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Chapter category: Viruses

A Glance at Evolution through the Genomic Window

Chapter authors:
Eugene D. Sverdlov

A large number of various genomes sequenced recently for the first time make it possible to analyze evolutionary changes at a whole genome level, unlike a single gene level. Intra- and interspecies comparisons of the sequenced genomes demonstrated that the organism’s complexities did not directly correlate with the number of genes and suggested the importance of combinatorial interactions in cells and organisms as a major player in the complexity of live systems. They made it possible to reveal conserved and variable elements of the genomes and to suppose that tens of thousands of proteins are made of just about 1,500-2,000 discrete structural protein units called domains or modules. Different modular proteins are formed from these modules taken in different combinations, and this shuffling might play an extremely important role in the genesis of evolutionary novelties. The new domain architectures (defined as the linear arrangement of domains within a polypeptide) have emerged in evolution by shuffling, adding or deleting domains, resulting in new proteins composed of old parts. More complex organisms seem to contain more various protein architectures than the simpler ones. Whole genome comparisons allowed one to elucidate the role of gene duplications, gross genome rearrangements, transposable elements and other genomic changes in genome divergency, thus forming a solid basis for understanding genetic mechanisms of evolution. Whole genome analyses developed in parallel and interdependently with the development of new concepts of evolution such as evolutionary developmental biology (Evo-Devo) aimed at explaining how developmental processes and mechanisms become modified in evolution, and how these modifications produce changes in animal morphology and body plans. Among these new concepts can be found such fruitful notions as (i) a universal principle of modular organization at various levels of living systems, particular modules being changed and co-opted into new functions without affecting other modules, (ii) a concept of network-like organization of cellular regulatory systems with cis-regulatory elements of the genome functioning as major nodes of the networks, and a crucial evolutionary role of changes in the regulatory systems, (iii) an assumption of increase in functional load per regulatory gene with increasing the complexity of the organism, (iv) an idea of evolvability as a universal feature of the living entities, and a very important concept (v) that not only natural selection, but also internal developmental biases can form the basis for evolutionary changes.

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