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Using large-scale comparative genomics with appropriate algorithms and databases, described briefly, we present a phylogeny of microbial species that takes into account
both vertical and horizontal gene transfer (HGT) events. So far, all phylogenetic reconstructions have presented microbial relationships as trees rather than networks. This first attempt to reconstruct such an evolutionary network is termed as the "net of life". We use available reconstruction methods to infer vertical inheritance, and use an ancestral state inference algorithm to map HGT events on the tree. We demonstrate that vertical inheritance constitutes the bulk of gene transfer on the tree of life. We term the bulk of horizontal gene flow between species as "vines", and show that multiple, yet tiny, vines interconnect throughout the tree. These results strongly suggest that the HGT network is a scale-free graph, a finding with important implications for genome evolution. Finally, we propose that genes might propagate extremely rapidly across microbial species through the HGT network, using certain organisms as hubs. Open problems and possible future directions for research will also be discussed.
Further reading: Ouzounis CA (2005) Ancestral state reconstructions for genomes. Curr. Opin. Genet. Devel. 15, 595-600. Kunin V, Goldovsky L, Darzentas N, Ouzounis CA (2005) The net of life: Reconstructing the microbial phylogenetic network. Genome Research 15, 954-959. Kunin V, Ouzounis CA (2003) The balance of driving forces during genome evolution in prokaryotes. Genome Research 13, 1589-1594. |
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