Epigenetics and evolution

Epigenetic mechanisms traditionally have been studied in the domains of development and disease, but they may also play important roles in ecological and evolutionary processes. In this article, we revisit historical as well as recent studies that indicate significant impacts of epigenetic processes on evolution. Our main focus is DNA methylation, which is a prevalent chemical modification of genomic DNA. First, it has been long known that DNA methylation acts as a major mutational facilitator in animal genomes and influences nucleotide compositions of genomes. More recently, genome-wide analyses have demonstrated that the current levels of DNA methylation can be predicted from the evolutionary signatures of DNA methylation, indicating that these two processes are intimately correlated. Indeed, the recent explosive growth in the knowledge of genomic DNA methylation in wide-ranging taxa has revealed that patterns of DNA methylation are surprisingly conserved across deep phylogenies. Interestingly, comparative analyses of humans and closely related primate species show that genomic regions that do show evolutionary divergence of DNA methylation are enriched for developmental and tissue specializations. A key question is how epigenetic patterns transmit between generations and impact evolutionary dynamics. On the one hand, some studies report direct transmissions of epigenetic features to the next generation. On the other hand, it is becoming clear that genomic sequence variants exist that encode and presumably regulate distinctive epigenetic patterns. For instance, numerous single-nucleotide polymorphisms that affect DNA-methylation patterns have been discovered in human populations. These studies begin to unveil a dynamic interplay between genomic and epigenomic factors across long and short evolutionary timescales.

Bright solitons from the nonpolynomial Schrödinger equation with inhomogeneous defocusing nonlinearities

Extending the recent work on models with spatially nonuniform nonlinearities, we study bright solitons generated by the nonpolynomial self-defocusing (SDF) nonlinearity in the framework of the one-dimensional (1D) Muñoz-Mateo-Delgado (MM-D) equation (the 1D reduction of the Gross-Pitaevskii equation with the SDF nonlinearity), with the local strength of the nonlinearity growing at |x|→∞ faster than |x|. We produce numerical solutions and analytical ones, obtained by means of the Thomas-Fermi approximation, for nodeless ground states and for excited modes with one, two, three and four nodes, in two versions of the model, with steep (exponential) and mild (algebraic) nonlinear-modulation profiles. In both cases, the ground states and the single-node ones are completely stable, while the stability of the higher-order modes depends on their norm (in the case of the algebraic modulation, they are fully unstable). Unstable states spontaneously evolve into their stable lower-order counterparts.