Constraints, Plasticity, and Universal Patterns in Genome and Phenome Evolution
Evolutionary genomics identifies multiple constraints that differentially affect different parts of the genomes of diverse life forms. The selective pressures that shape the evolution of viral, prokaryotic, and eukaryotic genomes differ dramatically, and
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Constraints, Plasticity, and Universal Patterns in Genome and Phenome Evolution Eugene V. Koonin and Yuri I. Wolf
Abstract Evolutionary genomics identifies multiple constraints that differentially affect different parts of the genomes of diverse life forms. The selective pressures that shape the evolution of viral, prokaryotic, and eukaryotic genomes differ dramatically, and substantial differences exist even between animal and bacterial lineages. Constraints on protein evolution appear to be more universal and could be determined by the fundamental physics of protein folding. Some key features of the molecular phenome such as protein abundance turn out to be unexpectedly conserved and hence strongly constrained. The constraints that shape the evolution of genomes and phenomes are complemented by the plasticity and robustness of genome architecture, expression, and regulation. Several universal “laws” of genome and phenome evolution were detected, some of which seem to be dictated by selective constraints and others by neutral process.
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Introduction
In principle, the entire genome of any life form can be perceived as evolving under constraints (purifying selection) the strength of which varies from 0 (unconstrained evolution) to 1 (absolute conservation). Moreover, constraints affect evolution at all levels of biological organization, from genome sequence to genome architecture to gene expression to molecular interactions to actual organismal phenotypes (Kimura 1983; Lynch 2007c). Generally, constraints on the rates and paths of evolution can be divided into genomic, those that are manifest at the level of the genome sequence and architecture, and phenomic, those that pertain to phenotypic characteristics (although ultimately realized through genomic changes as well). Comparative E.V. Koonin and Y.I. Wolf National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA e-mail: [email protected]
P. Pontarotti (ed.), Evolutionary Biology – Concepts, Molecular and Morphological Evolution, DOI 10.1007/978-3-642-12340-5_2, # Springer-Verlag Berlin Heidelberg 2010
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E.V. Koonin and Y.I. Wolf
genomics and systems biology produce massive amounts of diverse data that provide for previously inconceivable insights into the patterns and processes of genome and phenome evolution (Kitano 2002; Medina 2005; Koonin and Wolf 2006; Lynch 2007c; Loewe 2009; Yamada and Bork 2009). Comparative genomics allows us, at least in principle, to measure the strength of constraints that affect different classes of sites in genomes and to elucidate the biological nature of these constraints. However, genome comparison does more than that as it gives us material to address evolutionary constraints beyond the traditional aspect of sequence conservation to higher level questions such as: how constrained in evolution are gene repertoires of organisms, genome architecture, evolution rate itself, and more? The massive influx of data from systems biology takes th
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