Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with “non-coding” DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called “non-coding” RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
Highlights
Introduction and GoalsOver the past 40 years, several books and numerous review articles have detailed the molecular mechanisms that cells utilize to alter their genomes [1,2,3,4,5,6,7,8]
While early theories of protein evolution were based on the sequential accumulation of individual amino acid changes, the last three decades have revolutionized our understanding of protein organization, protein coding in the genome, and cellular activities that reorganize and innovate protein coding DNA elements
“. . . human-specific de novo protein-coding gene, FLJ33706 . . . originated from noncoding DNA sequences: insertion of repeat elements especially Alu contributed to the formation of the first coding exon and six standard splice junctions on the branch leading to humans and chimpanzees, and two subsequent substitutions in the human lineage escaped two stop codons and created an open reading frame of 194 amino acids.”
Summary
Over the past 40 years, several books and numerous review articles have detailed the molecular mechanisms that cells utilize to alter their genomes [1,2,3,4,5,6,7,8]. These “natural genetic engineering” (NGE) processes are biochemical tools that living organisms possess to make adaptive use of their DNA databases as “Read-Write Genomes” [9]. Previous reviews have summarized the outline of the basic arguments presented below [10,11,12], but this article presents each topic in greater depth and detail than earlier publications
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