Evolved RNA Secondary Structure and the Rooting of the Universal Tree
of Life
Gustavo Caetano-AnolleĢs
Laboratory of Molecular Ecology and Evolution and Division of Molecular Biology, Department of Biology, University of Oslo,
N-0316 Oslo, Norway
Received: 13 September 2000 / Accepted: 27 August 2001
Abstract. The origin and diversification of RNA sec-
ondary structure were traced using cladistic methods.
Structural components were coded as polarized and or-
dered multi-state characters, following a model of char-
acter state transformation outlined by considerations in
statistical mechanics. Several classes of functional RNA
were analyzed, including ribosomal RNA (rRNA). Con-
siderable phylogenetic signal was present in their sec-
ondary structure. The intrinsically rooted phylogenies re-
constructed from evolved RNA structure depicted those
derived from nucleic acid sequence at all taxonomical
levels, and grouped organisms in concordance with tra-
ditional classification, especially in the archaeal and eu-
karyal domains. Natural selection appears therefore to
operate early in the information flow that originates in
sequence and ends in an adapted phenotype. When ex-
amining the hierarchical classification of the living
world, phylogenetic analysis of secondary structure of
the small and large rRNA subunits reconstructed a uni-
versal tree of life that branched in three monophyletic
groups corresponding to Eucarya, Archaea, and Bacteria,
and was rooted in the eukaryotic branch. Ribosomal
characters involved in the translational cycle could be
easily traced and showed that transfer RNA (tRNA)
binding domains in the large rRNA subunit evolved con-
currently with the rest of the rRNA molecule. Results
suggest it is equally parsimonious to consider that an-
cestral unicellular eukaryotes or prokaryotes gave rise to
all extant life forms and provide a rare insight into the
early evolution of nucleic acid and protein biosynthesis.
Key words: Cladistic analysis — Molecular evolution
— Ribosomal RNA — Secondary structu