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Transfer RNA transforms tree of life

A comparison of transfer RNAs has revealed the roots of the tree of life, indicating ancient origins for Archaea and viruses, according to research published yesterday in linkurl:PLoS Computational Biology.;http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000018 Since the discovery that ribosomal RNA can reveal evolutionary relationships between organisms, researchers have split the universal tree of life into three main branches: the superkingdoms Archaea, Bacteria, an

By | March 7, 2008

A comparison of transfer RNAs has revealed the roots of the tree of life, indicating ancient origins for Archaea and viruses, according to research published yesterday in linkurl:PLoS Computational Biology.;http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000018 Since the discovery that ribosomal RNA can reveal evolutionary relationships between organisms, researchers have split the universal tree of life into three main branches: the superkingdoms Archaea, Bacteria, and Eukarya. But the root of the tree has remained linkurl:controversial.;http://www.the-scientist.com/article/display/13255/ Also, this tripartite tree of "life" has omitted viruses, which have long been considered as "not living." To resolve the timeline of diversification and the origin of viruses, therefore, a new molecular marker was needed. Enter tRNA. "Transfer RNAs are ancient molecules," said Gustavo Caetano-Anollés of the University of Illinois at Urbana-Champaign. "They're molecular fossils." Caetano-Anollés and his colleague Feng-Jie Sun investigated the sequence and structure of hundreds of tRNAs to probe for deep evolutionary relationships in the tree of life. When they tried standard phylogenetic methods, however, no clear patterns emerged. So they grouped together tRNAs from the same superkingdoms and from viruses, assuming that the different taxa must have evolved independently, and looked for trees that required the fewest evolutionary steps. "We bombarded the system with alternative hypotheses and chose the ones that fit the data best," Caetano-Anollés told The Scientist. Consistently, the trees with the fewest steps showed Archaea as most ancient, followed by viruses, Eukarya, and Bacteria. And viruses were not only very old; they were also tightly linked to Archaea. linkurl:Russell Doolittle;http://biology.ucsd.edu/faculty/doolittle.html of the University of California at San Diego, who was not involved with the work, called the results "provocative." But he cautioned that the analysis might be prone to a tree reconstruction artifact known as "long branch attraction," where rapidly evolving lineages seem to be closely related regardless of their true evolutionary relationships. Doolittle also told The Scientist that he was "surprised there were enough virus tRNAs to do this." Caetano-Anollés conceded that only around 20 viral tRNAs were included, but he argued that the results are robust because the viral tRNAs clustered together even when he divided viruses infecting Eukarya or Bacteria into separate groups. So, does the tRNA-derived phylogeny match the true tree of life? Last year, Caetano-Anollés also published a paper in linkurl:Genome Research;http://www.genome.org/cgi/content/abstract/17/11/1572 that supports the ancient origin of Archaea based on proteome architecture, although that study did not consider viruses. Whether the timeline of these molecules matches the timeline of organismal diversification, however, remains to be seen. "You could take different molecules and get a different topology," says Caetano-Anollés. "But tRNA is so old that it might represent very ancient relationships, such as the rooting of the tree of life."

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