Home > Archives > Additional Archives > Eugene Koonin   Eugene Koonin Senior Investigator National Center for Biotechnology Information National Library of Medicine National Institutes of Health  Comparative Genomics and its Impact on the Evolution of Evolutionary Biology About 40 complete genome sequences of cellular life forms - bacteria, archaea and eukaryotes - are currently available, and many more are in the pipeline. Comparative analysis of these genome is central to our understanding of gene functions and ushering biology in the era of functional genomics. At a more fundamental level, it appears that comparative analysis of the sequenced genomes has already affected our ideas on the nature of biological evolution to such an extent that it may be appropriate to claim a paradigm shift in evolutionary biology. Probably the principal finding that calls for such dramatic revision of our ideas of evolution is the discovery of the major role of horizontal gene transfer and lineage-specific gene loss, definitely throughout the prokaryotic world, but possibly also in eukaryotes. This demonstration casts some doubt on the very legitimacy of tree representations of the evolutionary history of species. At the same time, whole-genome comparisons provide for the possibility of constructing a new type of phylogenetic trees that could reveal weak phylogenetic signals from remote past in spite of the effects of horizontal gene transfer and gene loss. The major heuristic value of genome comparisons is that they allow systematic, large-scale testing of various hypotheses and models that address fundamental evolutionary problems. I will discuss the contribution of comparative genome analysis to the analysis of two such problems, the introns-late versus introns early controversy and the mode of evolution and reasons for evolutionary fixation of gene duplications. For more information, please see http://www.ncbi.nlm.nih.gov/COG/
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