What we have learned about evolutionary genome change in the past 7 decades

• Published in: BioSystems Vol. 215-216; p. 104669
• Main Author: Shapiro, James A.
• Format: Journal Article
• Language: English
• Published: Ireland Elsevier B.V 01.06.2022
• Subjects: Alternative end-joining; Animals; Biological Evolution; Chromoplexy; Chromothripsis; DNA Transposable Elements - genetics; Eukaryota - genetics; Evolution, Molecular; Functional non-coding ncRNAS; Genome shock; Genomics; Hybrid speciation; Hybridization, Genetic; Transposable elements; Hybrid speciation; Alternative end-joining; Functional non-coding ncRNAS; Genome shock; Chromoplexy; Transposable elements; Chromothripsis
• ISSN: 0303-2647; 1872-8324; 1872-8324
• DOI: 10.1016/j.biosystems.2022.104669

Cytogenetics and genomics have completely transformed our understanding of evolutionary genome change since the early 1950s. The point of this paper is to outline some of the empirical findings responsible for that transformation. The discovery of transposable elements (TEs) in maize by McClintock, and their subsequent rediscovery in all forms of life, tell us that organisms have the inherent capacity to evolve dispersed genomic networks encoding complex cellular and multicellular adaptations. Genomic analysis confirms the role of TEs in wiring novel networks at major evolutionary transitions. TEs and other forms of repetitive DNA are also important contributors to genome regions that serve as transcriptional templates for regulatory and other biologically functional noncoding ncRNAs. The many functions documented for ncRNAs shows the concept of abundant “selfish” or “junk” DNA in complex genomes is mistaken. Natural and artificial speciation by interspecific hybridization demonstrates that TEs and other biochemical systems of genome restructuring are subject to rapid activation and can generate changes throughout the genomes of the novel species that emerge. In addition to TEs and hybrid species, cancer cells have taught us important lessons about chromothripsis, chromoplexy and other forms of non-random multisite genome restructuring. In many of these restructured genomes, alternative end-joining processes display the capacities of eukaryotes to generate novel combinations of templated and untemplated DNA sequences at the sites of break repair. Sequence innovation by alternative end-joining is widespread among eukaryotes from single cells to advanced plants and animals. In sum, the cellular and genomic capacities of eukaryotic cells have proven to be capable of executing rapid macroevolutionary change under a variety of conditions.