Engines of innovation: biological origins of genome evolution

Abstract

Genome change does not occur accidentally. The conventional Modern Synthesis view of gradual evolution guided solely by natural selection fails to incorporate many important lessons from direct examination of genome structure by cytogeneticists and modern genomic sequencers. Among other discoveries is the major role that interspecific hybridization has played in the rapid generation of new species. Interspecific hybrids display altered epigenetic regulation and genome expression, great genome variability (including activation of transposable elements and chromosome rearrangements), and frequently whole genome duplication (WGD) as well. These changes produce novel species with adaptively altered phenotypes and reproductive isolation due to meiotic incompatibility with the progenitor species. Genomics has revealed that hybrid speciation and WGD have been widespread among all types of eukaryotes, from yeast and diatoms to flowering plants and primates. The maintenance of the biological responses to interspecific hybridization across virtually all eukaryotic history indicates that eukaryotes have continuously inheritted a capability for rapid evolutionary change. In other words, the best-documented path to the origin of species we have is an inherited biological process, not a series of accidents.

The potential for plant growth-promoting bacteria to impact crop productivity in future agricultural systems is linked to understanding the principles of microbial ecology

“…The suggested common name of the event is horizontal gene or horizontal gene (DNA) transfer (HGT or HDT) (De La Cruiz and Davies, 2000;Shapiro, 2021). The genetic changes in rhizobacteria and plants can be acquired through various mechanisms including, but not limited to, HGT (Batstone, 2022) and DNA methylation and random mutagenesis (Figure 2) (Wall et al, 2015;Gilbert and Hadfield, 2022;Shapiro, 2022).…”

“…Massive endosymbiotic bacteria in the nucleus led to the origin of eukaryotes (De La Cruiz and Davies, 2000). HGT transfers may cause major adaptive changes and involve DNA segments encoding whole proteins, or encode only a few individual domains, and have been documented across virtually all taxonomic units (Shapiro, 2022). Identification of HGT events can be performed by comparing the single-nucleotide polymorphism patterns of pangenomes, or coding sequence compositions, gene phylogeny, and genome compositions.…”

“…Identification of HGT events can be performed by comparing the single-nucleotide polymorphism patterns of pangenomes, or coding sequence compositions, gene phylogeny, and genome compositions. The comparative analysis shows that even though HGT-mediated microevolution takes place in all environments, HGT is considered the evolutionarily important mechanism under situations of selection pressure in harsh environments or population interactions over long periods of time (Shapiro, 2021(Shapiro, , 2022. Thus, rhizobacteria of the wild relatives at the centers of origin can be seen as mediators of plant and ecosystem genetic diversity (Bashan, 1998;Timmusk et al, 2011Timmusk et al, , 2014Perez-Jaramillo et al, 2018;Timmusk and de-Bashan, 2022).…”

Evolutionary Implications of Multi-Scale Intelligence

“…This view has been revised by, e.g., Waddington 55,56 , and more recent works [57][58][59][60][61][62][63][64][65][66] , and has been the subject of vigorous debate 40,63,[67][68][69][70][71][72] with respect to its capabilities for discovery, its optimal locus of control, and the degree to which various aspects are random (uncorrelated to the probability of future fitness improvements). Important open questions concern ways in which the properties of development -the layer between the mutated genotype and the selected phenotype -are evolved and in turn affect the evolutionary process 36,39,45,46,[73][74][75][76][77][78] .…”

Evolutionary Implications of Self-Assembling Cybernetic Materials with Collective Problem-Solving Intelligence at Multiple Scales

“…Based on a phenotypic fitness criterion, the corresponding genotypes, composed of the initial cell states (bottom left) and the functional ANN parameters (top right, are subject to evolutionary reproduction-recombination and mutation operations-to form the next generation of cellular phenotypes that successively "compute" the corresponding system-level phenotypes via morphogenesis, etc. This view has been revised by Waddington [55,56], and more recent works [57][58][59][60][61][62][63][64][65][66], and has been the subject of vigorous debate [40,63,[67][68][69][70][71][72] with respect to its capabilities for discovery, its optimal locus of control, and the degree to which various aspects are random (uncorrelated to the probability of future fitness improvements). Important open questions concern ways in which the properties of development-the layer between the mutated genotype and the selected phenotype-are evolved and in turn affect the evolutionary process [36,39,45,46,[73][74][75][76][77][78].…”