing researchers to go much farther back, to the first known branchings of the evolutionary pathway marked by the origins of Bacteria, Eukaryotes (cells with nuclei, like those of our body), and a third branch called Archaea. The first archaeal species was discovered less than two decades ago, in deep-sea drilling efforts to find oil, and now a number of its relatives have been found in locales which are almost equally inhospitable to other forms of life.

"Since Archaea live under such harsh conditions, they may evolve slowly," says Christos Ouzounis, a researcher at the European Bioinformatics Institute (EBI) in Hinxton, England. The EBI, an Outstation of the European Molecular Biology Laboratory (EMBL) based in Heidelberg, Germany, is the home of several of the world's most important databases of genome information. Among Ouzounis´ projects has been the reconstruction of a hypothetical ancestor that Archaea, Bacteria, and Eukaryotes must have shared. Ouzounis and his colleagues have been steadily gathering evidence to show that present-day Archaea represent the most direct descendants of the ancestor of all three lineages. Drawing on the databases, they hope to fill in the details of when and how these splits occurred.

Although researchers have changed their focus from the larger features of organisms to genomes, the principles by which they draw their conclusions about familial relationships between species haven't changed much: the higher the similarity between species, the more closely related they are presumed to be. Just as naturalists had to examine organisms as a whole to reach firm conclusions -- dolphins may resemble fish by few criteria, though they are obviously mammals -- the best information can be drawn from whole genomes rather than single genes. Completely-analysed genomes for Archaea have only existed for about two years, and Ouzounis and his colleagues are among the first to explore these data in depth.

What most obviously unites Bacteria, Archaea, and Eukaryotes is the fact that they all perform all of a cell's vital functions. Thus these organisms share not only DNA -- each of them needs the molecular machinery to transcribe it into RNA, as well. According to Ouzounis, transcription is a fundamental cellular process which can be considered a part of the genetic "hardware" of an organism, as opposed to processes such as metabolism, which can be considered as genetic "software". Transcription appears to have endured billions of years of evolution and may go back as far as the life history of the lineages themselves. Recently Ouzounis and collaborator Nikos Kyrpides of the University of Illinois at Urbana-Champaign (USA) undertook a complete inventory of this machinery in the three evolutionary branches.

"It takes concerted action on the part of many molecules to transcribe a gene," Ouzounis says. "To regulate gene expression, cells need molecules which help the transcription machinery to recognise genes, or to help to guide it there, or actually do the job of transcription. The machinery itself is made of a complex of proteins which varies depending on the gene and the organism. So we found over 4000 proteins in the databases associated with transcription in either bacteria or eukaryotic cells."

Ouzounis and Kyrpides used this list to search for related genes in four complete archaeal genomes. As species evolve through mutations in DNA, the new variants of an organism maintain important cellular processes such as transcription, and these processes are usually carried out by descendents of the original proteins. So genes, which hold the codes for proteins, represent a record of evolution. Genes that are present in multiple descendents must have been present in their common ancestor.

"We found 280 genes in Archaea that can be associated with transcription," Ouzounis says. "168 of these have relatives only in Bacteria, while 51 are related only to eukaryotic genes. The rest have relatives in both organisms. In contrast, very little of this machinery is shared by Bacteria and Eukaryotes. Probably the only viable explanation is that transcription existed in Archaea before Bacteria and Eukaryotes were "invented" by evolution, and that modern Archaea have preserved more of the original transcription machinery than either of the two latter branches."

This revises earlier theories that Archaea and Eukaryotes descended from Bacteria, based on studies showing that bacterial genes had undergone a greater degree of mutation -- implying they were "older". But Ouzounis points out that strains of Bacteria evolve more quickly. Archaea reproduce slowly and evolve in environments with very stable conditions. The rate at which a species evolves depends both on its reproductive rate and the environment. Thus the only sure method of reconstruction these ancient evolutionary relationships is though a broader look at the genome.

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