| Abstract: | Summary. Tracing organismal histories on the timescale of the tree of life remains one of the challenging tasks in evolutionary biology.
The hotly debated questions include the evolutionary relationship between the three domains of life (e.g., which of the three
domains are sister domains, are the domains para-, poly-, or monophyletic) and the location of the root within the universal
tree of life. For the latter, many different points of view have been considered but so far no consensus has been reached.
The only widely accepted rationale to root the universal tree of life is to use anciently duplicated paralogous genes that
are present in all three domains of life. To date only few anciently duplicated gene families useful for phylogenetic reconstruction
have been identified. Here we present results from a systematic search for ancient gene duplications using twelve representative,
completely sequenced, archaeal and bacterial genomes. Phylogenetic analyses of identified cases show that the majority of
datasets support a root between Archaea and Bacteria; however, some datasets support alternative hypotheses, and all of them
suffer from a lack of strong phylogenetic signal. The results are discussed with respect to the impact of horizontal gene
transfer on the ability to reconstruct organismal evolution. The exchange of genetic information between divergent organisms
gives rise to mosaic genomes, where different genes in a genome have different histories. Simulations show that even low rates
of horizontal gene transfer dramatically complicate the reconstruction of organismal evolution, and that the different most
recent common molecular ancestors likely existed at different times and in different lineages.
Correspondence and reprints: Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, U.S.A.
Present address: Genome Atlantic, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia,
Canada. |
