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Biology 2016, 5(2), 27; doi:10.3390/biology5020027

Nothing in Evolution Makes Sense Except in the Light of Genomics: Read–Write Genome Evolution as an Active Biological Process

Department of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA
Academic Editor: John S. Torday
Received: 12 February 2016 / Revised: 20 May 2016 / Accepted: 2 June 2016 / Published: 8 June 2016
(This article belongs to the Special Issue Beyond the Modern Evolutionary Synthesis- what have we missed?)
View Full-Text   |   Download PDF [347 KB, uploaded 8 June 2016]   |  

Abstract

The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess “Read–Write Genomes” they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification. View Full-Text
Keywords: genome sequence; molecular phylogeny; repetitive DNA; symbiogenesis; hybrid speciation; whole genome duplication; horizontal DNA transfer; viviparity; mobile DNA elements; stem cell pluripotency genome sequence; molecular phylogeny; repetitive DNA; symbiogenesis; hybrid speciation; whole genome duplication; horizontal DNA transfer; viviparity; mobile DNA elements; stem cell pluripotency
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Shapiro, J.A. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read–Write Genome Evolution as an Active Biological Process. Biology 2016, 5, 27.

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