Genomic revolution of evolution and the role of epidemic sequences

Theories of evolution seeded by Lamarck and Darwin two centuries ago put forward inherited modifications of genomes while ignoring interactions between organisms living in the same ecosystem, and rearrangements (with recombinations and reassortments), introgressive evolution, transposable elements, and sequence losses within genomes. Here we summarized data that currently indicate a different, optimized, and broadly applicable vision of genome evolution. In fact, two paradigms coexist in evolutionary biology: one is that of linear, gradual evolution linked to mutations with selection in a given environment, as drawn by Darwin, Lamarck, and the Red Queen theory. Another is that of unpredictable, chaotic, leap-making evolution, as illustrated by the Court Jester theory. Key drivers of genome expansion comprise gains of sequences, among which invasions by either endogenous or exogenous transposable elements that resemble epidemics and determine defense countermeasures, as well as genome duplications and polyploidizations. Sympatric conditions with biological melting pots promote sequence gains and increase genome mosaicism. Sequence loss, which can involve degradation and non-repair, is another major player in evolution in reduced ecosystems, with allopatric conditions promoting specializations. “Fertile selfish sequences” are transmitted between biological entities and can multiply within genomes, while junk DNA consists of remnants of genes progressively degraded. Besides, coding density within genomes tends to decrease as organism complexity increases, regardless of genome size, and therefore the proportion of genomes that is functional is mostly unknown. Overall, current genomic data indicate that genetic evolution is chaotic and permanently creative and innovative, and that representing genomes as single sequences is not realistic, just as phylogenetic trees are an inaccurate representation of sequence evolution, which is more realistically represented by rhizomes or networks, as genomes are not unique but multiple, plastic, and mosaic. Beyond, chaotic intentionality and random purpose should be considered, and the question of the finality of evolution cannot truly be resolved. Finally, genomic data support an anthropocenic rather than anthropocentric paradigm of evolution.